From olibclarke at gmail.com  Mon Mar  2 08:13:16 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Mon, 2 Mar 2015 11:13:16 -0500
Subject: [Chimera-users] explicit parentheses in atom selections
Message-ID: <35A5A07F-28DA-450E-832E-D9A1A417F6EF@gmail.com>

Hi all,

Would it be possible at some point to allow the use of explicit parentheses when grouping selections on the command line? It would make it much easier/clearer when using multiple boolean operations (e.g "ligand z<5 &~ ligand &~ solvent? could be ?ligand z<5 &~(ligand | solvent)?). Is there a reason why this kind of syntax is not used at the moment?

Also, just a random thought for a future version - it would be really handy to have something like the ?Macro recorder? function of ImageJ or similar programs. This records whatever the user does using the GUI (while the recorder is active) and spits out the equivalent scripting commands to a dialog, where they can be saved and reused, or turned into a script. This can be a very powerful tool for learning the command line functionality of a complex application in an interactive manner.

Cheers,
Oliver.


From meng at cgl.ucsf.edu  Mon Mar  2 08:48:53 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 2 Mar 2015 08:48:53 -0800
Subject: [Chimera-users] explicit parentheses in atom selections
In-Reply-To: <35A5A07F-28DA-450E-832E-D9A1A417F6EF@gmail.com>
References: <35A5A07F-28DA-450E-832E-D9A1A417F6EF@gmail.com>
Message-ID: <CA6AE93C-1BBF-4882-9A1E-D0250FF91109@cgl.ucsf.edu>

Hi Oliver,
These are both things we have felt the need for and discussed in some depth.

My understanding is that with the current complicated atomspec parsing, it is not possible (with reasonable effort) to add parentheses, but they are definitely one of the things we intend to allow in atomspecs in the next-generation Chimera.  This next-generation software is already under development.

I have also advocated for a step-by-step record of all actions (whether by menu or command) as command equivalents or some other form that allows them to be easily reproduced.  Thanks for the additional reminder that this would be a useful feature.

Best,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 2, 2015, at 8:13 AM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Hi all,
> 
> Would it be possible at some point to allow the use of explicit parentheses when grouping selections on the command line? It would make it much easier/clearer when using multiple boolean operations (e.g "ligand z<5 &~ ligand &~ solvent? could be ?ligand z<5 &~(ligand | solvent)?). Is there a reason why this kind of syntax is not used at the moment?
> 
> Also, just a random thought for a future version - it would be really handy to have something like the ?Macro recorder? function of ImageJ or similar programs. This records whatever the user does using the GUI (while the recorder is active) and spits out the equivalent scripting commands to a dialog, where they can be saved and reused, or turned into a script. This can be a very powerful tool for learning the command line functionality of a complex application in an interactive manner.
> 
> Cheers,
> Oliver.




From olibclarke at gmail.com  Mon Mar  2 09:03:34 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Mon, 2 Mar 2015 12:03:34 -0500
Subject: [Chimera-users] explicit parentheses in atom selections
In-Reply-To: <CA6AE93C-1BBF-4882-9A1E-D0250FF91109@cgl.ucsf.edu>
References: <35A5A07F-28DA-450E-832E-D9A1A417F6EF@gmail.com>
	<CA6AE93C-1BBF-4882-9A1E-D0250FF91109@cgl.ucsf.edu>
Message-ID: <2B6F8607-A66A-4EAE-B4C3-DB06FF9E6B03@gmail.com>

Many thanks for the quick reply Elaine, and I look forward to seeing the next-gen Chimera, I?m sure it will be great!

In terms of command-line features that would be useful for the next-gen chimera, maybe you could have a look at IPython for inspiration? A more complex shell-like interface with tab-completion and an easily searchable history would be wonderful?

Oliver.
> On Mar 2, 2015, at 11:48 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Oliver,
> These are both things we have felt the need for and discussed in some depth.
> 
> My understanding is that with the current complicated atomspec parsing, it is not possible (with reasonable effort) to add parentheses, but they are definitely one of the things we intend to allow in atomspecs in the next-generation Chimera.  This next-generation software is already under development.
> 
> I have also advocated for a step-by-step record of all actions (whether by menu or command) as command equivalents or some other form that allows them to be easily reproduced.  Thanks for the additional reminder that this would be a useful feature.
> 
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Mar 2, 2015, at 8:13 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
>> Hi all,
>> 
>> Would it be possible at some point to allow the use of explicit parentheses when grouping selections on the command line? It would make it much easier/clearer when using multiple boolean operations (e.g "ligand z<5 &~ ligand &~ solvent? could be ?ligand z<5 &~(ligand | solvent)?). Is there a reason why this kind of syntax is not used at the moment?
>> 
>> Also, just a random thought for a future version - it would be really handy to have something like the ?Macro recorder? function of ImageJ or similar programs. This records whatever the user does using the GUI (while the recorder is active) and spits out the equivalent scripting commands to a dialog, where they can be saved and reused, or turned into a script. This can be a very powerful tool for learning the command line functionality of a complex application in an interactive manner.
>> 
>> Cheers,
>> Oliver.
> 




From olibclarke at gmail.com  Mon Mar  2 12:59:38 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Mon, 2 Mar 2015 15:59:38 -0500
Subject: [Chimera-users] rmsd calculation for pre aligned structures
Message-ID: <54E9A68D-E770-4C83-A311-D86D1E9590F8@gmail.com>

Hi,

I have two structures that are pre-aligned in another program, and I would like to calculate a per-residue rmsd between the two structures and assign this to an attribute that I can use to color one of the structures. 

Is there any way to do this at present? 

The mavRMSD attribute only seems to be calculated after matchmaker, not after using the regular ?rmsd? command. 

Perhaps there is a way to do a dummy run of matchmaker, somehow forcing both structures to remain fixed?

Best,
Oliver.


From meng at cgl.ucsf.edu  Mon Mar  2 13:33:57 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 2 Mar 2015 13:33:57 -0800
Subject: [Chimera-users] rmsd calculation for pre aligned structures
In-Reply-To: <54E9A68D-E770-4C83-A311-D86D1E9590F8@gmail.com>
References: <54E9A68D-E770-4C83-A311-D86D1E9590F8@gmail.com>
Message-ID: <DC5DAFE2-67A2-41C7-8F6C-5EF8A4AE7551@cgl.ucsf.edu>

Hi Oliver,
There isn't really any connection between mavRMSD and matchmaker.   You just need a sequence alignment associated with both structures (which I guess you were getting from Matchmaker), and then mavRMSD will show the actual separation between the residues in each column.  For example, if you then move one structure far away from the other, all the mavRMSD values will become high.

Instead of using Matchmaker to create the sequence alignment, you could open the two pre-aligned structures and then use Favorites? Sequence to show the sequence of one of them, and then from the sequence window (Multalign Viewer) menu, choose Edit? Add Sequence, From Structure (from the other structure) to create a two-sequence alignment.  Then just show the RMSD header of interest using the sequence window Headers menu.

You could use other ways of getting the sequence alignment.  If you already had a sequence alignment created outside of Chimera, you could just open it in Chimera and associate the two structures with the appropriate sequences, show RMSD header, etc.

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 2, 2015, at 12:59 PM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Hi,
> 
> I have two structures that are pre-aligned in another program, and I would like to calculate a per-residue rmsd between the two structures and assign this to an attribute that I can use to color one of the structures. 
> 
> Is there any way to do this at present? 
> 
> The mavRMSD attribute only seems to be calculated after matchmaker, not after using the regular ?rmsd? command. 
> 
> Perhaps there is a way to do a dummy run of matchmaker, somehow forcing both structures to remain fixed?
> 
> Best,
> Oliver.




From boris.steipe at utoronto.ca  Mon Mar  2 13:53:34 2015
From: boris.steipe at utoronto.ca (Boris Steipe)
Date: Mon, 2 Mar 2015 16:53:34 -0500
Subject: [Chimera-users] rmsd calculation for pre aligned structures
In-Reply-To: <54E9A68D-E770-4C83-A311-D86D1E9590F8@gmail.com>
References: <54E9A68D-E770-4C83-A311-D86D1E9590F8@gmail.com>
Message-ID: <0C81479E-C437-4360-9A6C-561142D804DB@utoronto.ca>

Oliver -
Are you sure this makes sense? Per-residue RMSD values are sensitive to domain shifts because they are influenced by global rotation/translation and don't really represent per-residue structural similarity. Of course this depends on what you want to achieve - but you may be better of using a rotation/translation invariant metric based on internal coordinates: distance differences or torsion angle differences.

Cheers,
Boris



On Mar 2, 2015, at 3:59 PM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Hi,
> 
> I have two structures that are pre-aligned in another program, and I would like to calculate a per-residue rmsd between the two structures and assign this to an attribute that I can use to color one of the structures. 
> 
> Is there any way to do this at present? 
> 
> The mavRMSD attribute only seems to be calculated after matchmaker, not after using the regular ?rmsd? command. 
> 
> Perhaps there is a way to do a dummy run of matchmaker, somehow forcing both structures to remain fixed?
> 
> Best,
> Oliver.
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From meng at cgl.ucsf.edu  Mon Mar  2 15:17:49 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 2 Mar 2015 15:17:49 -0800
Subject: [Chimera-users] rmsd calculation for pre aligned structures
In-Reply-To: <96DE28B3-E177-498C-80B4-49D97556755F@gmail.com>
References: <54E9A68D-E770-4C83-A311-D86D1E9590F8@gmail.com>
	<DC5DAFE2-67A2-41C7-8F6C-5EF8A4AE7551@cgl.ucsf.edu>
	<96DE28B3-E177-498C-80B4-49D97556755F@gmail.com>
Message-ID: <E50C1BC6-E708-4184-9870-0D72E9AEA7E1@cgl.ucsf.edu>

Hi Oliver,
In that case, you can just show the sequence of one protein, then use the sequence window menu: Structure? Associations to associate both structures with that one sequence, then sequence window Headers menu to show the RMSD of interest, etc.

This would work even if the sequences of the structures were slightly different, as long as they were both similar enough to the sequence in Multalign Viewer that Chimera could figure out the association accurately.
Elaine


On Mar 2, 2015, at 3:12 PM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Hi Elaine, thanks for the reply! This sounds like exactly the right solution. However, when I try to add a sequence in the sequence dialog, Chimera hangs on ?running Needleman-Wunsch?. 
> 
> I suspect this is because my sequences are so long (~5000 residues). 
> 
> But I don?t actually need to align them - they are already aligned as they are actually the same sequence, because I am looking at different conformations of the same protein. 
> 
> I guess I can create a dummy sequence alignment, with two identical sequences, but it would be nice to have some way of telling chimera not to align the sequences, or to allow for manual alignment in cases such as these - perhaps a ?Do not align? or ?align manually? checkbox in the add sequence dialog would do the trick.
> 
> Thanks again,
> Oliver.




From thrabe at sanfordburnham.org  Mon Mar  2 17:25:27 2015
From: thrabe at sanfordburnham.org (Thomas Hrabe)
Date: Tue, 3 Mar 2015 01:25:27 +0000
Subject: [Chimera-users] Select residue by array index, not residue id
Message-ID: <71E83167-ED05-4952-8215-D34593C83065@sanfordburnham.org>

Hi everyone,

is there a way to select a residue by it?s array index, starting at 0 -> sequence length rather than using the residue id?

Thank you in advance for your help,
Thomas



From pett at cgl.ucsf.edu  Tue Mar  3 11:11:08 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 3 Mar 2015 11:11:08 -0800
Subject: [Chimera-users] Select residue by array index, not residue id
In-Reply-To: <71E83167-ED05-4952-8215-D34593C83065@sanfordburnham.org>
References: <71E83167-ED05-4952-8215-D34593C83065@sanfordburnham.org>
Message-ID: <45F92E54-578C-49FF-8C40-78EC9E639EE8@cgl.ucsf.edu>

On Mar 2, 2015, at 5:25 PM, Thomas Hrabe <thrabe at sanfordburnham.org> wrote:

> Hi everyone,
> 
> is there a way to select a residue by it?s array index, starting at 0 -> sequence length rather than using the residue id?

Hi Thomas,
	I think the answer is no, using only normal Chimera commands.  However a simple Python script can do it, and such a script can be executed with the "runscript" command.  I have attached a script that takes a model number and a residue index as arguments and selects the corresponding residue.  If you put the script in your home directory then "runscript ~/selres.py 0 12" would select the 13th residue (input order) in model 0.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

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From sunyeping at aliyun.com  Tue Mar  3 23:14:57 2015
From: sunyeping at aliyun.com (sunyeping)
Date: Wed, 04 Mar 2015 15:14:57 +0800
Subject: [Chimera-users] =?utf-8?q?concatenate?=
Message-ID: <99054f98-a0c0-4232-b4ea-46c7c7dc05ac@aliyun.com>

Dear all,I am dealing with a EM map which is a double helical filament and composed of two protein chains winding each other. Each of the two chains is composed of multiple same protein subunits. Now I am trying to color one chain of the map with one color, and the other chain with another color. How should I do that?Besides, it is known that multiple such?double helixes can constitute a longer helix by a head-to-tail way. ?I can open several helixes in chimera, but how to concatenate they correctly into a long helix?Could you help me with these questions?With many thanks!??
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
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From emailanindito at yahoo.co.in  Wed Mar  4 01:44:44 2015
From: emailanindito at yahoo.co.in (Anindito Sen)
Date: Wed, 4 Mar 2015 09:44:44 +0000 (UTC)
Subject: [Chimera-users] Command for zooming in
Message-ID: <537142390.1799334.1425462284934.JavaMail.yahoo@mail.yahoo.com>

?Dear All,
What is the command for zooming into a portion of a density map ? This will be just using the command line ?for the zoom-in instead of using the middle mouse button.
Thanks
Andy



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From meng at cgl.ucsf.edu  Wed Mar  4 07:15:26 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 4 Mar 2015 07:15:26 -0800
Subject: [Chimera-users] Command for zooming in
In-Reply-To: <537142390.1799334.1425462284934.JavaMail.yahoo@mail.yahoo.com>
References: <537142390.1799334.1425462284934.JavaMail.yahoo@mail.yahoo.com>
Message-ID: <A32E9E8C-C09F-4A93-B6F6-E16879C6847A@cgl.ucsf.edu>

Hi Andy,
There is a ?scale? command (for example, ?scale 2? for double size)

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scale.html>

... or you can Z-translate with ?move z? (for example, ?move z 50? to move all models 50 A toward the viewer)

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/move.html>

See the links for additional command options.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 4, 2015, at 1:44 AM, Anindito Sen <emailanindito at yahoo.co.in> wrote:

>  Dear All,
> What is the command for zooming into a portion of a density map ? This will be just using the command line  for the zoom-in instead of using the middle mouse button.
> 
> Thanks
> 
> Andy




From meng at cgl.ucsf.edu  Wed Mar  4 07:34:05 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 4 Mar 2015 07:34:05 -0800
Subject: [Chimera-users] concatenate
In-Reply-To: <99054f98-a0c0-4232-b4ea-46c7c7dc05ac@aliyun.com>
References: <99054f98-a0c0-4232-b4ea-46c7c7dc05ac@aliyun.com>
Message-ID: <F2E1167A-0EF2-4119-855C-D211F4C542AE@cgl.ucsf.edu>

Dear Yeping Sun,

How you can refer to one chain or the other depends on how they are described in the input coordinate file (usually a PDB file).  If they are chains A and B you could use commands like:

color red :.A
color gold :.B

Or, maybe they are not different chains but different residue numbers, in which case you would have to use the residue numbers, something like:

color red :1-30
color gold :31-60

If you open one copy of the helical atomic structure, Chimera?s ?sym? command can open more copies to make a longer helix, but you would have to somehow tell it the correct symmetry information.  This can be done with the ?group? option of that command.  You can give helical symmetry directly (see the example in the manual page, link below) or, if your density map has the symmetry already assigned to it, you can just give its model number, e.g. ?group #1? if the map is model 1:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>

It might be hard to figure out the symmetry yourself.  You could try having Chimera guess the symmetry of the map with ?measure symmetry? command, but because it is more difficult for helical symmetry, you would still have to specify approximate parameters as input to that command:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#symmetry>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 3, 2015, at 11:14 PM, sunyeping <sunyeping at aliyun.com> wrote:

> Dear all,
> 
> I am dealing with a EM map which is a double helical filament and composed of two protein chains winding each other. Each of the two chains is composed of multiple same protein subunits. Now I am trying to color one chain of the map with one color, and the other chain with another color. How should I do that?
> 
> Besides, it is known that multiple such double helixes can constitute a longer helix by a head-to-tail way.  I can open several helixes in chimera, but how to concatenate they correctly into a long helix?
> 
> Could you help me with these questions?
> 
> With many thanks!  
> 
> Yeping Sun
> 
> Institute of Microbiology, Chinese Academy of Sciences




From pett at cgl.ucsf.edu  Wed Mar  4 13:29:06 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 4 Mar 2015 13:29:06 -0800
Subject: [Chimera-users] Request for support - UCSF Chimera
In-Reply-To: <CAHvTCeT9TjBJGwdHB4JSAO1bZbU=5uP4Kw=rZY_=NnZdJ_VvHg@mail.gmail.com>
References: <CAHvTCeT9TjBJGwdHB4JSAO1bZbU=5uP4Kw=rZY_=NnZdJ_VvHg@mail.gmail.com>
Message-ID: <4D6A43CE-C386-49DF-9132-D5B0B5CBABEF@cgl.ucsf.edu>

On Mar 4, 2015, at 10:14 AM, Nishant Ray Velagapudi <nishray at uw.edu> wrote:

> Hello Mr. Petterson,
> 
> I was looking for some help with using UCSF chimera and I was wondering if I can directly email you my question. If this is not the appropriate address, my apologies, and could you point me in the appropriate direction for support?

Hi Nishant,
	You should probably send questions like these to the chimera-users mailing list.  That way other people can benefit from the answer, and it also allows others to answer in the cases where I'm not really the best person for the question.

> My issue is that I want to automate the process of creating and saving structure based sequence alignments. It has been simple to open the file and align them, but I am not sure how to save the .fasta alignment file out. Here is what I have so far:
> 
> for fn in file_names:
> 	replyobj.status("Processing: " + fn)
> 	rc("open " + fn)
> 	rc(mm #0 #1 show true)
> 	rc("close " + fn)
> 
> The bold line is the problematic one - is there any way to write out the resulting alignment file in a programmatic fashion?

	Yes.  You can locate the MultAlign Viewer (MAV) instance using the code in this previous chimera-users mail:

http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010017.html

That message also describes how to save the alignment to a file, in conjunction with the info in this message:

http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010015.html

	You can search the chimera-users list from this page to see if your question has been asked previously:

http://www.cgl.ucsf.edu/chimera/docs/feedback.html

I hope this helps.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu


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From 21620101152414 at stu.xmu.edu.cn  Mon Mar  9 06:45:40 2015
From: 21620101152414 at stu.xmu.edu.cn (=?GB2312?B?wO7Wx7qj?=)
Date: Mon, 9 Mar 2015 21:45:40 +0800
Subject: [Chimera-users] How to lower the map size
Message-ID: <CD6D15AB-56A6-401B-9E1F-BC49BBA35C4F@stu.xmu.edu.cn>

Hi,

Now I have a density map with a dimension of 820*820*820, it is too large for me to perform image processes with Chimera. 
So I was wondering whether there is a way to decrease the map size rather than re-reconstruct the map with bined particle image.

please help me out! Thank you in advance!


Zhihai Li



From goddard at sonic.net  Mon Mar  9 10:02:38 2015
From: goddard at sonic.net (Tom Goddard)
Date: Mon, 9 Mar 2015 10:02:38 -0700
Subject: [Chimera-users] How to lower the map size
In-Reply-To: <CD6D15AB-56A6-401B-9E1F-BC49BBA35C4F@stu.xmu.edu.cn>
References: <CD6D15AB-56A6-401B-9E1F-BC49BBA35C4F@stu.xmu.edu.cn>
Message-ID: <AF895FB5-A360-4D33-B061-9DF017F1B674@sonic.net>

Hi Zhihai,

  If you set the ?step? value to 2 (above the histogram in the volume viewer dialog) then Chimera uses every other grid point along the 3 axes (8 times less data).  If you really want to produce a binned map (e.g. averaging 2x2x2 grid points to make a map half the size in each dimension), then use the Volume Filter dialog (menu Tools / Volume Data / Volume Filter) or the ?vop bin? command, then save the resulting map to a new file (Volume Viewer dialog menu File / Save Map As?).

	Tom


	
> On Mar 9, 2015, at 6:45 AM, ??? <21620101152414 at stu.xmu.edu.cn> wrote:
> 
> Hi,
> 
> Now I have a density map with a dimension of 820*820*820, it is too large for me to perform image processes with Chimera. 
> So I was wondering whether there is a way to decrease the map size rather than re-reconstruct the map with bined particle image.
> 
> please help me out! Thank you in advance!
> 
> 
> Zhihai Li
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From devicerandom at gmail.com  Wed Mar 11 05:24:53 2015
From: devicerandom at gmail.com (ms)
Date: Wed, 11 Mar 2015 13:24:53 +0100
Subject: [Chimera-users] Interaction interface between two residues and
	measure buriedArea
Message-ID: <55003415.8020800@gmail.com>

Dear all,

I am trying to understand what is the area buried between two residues 
(or between one residue and two other ones) in several structures. It 
seemed to me the best way to do this was to use the command "measure 
buriedArea :res1 :res2" on the full structure (once all non-protein 
components have been cleaned out of it). The overall trend of these 
measures seems consistent with visual inspection.

However I have a couple of questions about it:

1) I am unsure about what value is best to use/compare, buriedSAS and 
buriedSES. It seems to me that the difference between the two is 
essentially in the geometrical protocol used. Is there any general 
wisdom about what do they physically mean and how should I approach each 
value?

2) In some cases I receive *negative* values for buriedSAS and/or 
buriedSES. Looking on the ML it seems that it is a symptom of a buggy or 
failed area calculation (e.g. 
http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-April/005119.html 
). However it also says that I should see a "fallback" warning on the 
Reply Log -I see nothing of the sort. How do I troubleshoot this? Also 
in cases where the calculated value is positive, how can I be sure that 
the values are indeed meaningful?

Any other feedback on the kind of measurement I am trying to do is more 
than welcome.

Thanks a lot,
Massimo


From urszula.uciechowska at biotech.ug.edu.pl  Wed Mar 11 05:33:00 2015
From: urszula.uciechowska at biotech.ug.edu.pl (Urszula Uciechowska)
Date: Wed, 11 Mar 2015 13:33:00 +0100
Subject: [Chimera-users] join DNA base pairs
In-Reply-To: <55003415.8020800@gmail.com>
References: <55003415.8020800@gmail.com>
Message-ID: <449ec080c61dafebd84ddc0fdd084b7a.squirrel@poczta.ug.edu.pl>



Dear chimera users,

Is it possible to join the DNA bases? I could not find it in manual.

best regards
Urszula

University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Kladki 24
80-822 Gdansk
Poland


-----------------------------------------
Ta wiadomo?? zosta?a wys?ana z serwera Uniwersytetu Gda?skiego
http://www.ug.edu.pl/



From devicerandom at gmail.com  Wed Mar 11 06:56:23 2015
From: devicerandom at gmail.com (ms)
Date: Wed, 11 Mar 2015 14:56:23 +0100
Subject: [Chimera-users] join DNA base pairs
In-Reply-To: <449ec080c61dafebd84ddc0fdd084b7a.squirrel@poczta.ug.edu.pl>
References: <55003415.8020800@gmail.com>
	<449ec080c61dafebd84ddc0fdd084b7a.squirrel@poczta.ug.edu.pl>
Message-ID: <55004987.6040303@gmail.com>

On 3/11/15 1:33 PM, Urszula Uciechowska wrote:
> Dear chimera users,
>
> Is it possible to join the DNA bases? I could not find it in manual.
What do you actually mean?

>
> best regards
> Urszula
>
> University of Gdansk and Medical Univesity of Gdansk
> Department of Molecular and Cellular Biology
> ul. Kladki 24
> 80-822 Gdansk
> Poland
>
>
> -----------------------------------------
> Ta wiadomo?? zosta?a wys?ana z serwera Uniwersytetu Gda?skiego
> http://www.ug.edu.pl/
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



From urszula.uciechowska at biotech.ug.edu.pl  Wed Mar 11 07:25:36 2015
From: urszula.uciechowska at biotech.ug.edu.pl (Urszula Uciechowska)
Date: Wed, 11 Mar 2015 15:25:36 +0100
Subject: [Chimera-users] mutation DNA base pairs
In-Reply-To: <449ec080c61dafebd84ddc0fdd084b7a.squirrel@poczta.ug.edu.pl>
References: <55003415.8020800@gmail.com>
	<449ec080c61dafebd84ddc0fdd084b7a.squirrel@poczta.ug.edu.pl>
Message-ID: <fba03280268626aef5d48101e51ea5e9.squirrel@poczta.ug.edu.pl>


Dear chimera users,

I was wondering if its possible to mutate DNA base pair (G-C etc.)in
chimera using swapa command?

Thank you in advance for any suggestions
Urszula Uciechowska

>
>
> Dear chimera users,
>
> Is it possible to join the DNA bases? I could not find it in manual.
>
> best regards
> Urszula
>
> University of Gdansk and Medical Univesity of Gdansk
> Department of Molecular and Cellular Biology
> ul. Kladki 24
> 80-822 Gdansk
> Poland
>
>
> -----------------------------------------
> Ta wiadomo?? zosta?a wys?ana z serwera Uniwersytetu Gda?skiego
> http://www.ug.edu.pl/
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>


University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Kladki 24
80-822 Gdansk
Poland


-----------------------------------------
Ta wiadomo?? zosta?a wys?ana z serwera Uniwersytetu Gda?skiego
http://www.ug.edu.pl/



From meng at cgl.ucsf.edu  Wed Mar 11 09:37:27 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 11 Mar 2015 09:37:27 -0700
Subject: [Chimera-users] Interaction interface between two residues and
	measure buriedArea
In-Reply-To: <55003415.8020800@gmail.com>
References: <55003415.8020800@gmail.com>
Message-ID: <42DFF2D2-18F1-489A-A160-6953CCE3BCF7@cgl.ucsf.edu>

Hi Massimo,
(1) I am not aware of any clear-cut rules of which to use for what purposes.  SES is where the probe sphere (crudely representing water) touches, SAS is where the probe sphere center can go.  There have been some efforts to derive an energy value per unit area of hydrophobic surface buried, so if you were using that kind of multiplier you would of course use the measure for which it was developed.  Otherwise, you could just think about the geometric definitions and see if one or the other fits what you are trying to measure.  There are some pictures on the web illustrating the difference, e.g. Fig 3 here:
<http://ieeexplore.ieee.org/ieee_pilot/articles/06/ttg2009061391/figures.html>

(2) The fallback warning is something about certain calculations failing so that only a single component (e.g. outer envelope and not interior bubbles) is calculated, but it would still show up as a warning in the Reply Log, so I wouldn?t worry about the specifics.  I believe it is rare, but sometimes there are errors or visible singularities in the surface that occur without a warning going to the Reply Log.  I don?t think we can do or say much about this.  In Chimera, molecular surfaces are created with embedded software from the MSMS package.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces>

One issue is that you are stretching the functionality beyond its intended purposes.  Measure buriedarea was mainly intended for looking at intermolecular or interdomain interfaces, not for measuring the area of single residues packing against each other within a protein.  When you are using it on these smaller subparts, possibly with more tortuous shapes, I imagine there would be a greater chance of errors.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 11, 2015, at 5:24 AM, ms <devicerandom at gmail.com> wrote:

> Dear all,
> I am trying to understand what is the area buried between two residues (or between one residue and two other ones) in several structures. It seemed to me the best way to do this was to use the command "measure buriedArea :res1 :res2" on the full structure (once all non-protein components have been cleaned out of it). The overall trend of these measures seems consistent with visual inspection.
> 
> However I have a couple of questions about it:
> 
> 1) I am unsure about what value is best to use/compare, buriedSAS and buriedSES. It seems to me that the difference between the two is essentially in the geometrical protocol used. Is there any general wisdom about what do they physically mean and how should I approach each value?
> 
> 2) In some cases I receive *negative* values for buriedSAS and/or buriedSES. Looking on the ML it seems that it is a symptom of a buggy or failed area calculation (e.g. http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-April/005119.html ). However it also says that I should see a "fallback" warning on the Reply Log -I see nothing of the sort. How do I troubleshoot this? Also in cases where the calculated value is positive, how can I be sure that the values are indeed meaningful?
> 
> Any other feedback on the kind of measurement I am trying to do is more than welcome.
> Thanks a lot,
> Massimo




From meng at cgl.ucsf.edu  Wed Mar 11 09:41:22 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 11 Mar 2015 09:41:22 -0700
Subject: [Chimera-users] join DNA base pairs
In-Reply-To: <449ec080c61dafebd84ddc0fdd084b7a.squirrel@poczta.ug.edu.pl>
References: <55003415.8020800@gmail.com>
	<449ec080c61dafebd84ddc0fdd084b7a.squirrel@poczta.ug.edu.pl>
Message-ID: <3B14813A-2B8B-42FB-8CD3-C27C6C90E675@cgl.ucsf.edu>

Dear Urszula,
If you just wanted to add a bond, you can use the ?bond? command, for example ?bond sel? if you have selected the two atoms,
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html>

?or the Build Structure tool (in menu under Tools? Structure Editing), the Adjust Bonds section
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 11, 2015, at 5:33 AM, Urszula Uciechowska <urszula.uciechowska at biotech.ug.edu.pl> wrote:

> Dear chimera users,
> Is it possible to join the DNA bases? I could not find it in manual.
> best regards
> Urszula




From meng at cgl.ucsf.edu  Wed Mar 11 09:51:50 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 11 Mar 2015 09:51:50 -0700
Subject: [Chimera-users] mutation DNA base pairs
In-Reply-To: <fba03280268626aef5d48101e51ea5e9.squirrel@poczta.ug.edu.pl>
References: <55003415.8020800@gmail.com>
	<449ec080c61dafebd84ddc0fdd084b7a.squirrel@poczta.ug.edu.pl>
	<fba03280268626aef5d48101e51ea5e9.squirrel@poczta.ug.edu.pl>
Message-ID: <34C577A3-987A-4791-B301-471A8EF3819A@cgl.ucsf.edu>

Dear Urszula,
The command for mutating a DNA base is ?swapna? - you would have to use it twice, one time for each member of the pair.  
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapna.html>

For example, if your base pair was between residue 2 in chain A named DG and residue 23 in chain B named DC, to change them into DA-DT it would be something like:

swapna A :2.A preserve true
swapna T :23.B preserve true

Or you could omit ?preserve true? ? see the manual page linked above for details.  The pairing geometry might not be that good after the swap, but you could rotate the bonds manually if you wanted (see Build Structure tool, Adjust Torsions section):
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>

To get the heteroatom color-coding on the new bases (red oxygen and blue nitrogen) you could use command ?color byhet? 

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 11, 2015, at 7:25 AM, Urszula Uciechowska <urszula.uciechowska at biotech.ug.edu.pl> wrote:

> Dear chimera users,
> 
> I was wondering if its possible to mutate DNA base pair (G-C etc.)in
> chimera using swapa command?
> 
> Thank you in advance for any suggestions
> Urszula Uciechowska
> 




From olibclarke at gmail.com  Wed Mar 11 13:20:59 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Wed, 11 Mar 2015 16:20:59 -0400
Subject: [Chimera-users] binned color ranges for scolor?
Message-ID: <1849A551-8565-4266-9BD7-AD834F4A8B5A@gmail.com>

Hi all, 

I was wondering whether it is possible to use binned ranges for scolor? 

Specifically, I would like to color one volume by the density values of a second volume, but rather than using a continuous color palette, I would like to highlight several discrete bins with particular colors - e.g coloring all values between 2 and 4 red, and all values between 6 and 8 green, while leaving other voxels uncolored (or colored gray, for example). 

Is this currently possible? I couldn?t figure it out - both cmap and map range seem to give continuous coloring.

Best,
Oliver.


From meng at cgl.ucsf.edu  Wed Mar 11 13:43:05 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 11 Mar 2015 13:43:05 -0700
Subject: [Chimera-users] binned color ranges for scolor?
In-Reply-To: <1849A551-8565-4266-9BD7-AD834F4A8B5A@gmail.com>
References: <1849A551-8565-4266-9BD7-AD834F4A8B5A@gmail.com>
Message-ID: <A1988A67-8796-4A09-B2F6-546FBD0D1610@cgl.ucsf.edu>

Hi Oliver,
Yes, but only by doing it sort of manually, i.e., by giving the same color twice at the lower and upper bounds of the bin.  For example, to color red up to .19999, blue .2-.29999, yellow .3 and up:

scolor #0 volume #1 cmap .19999,red:.2,blue:.29999,blue:.3,yellow

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#options>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 11, 2015, at 1:20 PM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Hi all, 
> I was wondering whether it is possible to use binned ranges for scolor? 
> 
> Specifically, I would like to color one volume by the density values of a second volume, but rather than using a continuous color palette, I would like to highlight several discrete bins with particular colors - e.g coloring all values between 2 and 4 red, and all values between 6 and 8 green, while leaving other voxels uncolored (or colored gray, for example). 
> 
> Is this currently possible? I couldn?t figure it out - both cmap and map range seem to give continuous coloring.
> Best,
> Oliver.




From goddard at sonic.net  Wed Mar 11 15:18:28 2015
From: goddard at sonic.net (Tom Goddard)
Date: Wed, 11 Mar 2015 15:18:28 -0700
Subject: [Chimera-users] Interaction interface between two residues and
	measure buriedArea
In-Reply-To: <55003415.8020800@gmail.com>
References: <55003415.8020800@gmail.com>
Message-ID: <9943A754-F708-4C8E-AB95-D45596C62953@sonic.net>

Hi Massimo,

  I think buried solvent accessible area (SAS) is most often used when buried areas are reported.  Negative values of buried SAS are impossible, that would be a bug, probably a failure of the surface calculation, and if you see a case of that could you send me a Chimera session that demostrates it?  Unfortunately with erratic surface calculation (which does not always report when it goes awry) you cannot be certain the numbers are correct.  I think buried SES can give a negative value in weird cases because the toroidal surface patches created by the probe sphere rolling between the two sets of atoms could be large (e.g. the buried area between two spheres whose surfaces are separate by a bit less than the probe radius).

	Tom


> On Mar 11, 2015, at 5:24 AM, ms <devicerandom at gmail.com> wrote:
> 
> Dear all,
> 
> I am trying to understand what is the area buried between two residues (or between one residue and two other ones) in several structures. It seemed to me the best way to do this was to use the command "measure buriedArea :res1 :res2" on the full structure (once all non-protein components have been cleaned out of it). The overall trend of these measures seems consistent with visual inspection.
> 
> However I have a couple of questions about it:
> 
> 1) I am unsure about what value is best to use/compare, buriedSAS and buriedSES. It seems to me that the difference between the two is essentially in the geometrical protocol used. Is there any general wisdom about what do they physically mean and how should I approach each value?
> 
> 2) In some cases I receive *negative* values for buriedSAS and/or buriedSES. Looking on the ML it seems that it is a symptom of a buggy or failed area calculation (e.g. http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-April/005119.html ). However it also says that I should see a "fallback" warning on the Reply Log -I see nothing of the sort. How do I troubleshoot this? Also in cases where the calculated value is positive, how can I be sure that the values are indeed meaningful?
> 
> Any other feedback on the kind of measurement I am trying to do is more than welcome.
> 
> Thanks a lot,
> Massimo
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From devicerandom at gmail.com  Wed Mar 11 15:48:21 2015
From: devicerandom at gmail.com (ms)
Date: Wed, 11 Mar 2015 23:48:21 +0100
Subject: [Chimera-users] Interaction interface between two residues and
 measure buriedArea
In-Reply-To: <9943A754-F708-4C8E-AB95-D45596C62953@sonic.net>
References: <55003415.8020800@gmail.com>
	<9943A754-F708-4C8E-AB95-D45596C62953@sonic.net>
Message-ID: <5500C635.9090100@gmail.com>

Hi Tom,

Thanks for your reply.

On 11/03/15 23:18, Tom Goddard wrote:

> I think buried solvent accessible area (SAS) is most often used when
> buried areas are reported.

OK, thanks. Any justification in the literature for that, just to be on 
the safe side?

> Negative values of buried SAS are
> impossible, that would be a bug, probably a failure of the surface
> calculation,

OK.

> and if you see a case of that could you send me a
> Chimera session that demostrates it?

I will do it tomorrow.

> Unfortunately with erratic
> surface calculation (which does not always report when it goes awry)
> you cannot be certain the numbers are correct.

Understood. If so, is there any sanity check I can do to see if a 
calculation has more or less chances of being meaningful?

thanks,
Massimo

-- 
Massimo Sandal, Ph.D.
http://devicerandom.org


From goddard at sonic.net  Wed Mar 11 16:11:12 2015
From: goddard at sonic.net (Tom Goddard)
Date: Wed, 11 Mar 2015 16:11:12 -0700
Subject: [Chimera-users] Interaction interface between two residues and
	measure buriedArea
In-Reply-To: <5500C635.9090100@gmail.com>
References: <55003415.8020800@gmail.com>
	<9943A754-F708-4C8E-AB95-D45596C62953@sonic.net>
	<5500C635.9090100@gmail.com>
Message-ID: <DCC95EB6-2C46-48B8-BD3F-05CAD2E5E05D@sonic.net>

Hi Massimo,

 I think the reason buried solvent accessible area is usually reported is because it is probably better correlated with the solvation energy, how much energy is related to the water / protein interface, then solvent excluded area.  This makes some sense to me because the SAS surface is where the ?probe? sphere representing a water molecule is centered so it roughly says how many spheres or water molecules you can pack against the protein.  This is all just my guess.  The only case where I have read literature on this topic is studies that try to identify biologically meaningful protein-protein interfaces in X-ray crystal structures by measuring buried areas.

  A sanity check on your buried area values (after checking that they are positive) is try changing the probe radius by a small bit and see if you get just a small change in buried area.  This will cause different surfaces to be computed but should result in a small area change if the calculation is correct.  The default probe radius is 1.4 Angstroms, so try ?measure buried #0 #1 probe 1.45?.

	Tom


> On Mar 11, 2015, at 3:48 PM, ms wrote:
> 
> Hi Tom,
> 
> Thanks for your reply.
> 
> On 11/03/15 23:18, Tom Goddard wrote:
> 
>> I think buried solvent accessible area (SAS) is most often used when
>> buried areas are reported.
> 
> OK, thanks. Any justification in the literature for that, just to be on the safe side?
> 
>> Negative values of buried SAS are
>> impossible, that would be a bug, probably a failure of the surface
>> calculation,
> 
> OK.
> 
>> and if you see a case of that could you send me a
>> Chimera session that demostrates it?
> 
> I will do it tomorrow.
> 
>> Unfortunately with erratic
>> surface calculation (which does not always report when it goes awry)
>> you cannot be certain the numbers are correct.
> 
> Understood. If so, is there any sanity check I can do to see if a calculation has more or less chances of being meaningful?
> 
> thanks,
> Massimo
> 
> -- 
> Massimo Sandal, Ph.D.
> http://devicerandom.org
> 




From urszula.uciechowska at biotech.ug.edu.pl  Thu Mar 12 07:47:28 2015
From: urszula.uciechowska at biotech.ug.edu.pl (Urszula Uciechowska)
Date: Thu, 12 Mar 2015 15:47:28 +0100
Subject: [Chimera-users] join DNA base pairs
In-Reply-To: <449ec080c61dafebd84ddc0fdd084b7a.squirrel@poczta.ug.edu.pl>
References: <55003415.8020800@gmail.com>
	<449ec080c61dafebd84ddc0fdd084b7a.squirrel@poczta.ug.edu.pl>
Message-ID: <1ccc5b5b3b66a21d5aee779351dea783.squirrel@poczta.ug.edu.pl>

Dear chimera users,

 Is it possible to join the DNA bases? I could not find it in manual. I
would like to join the Guanine with Thymine. I saw in the Build
Structure/Join Models form other bond. However is not working for me in
this case.

 best regards
 Urszula


University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Kladki 24
80-822 Gdansk
Poland


-----------------------------------------
Ta wiadomo?? zosta?a wys?ana z serwera Uniwersytetu Gda?skiego
http://www.ug.edu.pl/



From meng at cgl.ucsf.edu  Thu Mar 12 08:48:27 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 12 Mar 2015 08:48:27 -0700
Subject: [Chimera-users] join DNA base pairs
In-Reply-To: <1ccc5b5b3b66a21d5aee779351dea783.squirrel@poczta.ug.edu.pl>
References: <55003415.8020800@gmail.com>
	<449ec080c61dafebd84ddc0fdd084b7a.squirrel@poczta.ug.edu.pl>
	<1ccc5b5b3b66a21d5aee779351dea783.squirrel@poczta.ug.edu.pl>
Message-ID: <5BDD0DD6-DE35-459D-975C-9CCBFE4CAA3D@cgl.ucsf.edu>

Dear Urszula,
Build Structure/Join Models is only for when the two parts are in two different models (if you opened those parts from two separate files, for example).

If the bases are in the same model already, you would instead use Build Structure/Adjust Bonds, or the "bond" command, as suggested in my previous reply:

<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-March/010766.html>

Or, if you are building starting from nothing, use Build Structure/Start Structure.  It can build helical DNA and/or RNA.

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 12, 2015, at 7:47 AM, "Urszula Uciechowska" <urszula.uciechowska at biotech.ug.edu.pl> wrote:

> Dear chimera users,
> 
> Is it possible to join the DNA bases? I could not find it in manual. I
> would like to join the Guanine with Thymine. I saw in the Build
> Structure/Join Models form other bond. However is not working for me in
> this case.
> 
> best regards
> Urszula




From msufian at outlook.com  Thu Mar 12 05:10:26 2015
From: msufian at outlook.com (Muhammad Sufian)
Date: Thu, 12 Mar 2015 17:10:26 +0500
Subject: [Chimera-users] UCSF Chimera error: X Error of failed request:
 BadDrawable (invalid Pixmap or Window parameter)
Message-ID: <BAY180-W655B5B2B5871CE3AB47474B7060@phx.gbl>




Dear all Chimera users,

I tried to install following version of Chimera;
  chimera-1.10.1-linux_x86_64.bin

but after installation, following error appeared after its execution;
sufian at system01:/usr/local/chimera/bin> ./chimera
X Error of failed request:  BadDrawable (invalid Pixmap or Window parameter)
  Major opcode of failed request:  72 (X_PutImage)
  Resource id in failed request:  0x2200064
  Serial number of failed request:  1357
  Current serial number in output stream:  1363

I also tried to install Chimera 1.9, but got same error. My system specifications are;
  Processor: x86_64 
  Operating-system: GNU/Linux (OpenSUSE 12.1)
  Kernel: Linux 3.4.63-2.44-desktop

Kindly guide me how to resolve this issue.

Regards.


Muhammad SufianM.Phil. scholar (Molecular Medicine),Computational Biology Laboratory,Lab no. P-103, PCMD-Extension,Dr. Panjwani Center for Molecular Medicine and Drug ResearchInternational Center for Chemical and Biological SciencesUniversity of Karachi, Karachi, Pakistan
 		 	   		  
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From t.f.leong at dundee.ac.uk  Thu Mar 12 07:34:06 2015
From: t.f.leong at dundee.ac.uk (Tein Leong (PG Research))
Date: Thu, 12 Mar 2015 14:34:06 +0000
Subject: [Chimera-users] Selecting just 1 carbohydrate chain
Message-ID: <E514F20F-CEE3-4485-A7FE-6BF461E5A61E@dundee.ac.uk>

Hello,

Thank you for the amazing programme. I?m using it for the first time and I can do most of the things I needed to do. I am writing to ask if it is possible to ?color? just one carbohydrate chain ?
I?m coloring an antibody crystal structure which is made up of two heavy chains. Each chain has a carbohydrate attached. I wanted to color both carbohydrate in different colors but I?m unable to do so. When I go to ?Select? > ?Residue? , the programme can only select all carbohydrate residues. Please advice.

Thanks !

Best wishes,
Tein Foong Leong
PhD Student
Jacqui Wood Cancer Centre, Level 7
Ninewells Hospital
University of Dundee
DD1 9SY




The University of Dundee is a registered Scottish Charity, No: SC015096



From meng at cgl.ucsf.edu  Thu Mar 12 11:07:56 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 12 Mar 2015 11:07:56 -0700
Subject: [Chimera-users] Selecting just 1 carbohydrate chain
In-Reply-To: <E514F20F-CEE3-4485-A7FE-6BF461E5A61E@dundee.ac.uk>
References: <E514F20F-CEE3-4485-A7FE-6BF461E5A61E@dundee.ac.uk>
Message-ID: <8A41566A-A15C-4063-88DC-5FCBBCAE61A5@cgl.ucsf.edu>

Hello Tein Foong Leong,
There are many ways to specify only a particular residue or chain.  You can see the residue number and chain ID of a residue by hovering the cursor over it and seeing the information that pops up.

(A) One way is by residue number and chain ID in the command line (show command line from the Favorites menu).  For example, command:

color red :15.C

? colors only residue number 15 in chain C.  

(B) Or, you might want to select the residue interactively in the Chimera window.  You can select an atom with Ctrl-click and then press keyboard up arrow to expand the selection (see green highlights) to the whole residue, or up arrow again to whole chain (or down arrow to go back down if you overshoot).  You can select an atom in one residue with Ctrl-click and then another atom in another residue with Shift-Ctrl-click?. then up arrow will expand to both of those whole residues.

(C ) Or, with select menu you could first select all carbohydrates and then deselect only the ones with a specific chain ID with either a command (for example, "~select :.B" would deselect chain B only) or the menu:

menu: Select? Selection Mode? subtract
menu: Select? Chain? B
menu: Select? Selection Mode? replace

(the latter to change the mode back to replace so that you don't get confused later by the subtraction mode)

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 12, 2015, at 7:34 AM, "Tein Leong (PG Research)" <t.f.leong at dundee.ac.uk> wrote:

> Hello,
> 
> Thank you for the amazing programme. I?m using it for the first time and I can do most of the things I needed to do. I am writing to ask if it is possible to ?color? just one carbohydrate chain ?
> I?m coloring an antibody crystal structure which is made up of two heavy chains. Each chain has a carbohydrate attached. I wanted to color both carbohydrate in different colors but I?m unable to do so. When I go to ?Select? > ?Residue? , the programme can only select all carbohydrate residues. Please advice.
> 
> Thanks !
> 
> Best wishes,
> Tein Foong Leong
> PhD Student
> Jacqui Wood Cancer Centre, Level 7
> Ninewells Hospital
> University of Dundee
> DD1 9SY




From gregc at cgl.ucsf.edu  Thu Mar 12 12:58:00 2015
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Thu, 12 Mar 2015 12:58:00 -0700
Subject: [Chimera-users] UCSF Chimera error: X Error of failed request:
 BadDrawable (invalid Pixmap or Window parameter)
In-Reply-To: <BAY180-W655B5B2B5871CE3AB47474B7060@phx.gbl>
References: <BAY180-W655B5B2B5871CE3AB47474B7060@phx.gbl>
Message-ID: <5501EFC8.4070704@cgl.ucsf.edu>

Try running "chimera --debug", it should give a clue where in the 
initialization process chimera died.  That said, it is most likely a 
graphics driver bug.  Run "lspci | grep VGA" to see what kind of 
graphics card you have.  Then, if OpenSUSE has a tool or package for 
that graphics card, install it.  If not, if you have ATI/AMD or NVIDIA 
graphics, you will download the right driver from amd.com or nvidia.com, 
respectively, and install it.  If you have Intel graphics, upgrade your 
system to OpenSUSE 13.2.

     Best of luck and please let me know if updating the graphics driver 
fixes the bug,

     Greg

On 03/12/2015 05:10 AM, Muhammad Sufian wrote:
> Dear all Chimera users,
>
> I tried to install following version of Chimera;
> *chimera-1.10.1-linux_x86_64.bin*
>
> but after installation, following error appeared after its execution;
> *sufian at system01:/usr/local/chimera/bin> ./chimera
> X Error of failed request: BadDrawable (invalid Pixmap or Window 
> parameter)
>   Major opcode of failed request:  72 (X_PutImage)
>   Resource id in failed request: 0x2200064
>   Serial number of failed request: 1357
>   Current serial number in output stream:  1363*
>
> I also tried to install Chimera 1.9, but got same error. My system 
> specifications are;
>   Processor: x86_64
>   Operating-system: GNU/Linux (OpenSUSE 12.1)
>   Kernel: Linux 3.4.63-2.44-desktop
>
> Kindly guide me how to resolve this issue.
>
> Regards.
>
>
> *Muhammad Sufian*
> M.Phil. scholar (Molecular Medicine),
> Computational Biology Laboratory,
> Lab no. P-103, PCMD-Extension,
> Dr. Panjwani Center for Molecular Medicine and Drug Research
> International Center for Chemical and Biological Sciences
> University of Karachi, Karachi, Pakistan
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From gregc at cgl.ucsf.edu  Fri Mar 13 09:17:07 2015
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Fri, 13 Mar 2015 09:17:07 -0700
Subject: [Chimera-users] UCSF Chimera error: X Error of failed request:
 BadDrawable (invalid Pixmap or Window parameter)
In-Reply-To: <BAY180-W15B8ABFBC7963404041EB0B7070@phx.gbl>
References: <BAY180-W655B5B2B5871CE3AB47474B7060@phx.gbl>,
	<5501EFC8.4070704@cgl.ucsf.edu>
	<BAY180-W15B8ABFBC7963404041EB0B7070@phx.gbl>
Message-ID: <55030D83.1020001@cgl.ucsf.edu>

I'm sorry, the Matrix graphics is more of a hindrance than a help. It 
uses the software only OpenGL driver, Mesa, to do its 3D drawing.  And 
the easiest way to get a newer version of Mesa on your system is to 
update it to OpenSUSE 13.2 or the latest Ubuntu.  If you have the option 
of installing an AMD or NVIDIA graphics card in your system, do so, and 
install the proprietary driver.  It will be like going from walking to 
driving a car -- much faster, and you can buy a budget car, a regular 
car, or race car, depending on your budget. :-)

     HTH,

     Greg

On 3/13/2015 12:27 AM, Muhammad Sufian wrote:
> Dear Greg,
>
> I have tried debugging Chimera and the issue is related to OpenGL;
>
> *sufian at system01:~> chimera --debug
>   initializing general preferences
>   loading Tix
>   initializing graphics
>   create application
>   loading Pmw
>   creating main window
>   creating menus
>   creating toolbar
>   creating viewer
>   initializing OpenGL
> X Error of failed request: BadDrawable (invalid Pixmap or Window 
> parameter)
>     Major opcode of failed request:  72 (X_PutImage)
>     Resource id in failed request: 0x4000064
>     Serial number of failed request:  2678
>     Current serial number in output stream: 2682*
>
> Then I checked for PCI as per your mentioned command;
>
> *sufian at system01:~ # lspci | grep VGA
> 03:00.0 VGA compatible controller: Matrox Electronics Systems Ltd. MGA 
> G200EV*
>
> I checked *yast2* for any driver update, and it was up to date. I 
> don't want to switch to *OpenSUSE 13.2* for now.
> Is there any earlier version of Chimera specific to my VGA ? I have 
> also tried Chimera 1.8, but got same error.
>
> Kindly guide me.
>
>
> *Muhammad Sufian*
>
>
> ------------------------------------------------------------------------
> Date: Thu, 12 Mar 2015 12:58:00 -0700
> From: gregc at cgl.ucsf.edu
> To: msufian at outlook.com; chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] UCSF Chimera error: X Error of failed 
> request: BadDrawable (invalid Pixmap or Window parameter)
>
> Try running "chimera --debug", it should give a clue where in the 
> initialization process chimera died.  That said, it is most likely a 
> graphics driver bug.  Run "lspci | grep VGA" to see what kind of 
> graphics card you have.  Then, if OpenSUSE has a tool or package for 
> that graphics card, install it.  If not, if you have ATI/AMD or NVIDIA 
> graphics, you will download the right driver from amd.com or 
> nvidia.com, respectively, and install it.  If you have Intel graphics, 
> upgrade your system to OpenSUSE 13.2.
>
>     Best of luck and please let me know if updating the graphics 
> driver fixes the bug,
>
>     Greg
>
> On 03/12/2015 05:10 AM, Muhammad Sufian wrote:
>
>     Dear all Chimera users,
>
>     I tried to install following version of Chimera;
>     *chimera-1.10.1-linux_x86_64.bin*
>
>     but after installation, following error appeared after its execution;
>     *sufian at system01:/usr/local/chimera/bin> ./chimera
>     X Error of failed request:  BadDrawable (invalid Pixmap or Window
>     parameter)
>       Major opcode of failed request:  72 (X_PutImage)
>       Resource id in failed request:  0x2200064
>       Serial number of failed request:  1357
>       Current serial number in output stream:  1363*
>
>     I also tried to install Chimera 1.9, but got same error. My system
>     specifications are;
>       Processor: x86_64
>       Operating-system: GNU/Linux (OpenSUSE 12.1)
>       Kernel: Linux 3.4.63-2.44-desktop
>
>     Kindly guide me how to resolve this issue.
>
>     Regards.
>
>
>     *Muhammad Sufian*
>     M.Phil. scholar (Molecular Medicine),
>     Computational Biology Laboratory,
>     Lab no. P-103, PCMD-Extension,
>     Dr. Panjwani Center for Molecular Medicine and Drug Research
>     International Center for Chemical and Biological Sciences
>     University of Karachi, Karachi, Pakistan
>
>
>     _______________________________________________
>     Chimera-users mailing list
>     Chimera-users at cgl.ucsf.edu  <mailto:Chimera-users at cgl.ucsf.edu>
>     http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>

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From msufian at outlook.com  Fri Mar 13 00:27:11 2015
From: msufian at outlook.com (Muhammad Sufian)
Date: Fri, 13 Mar 2015 12:27:11 +0500
Subject: [Chimera-users] UCSF Chimera error: X Error of failed request:
 BadDrawable (invalid Pixmap or Window parameter)
In-Reply-To: <5501EFC8.4070704@cgl.ucsf.edu>
References: <BAY180-W655B5B2B5871CE3AB47474B7060@phx.gbl>,
	<5501EFC8.4070704@cgl.ucsf.edu>
Message-ID: <BAY180-W15B8ABFBC7963404041EB0B7070@phx.gbl>

Dear Greg,

I have tried debugging Chimera and the issue is related to OpenGL;

sufian at system01:~> chimera --debug
  initializing general preferences
  loading Tix
  initializing graphics
  create application
  loading Pmw
  creating main window
  creating menus
  creating toolbar
  creating viewer
  initializing OpenGL
  X Error of failed request:  BadDrawable (invalid Pixmap or Window parameter)
    Major opcode of failed request:  72 (X_PutImage)
    Resource id in failed request:  0x4000064
    Serial number of failed request:  2678
    Current serial number in output stream:  2682

Then I checked for PCI as per your mentioned command;

sufian at system01:~ # lspci | grep VGA
03:00.0 VGA compatible controller: Matrox Electronics Systems Ltd. MGA G200EV

I checked yast2 for any driver update, and it was up to date. I don't want to switch to OpenSUSE 13.2 for now. 
Is there any earlier version of Chimera specific to my VGA ? I have also tried Chimera 1.8, but got same error.

Kindly guide me.


Muhammad Sufian

Date: Thu, 12 Mar 2015 12:58:00 -0700
From: gregc at cgl.ucsf.edu
To: msufian at outlook.com; chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] UCSF Chimera error: X Error of failed request: BadDrawable (invalid Pixmap or Window parameter)


  
    
  
  
    Try running "chimera --debug", it should give a clue where in the
    initialization process chimera died.  That said, it is most likely a
    graphics driver bug.  Run "lspci | grep VGA" to see what kind of
    graphics card you have.  Then, if OpenSUSE has a tool or package for
    that graphics card, install it.  If not, if you have ATI/AMD or
    NVIDIA graphics, you will download the right driver from amd.com or
    nvidia.com, respectively, and install it.  If you have Intel
    graphics, upgrade your system to OpenSUSE 13.2.

    

        Best of luck and please let me know if updating the graphics
    driver fixes the bug,

    

        Greg

    

    On 03/12/2015 05:10 AM, Muhammad Sufian
      wrote:

    
    
      
        
        Dear all Chimera users,

            

            I tried to install following version of Chimera;

             
                  chimera-1.10.1-linux_x86_64.bin

            

            but after installation, following error appeared after its
            execution;

            sufian at system01:/usr/local/chimera/bin>
                  ./chimera

                X Error of failed request: 
                  BadDrawable (invalid Pixmap or Window parameter)

                  Major opcode of failed request:  72
                  (X_PutImage)

                  Resource id in failed request: 
                  0x2200064

                  Serial number of failed request: 
                  1357

                  Current serial number in output
                  stream:  1363

            

            I also tried to install Chimera 1.9, but got same error. My
            system specifications are;

              Processor: x86_64 

              Operating-system: GNU/Linux (OpenSUSE 12.1)

              Kernel: Linux 3.4.63-2.44-desktop

            

            Kindly guide me how to resolve this issue.

            

            Regards.

          
          

            
          

              
          Muhammad Sufian
          M.Phil. scholar
              (Molecular Medicine),
          Computational
              Biology Laboratory,
          
            Lab no. P-103,
                PCMD-Extension,
            Dr. Panjwani
                Center for Molecular Medicine and Drug Research
            International
                Center for Chemical and Biological Sciences
          
          University of
              Karachi, Karachi, Pakistan
        
      
      

      
      

      _______________________________________________
Chimera-users mailing list
Chimera-users at cgl.ucsf.edu
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

    
    
 		 	   		  
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From msufian at outlook.com  Sat Mar 14 05:24:55 2015
From: msufian at outlook.com (Muhammad Sufian)
Date: Sat, 14 Mar 2015 17:24:55 +0500
Subject: [Chimera-users] UCSF Chimera error: X Error of failed request:
 BadDrawable (invalid Pixmap or Window parameter)
In-Reply-To: <55030D83.1020001@cgl.ucsf.edu>
References: <BAY180-W655B5B2B5871CE3AB47474B7060@phx.gbl>,
	<5501EFC8.4070704@cgl.ucsf.edu>
	<BAY180-W15B8ABFBC7963404041EB0B7070@phx.gbl>,
	<55030D83.1020001@cgl.ucsf.edu>
Message-ID: <BAY180-W59D4E6D100ED14BABB2ED6B7040@phx.gbl>

Thank you Greg for your kind help.
For now, I don;t want to change my graphics card and I have latest graphics driver for Mesa, so I have decided to update OpenSUSE.
But is it necessary to install 13.2 ?
Can't I go for 13.1 ?
Is there any way to check which earliest version is compatible for my workstation and Chimera graphics ?

Muhammad Sufian

Date: Fri, 13 Mar 2015 09:17:07 -0700
From: gregc at cgl.ucsf.edu
To: msufian at outlook.com; chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] UCSF Chimera error: X Error of failed request: BadDrawable (invalid Pixmap or Window parameter)


  
    
  
  
    I'm sorry, the Matrix graphics is more of a hindrance than a help. 
    It uses the software only OpenGL driver, Mesa, to do its 3D
    drawing.  And the easiest way to get a newer version of Mesa on your
    system is to update it to OpenSUSE 13.2 or the latest Ubuntu.  If
    you have the option of installing an AMD or NVIDIA graphics card in
    your system, do so, and install the proprietary driver.  It will be
    like going from walking to driving a car -- much faster, and you can
    buy a budget car, a regular car, or race car, depending on your
    budget. :-)

    

        HTH,

    

        Greg

    

    On 3/13/2015 12:27 AM, Muhammad Sufian
      wrote:

    
    
      
      Dear Greg,

        

        I have tried debugging Chimera and the issue is related to
        OpenGL;

        

        sufian at system01:~>
            chimera --debug

            initializing general preferences

            loading Tix

            initializing graphics

            create application

            loading Pmw

            creating main window

            creating menus

            creating toolbar

            creating viewer

            initializing OpenGL

            X Error of failed request: 
              BadDrawable (invalid Pixmap or Window parameter)

              Major opcode of failed request:  72
            (X_PutImage)

              Resource id in failed request: 
            0x4000064

              Serial number of failed request:  2678

              Current serial number in output stream: 
            2682

        

        Then I checked for PCI as per your mentioned command;

        

        sufian at system01:~
            # lspci | grep VGA

          03:00.0 VGA compatible controller: Matrox
            Electronics Systems Ltd. MGA G200EV

        

        I checked yast2 for
        any driver update, and it was up to date. I don't want to switch
        to OpenSUSE 13.2 for now. 

        Is there any earlier version of Chimera specific to my VGA ? I
        have also tried Chimera 1.8, but got same error.

        

        Kindly guide me.

        

          
        

            
        Muhammad Sufian
        

        

        
          Date: Thu, 12 Mar 2015 12:58:00 -0700

          From: gregc at cgl.ucsf.edu

          To: msufian at outlook.com; chimera-users at cgl.ucsf.edu

          Subject: Re: [Chimera-users] UCSF Chimera error: X Error of
          failed request: BadDrawable (invalid Pixmap or Window
          parameter)

          

          Try running "chimera --debug", it should give a clue where in
          the initialization process chimera died.  That said, it is
          most likely a graphics driver bug.  Run "lspci | grep VGA" to
          see what kind of graphics card you have.  Then, if OpenSUSE
          has a tool or package for that graphics card, install it.  If
          not, if you have ATI/AMD or NVIDIA graphics, you will download
          the right driver from amd.com or nvidia.com, respectively, and
          install it.  If you have Intel graphics, upgrade your system
          to OpenSUSE 13.2.

          

              Best of luck and please let me know if updating the
          graphics driver fixes the bug,

          

              Greg

          

          On 03/12/2015 05:10 AM,
            Muhammad Sufian wrote:

          
          
            
              
              Dear all Chimera users,

                  

                  I tried to install following version of Chimera;

                   
                        chimera-1.10.1-linux_x86_64.bin

                  

                  but after installation, following error appeared after
                  its execution;

                  sufian at system01:/usr/local/chimera/bin>

                        ./chimera

                      X Error of failed
                        request:  BadDrawable (invalid Pixmap or Window
                        parameter)

                        Major opcode of
                        failed request:  72 (X_PutImage)

                        Resource id in
                        failed request:  0x2200064

                        Serial number of
                        failed request:  1357

                        Current serial
                        number in output stream:  1363

                  

                  I also tried to install Chimera 1.9, but got same
                  error. My system specifications are;

                    Processor: x86_64 

                    Operating-system: GNU/Linux (OpenSUSE 12.1)

                    Kernel: Linux 3.4.63-2.44-desktop

                  

                  Kindly guide me how to resolve this issue.

                  

                  Regards.

                
                

                  
                

                    
                Muhammad Sufian
                M.Phil.
                    scholar (Molecular Medicine),
                Computational
                    Biology Laboratory,
                
                  Lab no.
                      P-103, PCMD-Extension,
                  Dr.
                      Panjwani Center for Molecular Medicine and Drug
                      Research
                  International

                      Center for Chemical and Biological Sciences
                
                University of
                    Karachi, Karachi, Pakistan
              
            
            

            
            

            _______________________________________________
Chimera-users mailing list
Chimera-users at cgl.ucsf.edu
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

          
          

        
      
    
    
 		 	   		  
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From smith_liu123 at 163.com  Sun Mar 15 18:03:34 2015
From: smith_liu123 at 163.com (Smith Liu)
Date: Mon, 16 Mar 2015 09:03:34 +0800 (CST)
Subject: [Chimera-users] a question related to segment map
Message-ID: <552145bb.8190.14c201b7c3f.Coremail.smith_liu123@163.com>

Dear All,
 
After I segment a map into diffrent color, will you please tell me in detail how can I erase some specific parts of the map which I do not nee for some purpose?
 
Smith
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From meng at cgl.ucsf.edu  Mon Mar 16 08:59:52 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 16 Mar 2015 08:59:52 -0700
Subject: [Chimera-users] a question related to segment map
In-Reply-To: <552145bb.8190.14c201b7c3f.Coremail.smith_liu123@163.com>
References: <552145bb.8190.14c201b7c3f.Coremail.smith_liu123@163.com>
Message-ID: <487D320F-AF22-4482-8226-CA1F64C16DED@cgl.ucsf.edu>

Dear Smith,

After  you get a segmentation (set of colored surfaces) that you like, you can write a new map that contains only the parts that you want. 

(1) select the surfaces that enclose the parts that you want:  Ctrl-click on one colored surface, then Shift-Ctrl-click on others to add them to the selection
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html#pickselect>

(2) use Segment Map menu "File? Save selected regions to .mrc file"  to save a new density map masked by the selected surfaces.  Also in that menu is a choice to save each surface-enclosed region to a separate map file.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/segment.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/segment.html#menu-file>

There's also a tutorial on using Segment Map, but I don't see anything in it about map-erasing:
<http://www.cgl.ucsf.edu/chimera/data/segger-howto-jun2010/segger.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 15, 2015, at 6:03 PM, Smith Liu <smith_liu123 at 163.com> wrote:

> Dear All,
>  
> After I segment a map into diffrent color, will you please tell me in detail how can I erase some specific parts of the map which I do not nee for some purpose?
>  
> Smith
> 




From gregc at cgl.ucsf.edu  Mon Mar 16 12:27:22 2015
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Mon, 16 Mar 2015 12:27:22 -0700
Subject: [Chimera-users] UCSF Chimera error: X Error of failed request:
 BadDrawable (invalid Pixmap or Window parameter)
In-Reply-To: <BAY180-W59D4E6D100ED14BABB2ED6B7040@phx.gbl>
References: <BAY180-W655B5B2B5871CE3AB47474B7060@phx.gbl>,
	<5501EFC8.4070704@cgl.ucsf.edu>
	<BAY180-W15B8ABFBC7963404041EB0B7070@phx.gbl>,
	<55030D83.1020001@cgl.ucsf.edu>
	<BAY180-W59D4E6D100ED14BABB2ED6B7040@phx.gbl>
Message-ID: <55072E9A.6080501@cgl.ucsf.edu>

Unfortunately, we haven't been testing every revision of Mesa to see 
which ones work.  I do know that sometimes it works for a few revisions, 
then breaks, then works again.  Mesa has improved a lot in the last few 
years (since it is the only way to get an Intel graphics driver on Linux 
and Intel has funded improvements to Mesa), so right now it usually 
works.  OpenSUSE 13.1 with Mesa 9.2.5 is from 2013-11-19, so it should 
be fine.

If I understand what I read about OpenSUSE 13.2 correctly, its 
advantage/disadvantage is that it is a rolling release.  That is, if 
there is a newer version of a particular software package, it will be 
available immediately, instead of having to wait for the next OpenSUSE 
release.  I consider this a huge advantage for desktop users because 
desktop graphics is constantly improving, sometimes with newer versions 
of the Linux kernel, but usually with improvements to Mesa.  OpenSUSE 
13.2 currently has Mesa 10.3.7.

     HTH,

     Greg

On 03/14/2015 05:24 AM, Muhammad Sufian wrote:
> Thank you Greg for your kind help.
> For now, I don;t want to change my graphics card and I have latest 
> graphics driver for Mesa, so I have decided to update OpenSUSE.
> But is it necessary to install 13.2 ?
> Can't I go for 13.1 ?
> Is there any way to check which earliest version is compatible for my 
> workstation and Chimera graphics ?
>
> *Muhammad Sufian*
>
>
> ------------------------------------------------------------------------
> Date: Fri, 13 Mar 2015 09:17:07 -0700
> From: gregc at cgl.ucsf.edu
> To: msufian at outlook.com; chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] UCSF Chimera error: X Error of failed 
> request: BadDrawable (invalid Pixmap or Window parameter)
>
> I'm sorry, the Matrix graphics is more of a hindrance than a help.  It 
> uses the software only OpenGL driver, Mesa, to do its 3D drawing.  And 
> the easiest way to get a newer version of Mesa on your system is to 
> update it to OpenSUSE 13.2 or the latest Ubuntu.  If you have the 
> option of installing an AMD or NVIDIA graphics card in your system, do 
> so, and install the proprietary driver.  It will be like going from 
> walking to driving a car -- much faster, and you can buy a budget car, 
> a regular car, or race car, depending on your budget. :-)
>
>     HTH,
>
>     Greg
>
> On 3/13/2015 12:27 AM, Muhammad Sufian wrote:
>
>     Dear Greg,
>
>     I have tried debugging Chimera and the issue is related to OpenGL;
>
>     *sufian at system01:~> chimera --debug
>       initializing general preferences
>       loading Tix
>       initializing graphics
>       create application
>       loading Pmw
>       creating main window
>       creating menus
>       creating toolbar
>       creating viewer
>       initializing OpenGL
>     X Error of failed request:  BadDrawable (invalid Pixmap or Window
>     parameter)
>         Major opcode of failed request: 72 (X_PutImage)
>         Resource id in failed request: 0x4000064
>         Serial number of failed request: 2678
>         Current serial number in output stream:  2682*
>
>     Then I checked for PCI as per your mentioned command;
>
>     *sufian at system01:~ # lspci | grep VGA
>     03:00.0 VGA compatible controller: Matrox Electronics Systems Ltd.
>     MGA G200EV*
>
>     I checked *yast2* for any driver update, and it was up to date. I
>     don't want to switch to *OpenSUSE 13.2* for now.
>     Is there any earlier version of Chimera specific to my VGA ? I
>     have also tried Chimera 1.8, but got same error.
>
>     Kindly guide me.
>
>
>     *Muhammad Sufian*
>
>
>     ------------------------------------------------------------------------
>     Date: Thu, 12 Mar 2015 12:58:00 -0700
>     From: gregc at cgl.ucsf.edu <mailto:gregc at cgl.ucsf.edu>
>     To: msufian at outlook.com <mailto:msufian at outlook.com>;
>     chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>
>     Subject: Re: [Chimera-users] UCSF Chimera error: X Error of failed
>     request: BadDrawable (invalid Pixmap or Window parameter)
>
>     Try running "chimera --debug", it should give a clue where in the
>     initialization process chimera died.  That said, it is most likely
>     a graphics driver bug.  Run "lspci | grep VGA" to see what kind of
>     graphics card you have.  Then, if OpenSUSE has a tool or package
>     for that graphics card, install it.  If not, if you have ATI/AMD
>     or NVIDIA graphics, you will download the right driver from
>     amd.com or nvidia.com, respectively, and install it.  If you have
>     Intel graphics, upgrade your system to OpenSUSE 13.2.
>
>         Best of luck and please let me know if updating the graphics
>     driver fixes the bug,
>
>         Greg
>
>     On 03/12/2015 05:10 AM, Muhammad Sufian wrote:
>
>         Dear all Chimera users,
>
>         I tried to install following version of Chimera;
>         *chimera-1.10.1-linux_x86_64.bin*
>
>         but after installation, following error appeared after its
>         execution;
>         *sufian at system01:/usr/local/chimera/bin> ./chimera
>         X Error of failed request:  BadDrawable (invalid Pixmap or
>         Window parameter)
>           Major opcode of failed request:  72 (X_PutImage)
>           Resource id in failed request:  0x2200064
>           Serial number of failed request:  1357
>           Current serial number in output stream:  1363*
>
>         I also tried to install Chimera 1.9, but got same error. My
>         system specifications are;
>           Processor: x86_64
>           Operating-system: GNU/Linux (OpenSUSE 12.1)
>           Kernel: Linux 3.4.63-2.44-desktop
>
>         Kindly guide me how to resolve this issue.
>
>         Regards.
>
>
>         *Muhammad Sufian*
>         M.Phil. scholar (Molecular Medicine),
>         Computational Biology Laboratory,
>         Lab no. P-103, PCMD-Extension,
>         Dr. Panjwani Center for Molecular Medicine and Drug Research
>         International Center for Chemical and Biological Sciences
>         University of Karachi, Karachi, Pakistan
>
>
>         _______________________________________________
>         Chimera-users mailing list
>         Chimera-users at cgl.ucsf.edu  <mailto:Chimera-users at cgl.ucsf.edu>
>         http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>

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From samuel.hertig at ucsf.edu  Mon Mar 16 14:54:51 2015
From: samuel.hertig at ucsf.edu (Samuel Hertig)
Date: Mon, 16 Mar 2015 14:54:51 -0700
Subject: [Chimera-users] Chimera tutorial at VIZBI conference in Boston on
 Tuesday, March 24
Message-ID: <5507512B.6080007@ucsf.edu>

Dear Chimera users,

In case you are interested in learning the basics of Chimera and if you 
can make it to Boston on March 24, the RBVI will be teaching a small 
Chimera tutorial as part of the Visualizing Biological Data (VIZBI) 
conference.

Details and registration:

http://www.vizbi.org/2015/Program/#Tuesday

Best regards,

Sam Hertig, PhD
Postdoctoral researcher
Resource for Biocomputing, Visualization, and Informatics
University of California, San Francisco





From smith_liu123 at 163.com  Tue Mar 17 08:24:27 2015
From: smith_liu123 at 163.com (Smith Liu)
Date: Tue, 17 Mar 2015 23:24:27 +0800 (CST)
Subject: [Chimera-users] on color zone
Message-ID: <511586e2.11060.14c285603dd.Coremail.smith_liu123@163.com>

Dear All,
 
I have a mrc file for a protein complex with a 3-fragment sheets (from A to B, from B to C, from C to D, and they were connected by H-bonds). Will you please  introduce to me on how to use color zone to split to get the mrc file for each fragment of the sheets? I have tried to do it by myself, however I find the splitting was not  done based on fragment, i.e., I cannot get the mrc file for each fragment of the sheets.


I am looking forward to getting your reply.


Smith
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From meng at cgl.ucsf.edu  Tue Mar 17 08:57:08 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 17 Mar 2015 08:57:08 -0700
Subject: [Chimera-users] on color zone
In-Reply-To: <511586e2.11060.14c285603dd.Coremail.smith_liu123@163.com>
References: <511586e2.11060.14c285603dd.Coremail.smith_liu123@163.com>
Message-ID: <BB463726-5EE0-4DC3-92CF-42C9C41FD3CE@cgl.ucsf.edu>

Dear Smith,
The main thing is how to select or specify the set of atoms in each fragment.  Then you can color each of those sets of atoms a different color.  When that is done, then select all the atoms, use Color Zone, and then split.  However, it is impossible to give exact instructions of how to select or specify only the atoms in a fragment without knowing how tthey are described in your PDB file.  If you know that one fragment consists of residues 12-58 of chain A, then one way to select it would be to use command:

select :12-58.A
? then color using Actions menu, or, just use a command to do the whole thing without selecting:
color orange :12-58.A

Another way to select a range of residues would be to show a sequence window (Favorites? Sequence, choose chain of interest) and then click-drag to select a range of residues in the sequence window, which will also select them in the 3D structure.

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 17, 2015, at 8:24 AM, "Smith Liu" <smith_liu123 at 163.com> wrote:

> Dear All,
>  
> I have a mrc file for a protein complex with a 3-fragment sheets (from A to B, from B to C, from C to D, and they were connected by H-bonds). Will you please  introduce to me on how to use color zone to split to get the mrc file for each fragment of the sheets? I have tried to do it by myself, however I find the splitting was not  done based on fragment, i.e., I cannot get the mrc file for each fragment of the sheets.
> 
> I am looking forward to getting your reply.
> 
> Smith




From semchonok at gmail.com  Tue Mar 17 03:56:29 2015
From: semchonok at gmail.com (Dmitry)
Date: Tue, 17 Mar 2015 11:56:29 +0100
Subject: [Chimera-users] scale bar
Message-ID: <5508085D.2090006@gmail.com>

Dear developers,

How are you?

I have a question about scale bar. I am not completely sure that the 
scale bar I drew is correct.


What are the scale settings for drawing the scale bar?

By the default the scale bar is in Angstroms isn?t it?

In ImageJ there is a possibility to set the scale 1 pixel = X value 
(nm/?/etc)

Is there the same possibility in Chimera?


Thank you


Sincerely,

Dmitry

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From meng at cgl.ucsf.edu  Tue Mar 17 10:44:52 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 17 Mar 2015 10:44:52 -0700
Subject: [Chimera-users] scale bar
In-Reply-To: <5508085D.2090006@gmail.com>
References: <5508085D.2090006@gmail.com>
Message-ID: <8CAE5FCA-D06D-4BBB-8F42-E1DA9B291777@cgl.ucsf.edu>

Dear Dmitry,
Pretty good - I hope you are well too!

The scale bar length and thickness are in the physical distance units of your data, whatever those are.  If your structure is in angstroms, they will be in angstroms, but if your map is in nanometers, they will be in nanometers.

I'm not sure what your question is about the other settings, but we try to explain them all in the help, which you can see by clicking the Help button or viewing the copy at our website:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/scalebar/scalebar.html>

I don't think there is a control for scalebar pixels per unit distance.  I found a post from 2005 with python for setting the pixels per unit distance in the whole graphics window (not the scale bar), but I don't know if it would work with today's Chimera:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2005-May/000369.html>

One thing to keep in mind is that the scale bar is an object in 3 dimensions, so you want it at a similar depth to your structures and maps, because due to perspective, if it is in front it will look larger, if towards the back it will look smaller.  You may be able to see its depth in the Side View, or by rotating the main view 90 degrees (and then putting it back, of course), e.g. commands:

 turn y 90
turn y -90

Another possibility is to turn off perspective, instead using orthographic projection:

set projection ortho
set proj persp

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 17, 2015, at 3:56 AM, Dmitry <semchonok at gmail.com> wrote:

> Dear developers,
> How are you?
> 
> I have a question about scale bar. I am not completely sure that the scale bar I drew is correct.
> 
> What are the scale settings for drawing the scale bar?
> 
> By the default the scale bar is in Angstroms isn?t it?
> 
>  In ImageJ there is a possibility to set the scale 1 pixel = X value (nm/?/etc)
> 
>  Is there the same possibility in Chimera?
>  Thank you
> Sincerely,
> Dmitry




From thapamb at mail.uc.edu  Tue Mar 17 22:39:17 2015
From: thapamb at mail.uc.edu (Mahendra B Thapa)
Date: Wed, 18 Mar 2015 01:39:17 -0400
Subject: [Chimera-users] How to get prmtop file corresponding to a pdb file
Message-ID: <CAM_0UTiKNqmghZ6zrHZ7nfSqRK6yQoowOmX56UhUCkiSfS88zw@mail.gmail.com>

Dear Chimera users,

To get *Amber prmtop file* corresponding to a *pdb file using Chimera*, I
did the following steps:
1] tools -> Amber -> write prmtop
2] In a pop-up window 'save file in chimera', I gave file name, say,
aa.prmtop, then clicked save.
3] No charges message appeared, then I clicked 'Assign charges'.
4] In a pop-up window 'Add charge', I selected 'AM1-BCC' in other residues,
then clicked ok.
5] In a pop up window 'specify net charge', I selected 'AMI-BCC' in charge
method
6] I got 'chimera error' - failure running ANTECHEMBER for residue HIS.
Check reply log for details.
7] In reply log, '*Failure running ANTECHEMBER for residue HIS*' seen.

Any help in this issue will be a good help for me.

Thank you.
Mahendra Thapa
University of Cincinnati,OH
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From chewaka.87 at gmail.com  Wed Mar 18 02:08:18 2015
From: chewaka.87 at gmail.com (=?UTF-8?Q?Victor_Mu=C3=B1oz?=)
Date: Wed, 18 Mar 2015 10:08:18 +0100
Subject: [Chimera-users] How to get prmtop file corresponding to a pdb
	file
In-Reply-To: <CAM_0UTiKNqmghZ6zrHZ7nfSqRK6yQoowOmX56UhUCkiSfS88zw@mail.gmail.com>
References: <CAM_0UTiKNqmghZ6zrHZ7nfSqRK6yQoowOmX56UhUCkiSfS88zw@mail.gmail.com>
Message-ID: <CAMpXCU1oYs6KecLcomZzwwZS=8HRg2VWnBefsgHWEzLgQut3Yw@mail.gmail.com>

Dear Mahendra,

The error is due to HIS not being the standard residue name for Histidine
in the Amber force field. In Amber, histidine residues are named either
HIE, HID or HIP depending on their protonation state (
http://ambermd.org/Questions/HIS.html). Change the name of the histidines
on the PDB file accordingly to their protonation state and it should work
fine.

Kind regards,

Victor

2015-03-18 6:39 GMT+01:00 Mahendra B Thapa <thapamb at mail.uc.edu>:

> Dear Chimera users,
>
> To get *Amber prmtop file* corresponding to a *pdb file using Chimera*, I
> did the following steps:
> 1] tools -> Amber -> write prmtop
> 2] In a pop-up window 'save file in chimera', I gave file name, say,
> aa.prmtop, then clicked save.
> 3] No charges message appeared, then I clicked 'Assign charges'.
> 4] In a pop-up window 'Add charge', I selected 'AM1-BCC' in other
> residues, then clicked ok.
> 5] In a pop up window 'specify net charge', I selected 'AMI-BCC' in charge
> method
> 6] I got 'chimera error' - failure running ANTECHEMBER for residue HIS.
> Check reply log for details.
> 7] In reply log, '*Failure running ANTECHEMBER for residue HIS*' seen.
>
> Any help in this issue will be a good help for me.
>
> Thank you.
> Mahendra Thapa
> University of Cincinnati,OH
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
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From thapamb at mail.uc.edu  Wed Mar 18 05:04:57 2015
From: thapamb at mail.uc.edu (Mahendra B Thapa)
Date: Wed, 18 Mar 2015 08:04:57 -0400
Subject: [Chimera-users] FW: How to get prmtop file corresponding to a
	pdb file
In-Reply-To: <a6f3290cca5c4ef4a70dc8f554588370@DM2PR0101MB1085.prod.exchangelabs.com>
References: <CAM_0UTiKNqmghZ6zrHZ7nfSqRK6yQoowOmX56UhUCkiSfS88zw@mail.gmail.com>
	<CAMpXCU1oYs6KecLcomZzwwZS=8HRg2VWnBefsgHWEzLgQut3Yw@mail.gmail.com>
	<a6f3290cca5c4ef4a70dc8f554588370@DM2PR0101MB1085.prod.exchangelabs.com>
Message-ID: <CAM_0UTjJq4s4pkL92FVksrWKV1Whi2o-+euqvnDFWGRKs80iAg@mail.gmail.com>

Dear Dr. Victor,

Thank you for reminding me about the protonation state of HIS. As a trial,
I changed all HIS to HID and again repeated my previous steps. This time, I
got some python track back errors. I suspect the source of error could be
the initial pdb file which I used in chimera ; the pdb file was obtained
from other software (like online server), so some atom names were different
from that of AMBER. My goal was to get AMBER prmtop corresponding to pdb
files which were generated by  programs other than AMBER so that I could
use ambertools. So, may I need to convert all such pdb files compatible
with amber pdb format ?

Thank you for help,
Mahendra Thapa


On Wed, Mar 18, 2015 at 5:08 AM, Thapa, Mahendra (thapamb) <
thapamb at mail.uc.edu> wrote:

>
> ------------------------------
> *From:* Victor Mu?oz
> *Sent:* Wednesday, March 18, 2015 3:08:18 AM (UTC-06:00) Central America
> *To:* Thapa, Mahendra (thapamb)
> *Cc:* chimera-users at cgl.ucsf.edu
> *Subject:* Re: [Chimera-users] How to get prmtop file corresponding to a
> pdb file
>
>    Dear Mahendra,
>
>  The error is due to HIS not being the standard residue name for Histidine
> in the Amber force field. In Amber, histidine residues are named either
> HIE, HID or HIP depending on their protonation state (
> http://ambermd.org/Questions/HIS.html). Change the name of the histidines
> on the PDB file accordingly to their protonation state and it should work
> fine.
>
>  Kind regards,
>
>  Victor
>
> 2015-03-18 6:39 GMT+01:00 Mahendra B Thapa <thapamb at mail.uc.edu>:
>
>>       Dear Chimera users,
>>
>>  To get *Amber prmtop file* corresponding to a *pdb file using Chimera*,
>> I did the following steps:
>>  1] tools -> Amber -> write prmtop
>>  2] In a pop-up window 'save file in chimera', I gave file name, say,
>> aa.prmtop, then clicked save.
>>  3] No charges message appeared, then I clicked 'Assign charges'.
>>  4] In a pop-up window 'Add charge', I selected 'AM1-BCC' in other
>> residues, then clicked ok.
>>  5] In a pop up window 'specify net charge', I selected 'AMI-BCC' in
>> charge method
>>  6] I got 'chimera error' - failure running ANTECHEMBER for residue HIS.
>> Check reply log for details.
>>  7] In reply log, '*Failure running ANTECHEMBER for residue HIS*' seen.
>>
>>  Any help in this issue will be a good help for me.
>>
>>  Thank you.
>>  Mahendra Thapa
>>  University of Cincinnati,OH
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>>
>
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From chewaka.87 at gmail.com  Wed Mar 18 05:12:12 2015
From: chewaka.87 at gmail.com (=?UTF-8?Q?Victor_Mu=C3=B1oz?=)
Date: Wed, 18 Mar 2015 13:12:12 +0100
Subject: [Chimera-users] FW: How to get prmtop file corresponding to a
	pdb file
In-Reply-To: <CAM_0UTjJq4s4pkL92FVksrWKV1Whi2o-+euqvnDFWGRKs80iAg@mail.gmail.com>
References: <CAM_0UTiKNqmghZ6zrHZ7nfSqRK6yQoowOmX56UhUCkiSfS88zw@mail.gmail.com>
	<CAMpXCU1oYs6KecLcomZzwwZS=8HRg2VWnBefsgHWEzLgQut3Yw@mail.gmail.com>
	<a6f3290cca5c4ef4a70dc8f554588370@DM2PR0101MB1085.prod.exchangelabs.com>
	<CAM_0UTjJq4s4pkL92FVksrWKV1Whi2o-+euqvnDFWGRKs80iAg@mail.gmail.com>
Message-ID: <CAMpXCU1oXYY0wJW4pTvrWAZd8NEMV2+DeZYgng1LHW7V578Y6w@mail.gmail.com>

Dear Mahendra,

Yes, I would say you should do that. Try converting all the atom names from
whatever name they have to the appropriate one for AMBER. Pay special
attention to the terminal residues, as there may be some differences on the
atom names depending on how you generated the PDB files.

Kind regards,

Victor

2015-03-18 13:04 GMT+01:00 Mahendra B Thapa <thapamb at mail.uc.edu>:

> Dear Dr. Victor,
>
> Thank you for reminding me about the protonation state of HIS. As a trial,
> I changed all HIS to HID and again repeated my previous steps. This time, I
> got some python track back errors. I suspect the source of error could be
> the initial pdb file which I used in chimera ; the pdb file was obtained
> from other software (like online server), so some atom names were different
> from that of AMBER. My goal was to get AMBER prmtop corresponding to pdb
> files which were generated by  programs other than AMBER so that I could
> use ambertools. So, may I need to convert all such pdb files compatible
> with amber pdb format ?
>
> Thank you for help,
> Mahendra Thapa
>
>
> On Wed, Mar 18, 2015 at 5:08 AM, Thapa, Mahendra (thapamb) <
> thapamb at mail.uc.edu> wrote:
>
>>
>> ------------------------------
>> *From:* Victor Mu?oz
>> *Sent:* Wednesday, March 18, 2015 3:08:18 AM (UTC-06:00) Central America
>> *To:* Thapa, Mahendra (thapamb)
>> *Cc:* chimera-users at cgl.ucsf.edu
>> *Subject:* Re: [Chimera-users] How to get prmtop file corresponding to a
>> pdb file
>>
>>    Dear Mahendra,
>>
>>  The error is due to HIS not being the standard residue name for
>> Histidine in the Amber force field. In Amber, histidine residues are named
>> either HIE, HID or HIP depending on their protonation state (
>> http://ambermd.org/Questions/HIS.html). Change the name of the
>> histidines on the PDB file accordingly to their protonation state and it
>> should work fine.
>>
>>  Kind regards,
>>
>>  Victor
>>
>> 2015-03-18 6:39 GMT+01:00 Mahendra B Thapa <thapamb at mail.uc.edu>:
>>
>>>       Dear Chimera users,
>>>
>>>  To get *Amber prmtop file* corresponding to a *pdb file using Chimera*,
>>> I did the following steps:
>>>  1] tools -> Amber -> write prmtop
>>>  2] In a pop-up window 'save file in chimera', I gave file name, say,
>>> aa.prmtop, then clicked save.
>>>  3] No charges message appeared, then I clicked 'Assign charges'.
>>>  4] In a pop-up window 'Add charge', I selected 'AM1-BCC' in other
>>> residues, then clicked ok.
>>>  5] In a pop up window 'specify net charge', I selected 'AMI-BCC' in
>>> charge method
>>>  6] I got 'chimera error' - failure running ANTECHEMBER for residue HIS.
>>> Check reply log for details.
>>>  7] In reply log, '*Failure running ANTECHEMBER for residue HIS*' seen.
>>>
>>>  Any help in this issue will be a good help for me.
>>>
>>>  Thank you.
>>>  Mahendra Thapa
>>>  University of Cincinnati,OH
>>>
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>
>>>
>>
>
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From deligkaris at gmail.com  Wed Mar 18 07:01:28 2015
From: deligkaris at gmail.com (Christos Deligkaris)
Date: Wed, 18 Mar 2015 09:01:28 -0500
Subject: [Chimera-users] visualization of electrostatic potential
Message-ID: <CAAHQ3wmN_5p23-pfT9Do23j+ZHkdXYdL9iY6tsbOar4gYqvLpw@mail.gmail.com>

Dear Chimera Users,

I am interested in visualizing the electrostatic potential calculated by
the APBS tool Chimera provides and I have several questions regarding this.

1) We have been having troubles running the PDB2PQR/APBS tools (I am not
sure if we had trouble with both, it has been a few weeks) that Chimera
provides, and I believe we fixed this by changing the version number at the
very end of the web server address. Is there anything else we could have
done to fix this?

2) I noticed that the numbers that are displayed when I visualize the
APBS-calculated potential on the MSMS are very different from the numbers
shown when I use the volume viewer (I mapped the values to atoms and then
displayed those as labels). Why are those numbers not the same? Is it
because the volume data will map the potential near the atoms and display
that, whereas the potential on the surface (or actually 1.4 Angstroms from
the surface) will display the potential value on the surface? Should I
assume that the units are the same?

3) I am interested in finding the "patches" of the molecular surface the
have fairly positive potential. I am familiar with the PatchFinderPlus
server but I am interested in finding several patches, not just the largest
one. I have not found any tool related to this in Chimera, please let me
know if I am wrong. So,I found the redarea.py script avalaible from
Chimera's website and I am thinking about modifying it in order to do this.
The script iterates over all surface pieces. Is it possible to calculate
the distance between vertices and atoms? Is it possible to obtain the
potential value at a vortex? I think this would help me get started...

Thank you very much,

Christos Deligkaris, PhD
Assistant Professor of Physics, Drury University
900 N Benton Ave, Springfield MO, 65802
Office Phone: (417) 873-7234
www2.drury.edu/christos <http://www2.drury.edu/christos/index.html>
@DeligkarisGroup <https://twitter.com/DeligkarisGroup> +ChristosDeligkaris
<http://google.com/+ChristosDeligkaris>
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From meng at cgl.ucsf.edu  Wed Mar 18 09:28:19 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 18 Mar 2015 09:28:19 -0700
Subject: [Chimera-users] visualization of electrostatic potential
In-Reply-To: <CAAHQ3wmN_5p23-pfT9Do23j+ZHkdXYdL9iY6tsbOar4gYqvLpw@mail.gmail.com>
References: <CAAHQ3wmN_5p23-pfT9Do23j+ZHkdXYdL9iY6tsbOar4gYqvLpw@mail.gmail.com>
Message-ID: <1C6B308C-4E57-4C3B-A405-5B7DFFD1EFDB@cgl.ucsf.edu>

Dear Christos,

1) It would be great if you could provide any more details about this.  In general, when you have problems you can report them to chimera-bugs at cgl.ucsf.edu.  This sounds like something we need to look at and fix for everybody, if possible.   PDB2PQR and APBS are web services provided by a separate resource and we are not always aware when they make changes.  Also, I?m not sure what you meant by ?troubles? ? no results at all, or error messages, or strange results?

2) The units are the same, but as you guessed, the evaluations are at different locations.  When you map to atoms, the evaluation is at the atom center.  When you color the surface, the default evaluation for electrostatic potential is furthermore not even at the displayed solvent-excluded surface, but 1.4 further outward (the probe radius).  So even though the coloring is displayed on the solvent-excluded surface, it reflects values at approximately the solvent-accessible surface.  This additional projection is optional.  In the Surface Color dialog, click Options and see the ?surface offset? value.  
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html#options>
Or, if you?re using the ?scolor? command, it?s the ?offset? option:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#volume>

3) You found the ?redarea.py? post, which is the most similar to what you describe:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-December/009401.html>

See also the posts regarding ?surfvalues.py? for obtaining values for surface vertices:
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2011-February/006000.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 18, 2015, at 7:01 AM, Christos Deligkaris <deligkaris at gmail.com> wrote:

> Dear Chimera Users,
> 
> I am interested in visualizing the electrostatic potential calculated by the APBS tool Chimera provides and I have several questions regarding this.
> 
> 1) We have been having troubles running the PDB2PQR/APBS tools (I am not sure if we had trouble with both, it has been a few weeks) that Chimera provides, and I believe we fixed this by changing the version number at the very end of the web server address. Is there anything else we could have done to fix this?
> 
> 2) I noticed that the numbers that are displayed when I visualize the APBS-calculated potential on the MSMS are very different from the numbers shown when I use the volume viewer (I mapped the values to atoms and then displayed those as labels). Why are those numbers not the same? Is it because the volume data will map the potential near the atoms and display that, whereas the potential on the surface (or actually 1.4 Angstroms from the surface) will display the potential value on the surface? Should I assume that the units are the same?
> 
> 3) I am interested in finding the "patches" of the molecular surface the have fairly positive potential. I am familiar with the PatchFinderPlus server but I am interested in finding several patches, not just the largest one. I have not found any tool related to this in Chimera, please let me know if I am wrong. So,I found the redarea.py script avalaible from Chimera's website and I am thinking about modifying it in order to do this. The script iterates over all surface pieces. Is it possible to calculate the distance between vertices and atoms? Is it possible to obtain the potential value at a vortex? I think this would help me get started...
> 
> Thank you very much,
> 
> Christos Deligkaris, PhD
> Assistant Professor of Physics, Drury University
> 900 N Benton Ave, Springfield MO, 65802
> Office Phone: (417) 873-7234
> www2.drury.edu/christos @DeligkarisGroup +ChristosDeligkaris




From sitiazma at gmail.com  Tue Mar 17 10:46:11 2015
From: sitiazma at gmail.com (SA)
Date: Tue, 17 Mar 2015 10:46:11 -0700
Subject: [Chimera-users] Chimera service unavailable
Message-ID: <CADhvAm=KJwXHFH8ozWvENV6SbmBYYBSTsjV4AGKaDkabhXyuTg@mail.gmail.com>

Dear developer,

I am using Chimera PDB2PQR module. However, it is failed. The error message
is below:

  self.backend = Backend(service, url)
  File "/soft/chimera/Chimera64-1.10.1/share/WebServices/opal_client.py",
line 21, in __init__
    raise NonChimeraError("Web service appears "
NonChimeraError: Web service appears to be down.  See Reply Log for more
details.
Service 'opal:pdb2pqr_1.8' is unavailable.  See Reply Log for more details.

For your indormation, I am using the latest linux version of Chimera.

Thank you.

Siti
Postdocs
UCSD
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From goddard at sonic.net  Wed Mar 18 09:58:46 2015
From: goddard at sonic.net (Tom Goddard)
Date: Wed, 18 Mar 2015 09:58:46 -0700
Subject: [Chimera-users] visualization of electrostatic potential
In-Reply-To: <1C6B308C-4E57-4C3B-A405-5B7DFFD1EFDB@cgl.ucsf.edu>
References: <CAAHQ3wmN_5p23-pfT9Do23j+ZHkdXYdL9iY6tsbOar4gYqvLpw@mail.gmail.com>
	<1C6B308C-4E57-4C3B-A405-5B7DFFD1EFDB@cgl.ucsf.edu>
Message-ID: <4DC59E07-5F03-4455-8EFF-BDB9E2E6DB9F@sonic.net>

Hi Christos,

  The surface coloring and volume viewer APBS map values are the same.  You will get much higher values with Values at Atom Positions than used with surface coloring because the electrostatic potential at a point charge is infinite.  You will instead get very large values because potential is sampled on a grid, so values at atom positions are interpolated from nearby grid points.

  The Chimera Python script you found red_area.py and the one Elaine mentioned surfvalues.py show you most of what you need to access the potential values on or near the surface.  One extra ingredient is to find which atom a surface point is associated with ? that is given by surface.atomMap that is a dictionary mapping vertex array index to an atom object.  This is defined in your Chimera distribution file

	chimera/share/MoleculeSurface/msurf.py

(on Mac in Chimera.app/Contents/Resources/share/MoleculeSurface/msurf.py)

	Tom


> On Mar 18, 2015, at 9:28 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Dear Christos,
> 
> 1) It would be great if you could provide any more details about this.  In general, when you have problems you can report them to chimera-bugs at cgl.ucsf.edu.  This sounds like something we need to look at and fix for everybody, if possible.   PDB2PQR and APBS are web services provided by a separate resource and we are not always aware when they make changes.  Also, I?m not sure what you meant by ?troubles? ? no results at all, or error messages, or strange results?
> 
> 2) The units are the same, but as you guessed, the evaluations are at different locations.  When you map to atoms, the evaluation is at the atom center.  When you color the surface, the default evaluation for electrostatic potential is furthermore not even at the displayed solvent-excluded surface, but 1.4 further outward (the probe radius).  So even though the coloring is displayed on the solvent-excluded surface, it reflects values at approximately the solvent-accessible surface.  This additional projection is optional.  In the Surface Color dialog, click Options and see the ?surface offset? value.  
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html#options>
> Or, if you?re using the ?scolor? command, it?s the ?offset? option:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#volume>
> 
> 3) You found the ?redarea.py? post, which is the most similar to what you describe:
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-December/009401.html>
> 
> See also the posts regarding ?surfvalues.py? for obtaining values for surface vertices:
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2011-February/006000.html>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Mar 18, 2015, at 7:01 AM, Christos Deligkaris <deligkaris at gmail.com> wrote:
> 
>> Dear Chimera Users,
>> 
>> I am interested in visualizing the electrostatic potential calculated by the APBS tool Chimera provides and I have several questions regarding this.
>> 
>> 1) We have been having troubles running the PDB2PQR/APBS tools (I am not sure if we had trouble with both, it has been a few weeks) that Chimera provides, and I believe we fixed this by changing the version number at the very end of the web server address. Is there anything else we could have done to fix this?
>> 
>> 2) I noticed that the numbers that are displayed when I visualize the APBS-calculated potential on the MSMS are very different from the numbers shown when I use the volume viewer (I mapped the values to atoms and then displayed those as labels). Why are those numbers not the same? Is it because the volume data will map the potential near the atoms and display that, whereas the potential on the surface (or actually 1.4 Angstroms from the surface) will display the potential value on the surface? Should I assume that the units are the same?
>> 
>> 3) I am interested in finding the "patches" of the molecular surface the have fairly positive potential. I am familiar with the PatchFinderPlus server but I am interested in finding several patches, not just the largest one. I have not found any tool related to this in Chimera, please let me know if I am wrong. So,I found the redarea.py script avalaible from Chimera's website and I am thinking about modifying it in order to do this. The script iterates over all surface pieces. Is it possible to calculate the distance between vertices and atoms? Is it possible to obtain the potential value at a vortex? I think this would help me get started...
>> 
>> Thank you very much,
>> 
>> Christos Deligkaris, PhD
>> Assistant Professor of Physics, Drury University
>> 900 N Benton Ave, Springfield MO, 65802
>> Office Phone: (417) 873-7234
>> www2.drury.edu/christos @DeligkarisGroup +ChristosDeligkaris
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From pett at cgl.ucsf.edu  Wed Mar 18 11:32:30 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 18 Mar 2015 11:32:30 -0700
Subject: [Chimera-users] How to get prmtop file corresponding to a pdb
	file
In-Reply-To: <CAM_0UTiKNqmghZ6zrHZ7nfSqRK6yQoowOmX56UhUCkiSfS88zw@mail.gmail.com>
References: <CAM_0UTiKNqmghZ6zrHZ7nfSqRK6yQoowOmX56UhUCkiSfS88zw@mail.gmail.com>
Message-ID: <9D367753-2A48-416F-8617-346323833C5D@cgl.ucsf.edu>

Hi Mahendra,
	If your PDB file has standard PDB atom names, then Chimera will have no problem deciding if the HIS residues should be HID (delta protonated), HIE (epsilon protonated), or HIP (both) for Amber purposes.  Apparently your file does not have PDB standard names throughout.  In particular, the proton names in your HIS residues must be non-standard.  Chimera makes the HIS decision based on whether your residue has an HD1 proton, an HE2 proton, or both.  You need to correct such protons to have the right names.
	You could either do this by hand with an editor or, if you don't need the specific protonation state of your starting structure, by deleting all the hydrogens in Chimera ("del H") and then adding them back ("addh").  This assumes that your heavy atom names are standard.  If they are not, those would need to be fixed by hand.

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu


On Mar 17, 2015, at 10:39 PM, Mahendra B Thapa <thapamb at mail.uc.edu> wrote:

> Dear Chimera users,
> 
> To get Amber prmtop file corresponding to a pdb file using Chimera, I did the following steps:
> 1] tools -> Amber -> write prmtop
> 2] In a pop-up window 'save file in chimera', I gave file name, say, aa.prmtop, then clicked save.
> 3] No charges message appeared, then I clicked 'Assign charges'.
> 4] In a pop-up window 'Add charge', I selected 'AM1-BCC' in other residues, then clicked ok.
> 5] In a pop up window 'specify net charge', I selected 'AMI-BCC' in charge method
> 6] I got 'chimera error' - failure running ANTECHEMBER for residue HIS. Check reply log for details.
> 7] In reply log, 'Failure running ANTECHEMBER for residue HIS' seen.
> 
> Any help in this issue will be a good help for me.
> 
> Thank you.
> Mahendra Thapa
> University of Cincinnati,OH
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



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From pett at cgl.ucsf.edu  Wed Mar 18 15:54:55 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 18 Mar 2015 15:54:55 -0700
Subject: [Chimera-users] Chimera service unavailable
In-Reply-To: <CADhvAm=KJwXHFH8ozWvENV6SbmBYYBSTsjV4AGKaDkabhXyuTg@mail.gmail.com>
References: <CADhvAm=KJwXHFH8ozWvENV6SbmBYYBSTsjV4AGKaDkabhXyuTg@mail.gmail.com>
Message-ID: <6BC272E7-D742-4075-88C5-8917FE4B3C74@cgl.ucsf.edu>

Hi Siti,
	Yes, the interface for accessing PDB2PQR at the NBCR server changed.  The daily build of Chimera has changes that correspond to the new interface and should work for you.  Please try the daily build.  It's on the Chimera download page, a little bit below the production builds.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Mar 17, 2015, at 10:46 AM, SA <sitiazma at gmail.com> wrote:

> Dear developer,
> 
> I am using Chimera PDB2PQR module. However, it is failed. The error message is below:
> 
>   self.backend = Backend(service, url)
>   File "/soft/chimera/Chimera64-1.10.1/share/WebServices/opal_client.py", line 21, in __init__
>     raise NonChimeraError("Web service appears "
> NonChimeraError: Web service appears to be down.  See Reply Log for more details.
> Service 'opal:pdb2pqr_1.8' is unavailable.  See Reply Log for more details.
> 
> For your indormation, I am using the latest linux version of Chimera.
> 
> Thank you.
> 
> Siti
> Postdocs
> UCSD
> 
> 
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users







From smith_liu123 at 163.com  Wed Mar 18 18:12:08 2015
From: smith_liu123 at 163.com (Smith Liu)
Date: Thu, 19 Mar 2015 09:12:08 +0800 (CST)
Subject: [Chimera-users] how to convert mtz file to a file which can be
	openne by Chimera
Message-ID: <c33dddc.1ea6.14c2f966862.Coremail.smith_liu123@163.com>

Dear All,
 
Will you please tell me how to convert mtz file to a file which can be openne by Chimera?
 
Smith
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From smith_liu123 at 163.com  Wed Mar 18 23:10:00 2015
From: smith_liu123 at 163.com (Smith Liu)
Date: Thu, 19 Mar 2015 14:10:00 +0800 (CST)
Subject: [Chimera-users] problem related to open the chimera file by Coot
Message-ID: <25e5621d.62e0.14c30a71b2f.Coremail.smith_liu123@163.com>

Dear All,
 
I have fit a PDB file with a MRC by the Chimera. I saved both the fitted PDB file and the fitted MRC file by coot. When I open the fitted PDB file and the fitted MRC file  by Chimera at the same time, they still fit perfectly. However when I open the Chimera  fitted PDB file and the Chimera fitted MRC file by coot, the protein backbone (and the sidechains) does not fit the MRC file anymore.
 
Will you please tell me what should I do in order to have the Chimera fitted PDB file and the Chimera fitted MRC file still fit in Coot?
 
I am looking forward to getting your reply.
 
Smith
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From meng at cgl.ucsf.edu  Thu Mar 19 08:25:01 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 19 Mar 2015 08:25:01 -0700
Subject: [Chimera-users] how to convert mtz file to a file which can be
	openne by Chimera
In-Reply-To: <c33dddc.1ea6.14c2f966862.Coremail.smith_liu123@163.com>
References: <c33dddc.1ea6.14c2f966862.Coremail.smith_liu123@163.com>
Message-ID: <1E60529D-1E69-4DC7-922B-FBC93CAE2498@cgl.ucsf.edu>

Dear Smith,
Chimera does not read or convert mtz files.  

There are several older posts to this list that suggest some other program such as CCP4 fft to create a map file from an mtz file, for example:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-August/005470.html>
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2006-February/000700.html>

You can search the Chimera-users mail archive for topics like "mtz" from here:
<http://www.rbvi.ucsf.edu/chimera/docs/feedback.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 18, 2015, at 6:12 PM, "Smith Liu" <smith_liu123 at 163.com> wrote:

> Dear All,
>  
> Will you please tell me how to convert mtz file to a file which can be openne by Chimera?
>  
> Smith




From meng at cgl.ucsf.edu  Thu Mar 19 08:35:15 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 19 Mar 2015 08:35:15 -0700
Subject: [Chimera-users] problem related to open the chimera file by Coot
In-Reply-To: <25e5621d.62e0.14c30a71b2f.Coremail.smith_liu123@163.com>
References: <25e5621d.62e0.14c30a71b2f.Coremail.smith_liu123@163.com>
Message-ID: <6FC75CC5-FED9-42EE-A384-AFA21DBB340C@cgl.ucsf.edu>

Dear Smith,
It may be the same issue as discussed in this previous post -- if so, it is a Coot problem, but a workaround is described:

<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-February/010736.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 18, 2015, at 11:10 PM, "Smith Liu" <smith_liu123 at 163.com> wrote:

> Dear All,
>  
> I have fit a PDB file with a MRC by the Chimera. I saved both the fitted PDB file and the fitted MRC file by coot. When I open the fitted PDB file and the fitted MRC file  by Chimera at the same time, they still fit perfectly. However when I open the Chimera  fitted PDB file and the Chimera fitted MRC file by coot, the protein backbone (and the sidechains) does not fit the MRC file anymore.
>  
> Will you please tell me what should I do in order to have the Chimera fitted PDB file and the Chimera fitted MRC file still fit in Coot?
>  
> I am looking forward to getting your reply.
>  
> Smith




From devicerandom at gmail.com  Thu Mar 19 09:20:57 2015
From: devicerandom at gmail.com (massimo sandal)
Date: Thu, 19 Mar 2015 17:20:57 +0100
Subject: [Chimera-users] Interaction interface between two residues and
 measure buriedArea
In-Reply-To: <9943A754-F708-4C8E-AB95-D45596C62953@sonic.net>
References: <55003415.8020800@gmail.com>
	<9943A754-F708-4C8E-AB95-D45596C62953@sonic.net>
Message-ID: <CAGqFyoojjn3NjzS6XW0o1hVjWEAkSFzvVwiPMvPOojnYoc1eAw@mail.gmail.com>

Hi all,

Sorry for my late reply and many thanks, your comments really helped.
Elaine Meng, your links really helped a lot. Two things:

1) I actually re-checked my dataset and it seems I have no negative SAS
-only negative SES values sometimes.
2) Can someone confirm the SAS values are in units of angstrom squared?

thanks,
Massimo

2015-03-11 23:18 GMT+01:00 Tom Goddard <goddard at sonic.net>:

> Hi Massimo,
>
>   I think buried solvent accessible area (SAS) is most often used when
> buried areas are reported.  Negative values of buried SAS are impossible,
> that would be a bug, probably a failure of the surface calculation, and if
> you see a case of that could you send me a Chimera session that demostrates
> it?  Unfortunately with erratic surface calculation (which does not always
> report when it goes awry) you cannot be certain the numbers are correct.  I
> think buried SES can give a negative value in weird cases because the
> toroidal surface patches created by the probe sphere rolling between the
> two sets of atoms could be large (e.g. the buried area between two spheres
> whose surfaces are separate by a bit less than the probe radius).
>
>         Tom
>
>
> > On Mar 11, 2015, at 5:24 AM, ms <devicerandom at gmail.com> wrote:
> >
> > Dear all,
> >
> > I am trying to understand what is the area buried between two residues
> (or between one residue and two other ones) in several structures. It
> seemed to me the best way to do this was to use the command "measure
> buriedArea :res1 :res2" on the full structure (once all non-protein
> components have been cleaned out of it). The overall trend of these
> measures seems consistent with visual inspection.
> >
> > However I have a couple of questions about it:
> >
> > 1) I am unsure about what value is best to use/compare, buriedSAS and
> buriedSES. It seems to me that the difference between the two is
> essentially in the geometrical protocol used. Is there any general wisdom
> about what do they physically mean and how should I approach each value?
> >
> > 2) In some cases I receive *negative* values for buriedSAS and/or
> buriedSES. Looking on the ML it seems that it is a symptom of a buggy or
> failed area calculation (e.g.
> http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-April/005119.html ).
> However it also says that I should see a "fallback" warning on the Reply
> Log -I see nothing of the sort. How do I troubleshoot this? Also in cases
> where the calculated value is positive, how can I be sure that the values
> are indeed meaningful?
> >
> > Any other feedback on the kind of measurement I am trying to do is more
> than welcome.
> >
> > Thanks a lot,
> > Massimo
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >
>
>
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From meng at cgl.ucsf.edu  Thu Mar 19 09:40:50 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 19 Mar 2015 09:40:50 -0700
Subject: [Chimera-users] Interaction interface between two residues and
	measure buriedArea
In-Reply-To: <CAGqFyoojjn3NjzS6XW0o1hVjWEAkSFzvVwiPMvPOojnYoc1eAw@mail.gmail.com>
References: <55003415.8020800@gmail.com>
	<9943A754-F708-4C8E-AB95-D45596C62953@sonic.net>
	<CAGqFyoojjn3NjzS6XW0o1hVjWEAkSFzvVwiPMvPOojnYoc1eAw@mail.gmail.com>
Message-ID: <57F992EE-B7F1-46B3-AE4C-32794F0C1B6E@cgl.ucsf.edu>

Hi Massimo,
You're welcome!
Yes, the SES and SAS values are in angstroms squared, given atomic coordinates in angstroms.
Elaine

On Mar 19, 2015, at 9:20 AM, massimo sandal <devicerandom at gmail.com> wrote:

> Hi all,
> 
> Sorry for my late reply and many thanks, your comments really helped. Elaine Meng, your links really helped a lot. Two things:
> 
> 1) I actually re-checked my dataset and it seems I have no negative SAS -only negative SES values sometimes. 
> 2) Can someone confirm the SAS values are in units of angstrom squared? 
> 
> thanks,
> Massimo
> 




From olibclarke at gmail.com  Thu Mar 19 09:44:20 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Thu, 19 Mar 2015 12:44:20 -0400
Subject: [Chimera-users] Constraining map-to-map fitting based on symmetry?
Message-ID: <201AA7F2-33F8-424F-93AF-87D6432E3D25@gmail.com>

Hi,

If I have two maps of the same symmetry (say C4), and I align them using fit in map, is there any way to force chimera to keep the rotation axes of the two maps aligned, and to only search rotation around (and translation along) that axis, rather than arbitrary rotations?

Cheers,
Oliver.





From devicerandom at gmail.com  Thu Mar 19 09:56:26 2015
From: devicerandom at gmail.com (massimo sandal)
Date: Thu, 19 Mar 2015 17:56:26 +0100
Subject: [Chimera-users] Interaction interface between two residues and
 measure buriedArea
In-Reply-To: <57F992EE-B7F1-46B3-AE4C-32794F0C1B6E@cgl.ucsf.edu>
References: <55003415.8020800@gmail.com>
	<9943A754-F708-4C8E-AB95-D45596C62953@sonic.net>
	<CAGqFyoojjn3NjzS6XW0o1hVjWEAkSFzvVwiPMvPOojnYoc1eAw@mail.gmail.com>
	<57F992EE-B7F1-46B3-AE4C-32794F0C1B6E@cgl.ucsf.edu>
Message-ID: <CAGqFyorXdxM+GVL55DDff5JRvYRvmTLneDeJ9rob7yd_u7b2RQ@mail.gmail.com>

2015-03-19 17:40 GMT+01:00 Elaine Meng <meng at cgl.ucsf.edu>:

> Hi Massimo,
> You're welcome!
> Yes, the SES and SAS values are in angstroms squared, given atomic
> coordinates in angstroms.
>

Awesome, thanks a lot.
M.
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From goddard at sonic.net  Thu Mar 19 12:23:40 2015
From: goddard at sonic.net (Tom Goddard)
Date: Thu, 19 Mar 2015 12:23:40 -0700
Subject: [Chimera-users] Constraining map-to-map fitting based on
	symmetry?
In-Reply-To: <201AA7F2-33F8-424F-93AF-87D6432E3D25@gmail.com>
References: <201AA7F2-33F8-424F-93AF-87D6432E3D25@gmail.com>
Message-ID: <4EADC70B-BE2D-48F5-AE06-A4864CE7D156@sonic.net>

Hi Oliver,

  No there no way to restrain symmetry axes using Chimera map fitting.  You can optimize rotations only preventing any translation, but full rotations will be allowed.

  You could use the Chimera ?measure correlation? command with the rotationAxis and angleRange and plot options to measure the correlation value as one map is rotated relative to the other.  This doesn?t report the maximum correlation position but you could find the maximum in the tabulated values in the reply log.

	http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/measure.html#correlation

  Tom


> On Mar 19, 2015, at 9:44 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Hi,
> 
> If I have two maps of the same symmetry (say C4), and I align them using fit in map, is there any way to force chimera to keep the rotation axes of the two maps aligned, and to only search rotation around (and translation along) that axis, rather than arbitrary rotations?
> 
> Cheers,
> Oliver.
> 
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From phil.cruz at nih.gov  Thu Mar 19 13:16:32 2015
From: phil.cruz at nih.gov (Cruz, Phil (NIH/NIAID) [C])
Date: Thu, 19 Mar 2015 20:16:32 +0000
Subject: [Chimera-users] Total number of atoms in all submodels
Message-ID: <D130A6DF.94C7%cruzp2@mail.nih.gov>

Dear Chimera users,

When I fetch a biological unit into Chimera from PDB, the symmetry related units are placed into separate submodels.  I would like to find the total number of atoms in all submodels that make up the biological unit within a python script.

Constructs (and variations that I've tried) such as the following only give the number of atoms in each sub model:

numAtoms = len(openModels.list(modelTypes=[Molecule])[0].atoms)

Is there some way to get the grand total of atoms?

Alternatively, if the script could find the total number (or list) of the submodels, I could probably still handle it.

My example is the virus capsid 1ej6.

Thanks for any suggestions.


--
Phillip Cruz, Ph.D.
Contractor, Medical Science & Computing

Computational Structural Biologist
Computational Biology Section
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

31 Center Dr., Room 3B62
Bethesda, MD 20892-0485
Office:  301-451-1089
http://bioinformatics.niaid.nih.gov<http://bioinformatics.niaid.nih.gov/> (Within NIH)
http://exon.niaid.nih.gov<http://exon.niaid.nih.gov/> (Public)

Disclaimer:
The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.



From pett at cgl.ucsf.edu  Thu Mar 19 13:23:29 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 19 Mar 2015 13:23:29 -0700
Subject: [Chimera-users] Total number of atoms in all submodels
In-Reply-To: <D130A6DF.94C7%cruzp2@mail.nih.gov>
References: <D130A6DF.94C7%cruzp2@mail.nih.gov>
Message-ID: <C3026C7E-B9BE-43AF-9D89-127D3EE90531@cgl.ucsf.edu>

On Mar 19, 2015, at 1:16 PM, "Cruz, Phil (NIH/NIAID) [C]" <phil.cruz at nih.gov> wrote:

> numAtoms = len(openModels.list(modelTypes=[Molecule])[0].atoms)

Because of the "[0]" subscript in the above, you are only getting the first Molecule model in the list.  Try this:

numAtoms = sum([len(m.atoms) for m in openModels.list(modelTypes=[Molecule])])

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu


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From phil.cruz at nih.gov  Thu Mar 19 13:32:52 2015
From: phil.cruz at nih.gov (Cruz, Phil (NIH/NIAID) [C])
Date: Thu, 19 Mar 2015 20:32:52 +0000
Subject: [Chimera-users] Total number of atoms in all submodels
In-Reply-To: <C3026C7E-B9BE-43AF-9D89-127D3EE90531@cgl.ucsf.edu>
Message-ID: <D130AA8D.94E9%cruzp2@mail.nih.gov>

Eric,

Thanks, that works perfectly.

Phil

--
Phillip Cruz, Ph.D.
Contractor, Medical Science & Computing

Computational Structural Biologist
Computational Biology Section
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

31 Center Dr., Room 3B62
Bethesda, MD 20892-0485
Office:  301-451-1089
http://bioinformatics.niaid.nih.gov<http://bioinformatics.niaid.nih.gov/> (Within NIH)
http://exon.niaid.nih.gov<http://exon.niaid.nih.gov/> (Public)

Disclaimer:
The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

From: Eric Pettersen <pett at cgl.ucsf.edu<mailto:pett at cgl.ucsf.edu>>
Reply-To: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu> Mailing List" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
Date: Thursday, March 19, 2015 4:23 PM
To: "Cruz, Phil (NIH/NIAID) [C]" <phil.cruz at nih.gov<mailto:phil.cruz at nih.gov>>
Cc: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu> Mailing List" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
Subject: Re: [Chimera-users] Total number of atoms in all submodels

On Mar 19, 2015, at 1:16 PM, "Cruz, Phil (NIH/NIAID) [C]" <phil.cruz at nih.gov<mailto:phil.cruz at nih.gov>> wrote:

numAtoms = len(openModels.list(modelTypes=[Molecule])[0].atoms)

Because of the "[0]" subscript in the above, you are only getting the first Molecule model in the list.  Try this:

numAtoms = sum([len(m.atoms) for m in openModels.list(modelTypes=[Molecule])])

--Eric


                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        http://www.cgl.ucsf.edu





From nick.mihelas at gmail.com  Fri Mar 20 07:46:46 2015
From: nick.mihelas at gmail.com (Nicholas Michelarakis)
Date: Fri, 20 Mar 2015 14:46:46 +0000
Subject: [Chimera-users] Contour levels
Message-ID: <CAGTCbAT+g5krR3fnWNAZKy48VKJgFJ-Ng4fMnNgZaDo7M69kBw@mail.gmail.com>

Hello all,

Forgive me if this is a silly question but I was under the impression that
when you opened two density maps in volume viewer and used the Fit in Map
tool, with the Use only data above contour level option ticked, the
correlation would change according to the contour level you selected in the
volume viewer. In my case this does not happen.

If this is indeed a bug, I would be happy to provide further information.
Atm, I'm using Chimera 1.10.

Thank you very much in advance.

Best,
Nick
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From olibclarke at gmail.com  Fri Mar 20 07:54:13 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Fri, 20 Mar 2015 10:54:13 -0400
Subject: [Chimera-users] Constraining map-to-map fitting based on
	symmetry?
In-Reply-To: <4EADC70B-BE2D-48F5-AE06-A4864CE7D156@sonic.net>
References: <201AA7F2-33F8-424F-93AF-87D6432E3D25@gmail.com>
	<4EADC70B-BE2D-48F5-AE06-A4864CE7D156@sonic.net>
Message-ID: <3454ACCC-550D-404E-BAE2-25B9DF6AAF06@gmail.com>

Thanks Tom, I will try this. I think locking the rotation axis for map fitting to the symmetry axis would be a useful feature for a future version, though I understand that it?s a bit of a niche use case.

Best,
Oliver.
> On Mar 19, 2015, at 3:23 PM, Tom Goddard <goddard at sonic.net> wrote:
> 
> Hi Oliver,
> 
>  No there no way to restrain symmetry axes using Chimera map fitting.  You can optimize rotations only preventing any translation, but full rotations will be allowed.
> 
>  You could use the Chimera ?measure correlation? command with the rotationAxis and angleRange and plot options to measure the correlation value as one map is rotated relative to the other.  This doesn?t report the maximum correlation position but you could find the maximum in the tabulated values in the reply log.
> 
> 	http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/measure.html#correlation
> 
>  Tom
> 
> 
>> On Mar 19, 2015, at 9:44 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
>> 
>> Hi,
>> 
>> If I have two maps of the same symmetry (say C4), and I align them using fit in map, is there any way to force chimera to keep the rotation axes of the two maps aligned, and to only search rotation around (and translation along) that axis, rather than arbitrary rotations?
>> 
>> Cheers,
>> Oliver.
>> 
>> 
>> 
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
> 




From goddard at sonic.net  Fri Mar 20 09:30:20 2015
From: goddard at sonic.net (Tom Goddard)
Date: Fri, 20 Mar 2015 09:30:20 -0700
Subject: [Chimera-users] Contour levels
In-Reply-To: <CAGTCbAT+g5krR3fnWNAZKy48VKJgFJ-Ng4fMnNgZaDo7M69kBw@mail.gmail.com>
References: <CAGTCbAT+g5krR3fnWNAZKy48VKJgFJ-Ng4fMnNgZaDo7M69kBw@mail.gmail.com>
Message-ID: <75B33656-73E9-4120-A29D-D289F715FB8E@sonic.net>

Hi Nick,

  The option is ?use only data above contour level from *first* map?.  So the correlation should change if you adjust the contour of map #1 when fitting #1 in #2, but it will not change when the contour level of map #2 is changed.

	Tom


> On Mar 20, 2015, at 7:46 AM, Nicholas Michelarakis wrote:
> 
> Hello all,
> 
> Forgive me if this is a silly question but I was under the impression that when you opened two density maps in volume viewer and used the Fit in Map tool, with the Use only data above contour level option ticked, the correlation would change according to the contour level you selected in the volume viewer. In my case this does not happen.
> 
> If this is indeed a bug, I would be happy to provide further information. Atm, I'm using Chimera 1.10.
> 
> Thank you very much in advance.
> 
> Best,
> Nick    
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From goddard at sonic.net  Fri Mar 20 09:37:11 2015
From: goddard at sonic.net (Tom Goddard)
Date: Fri, 20 Mar 2015 09:37:11 -0700
Subject: [Chimera-users] Constraining map-to-map fitting based on
	symmetry?
In-Reply-To: <3454ACCC-550D-404E-BAE2-25B9DF6AAF06@gmail.com>
References: <201AA7F2-33F8-424F-93AF-87D6432E3D25@gmail.com>
	<4EADC70B-BE2D-48F5-AE06-A4864CE7D156@sonic.net>
	<3454ACCC-550D-404E-BAE2-25B9DF6AAF06@gmail.com>
Message-ID: <31145BC4-7FAA-4A44-BF98-9B23559436B3@sonic.net>

Hi Oliver,

  My suggestion for using ?measure correlation? only handled rotations about the axis, not translations along the axis.  I?ve added a feature request for fitting using just these 2 degrees of freedom.

	http://plato.cgl.ucsf.edu/trac/chimera/ticket/13829 <http://plato.cgl.ucsf.edu/trac/chimera/ticket/13829>

I think it is not that uncommon a case. But we are working hard on Chimera 2 so I don?t think this will be added soon. Thanks for the suggestion.

	Tom


> On Mar 20, 2015, at 7:54 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Thanks Tom, I will try this. I think locking the rotation axis for map fitting to the symmetry axis would be a useful feature for a future version, though I understand that it?s a bit of a niche use case.
> 
> Best,
> Oliver.
>> On Mar 19, 2015, at 3:23 PM, Tom Goddard <goddard at sonic.net> wrote:
>> 
>> Hi Oliver,
>> 
>> No there no way to restrain symmetry axes using Chimera map fitting.  You can optimize rotations only preventing any translation, but full rotations will be allowed.
>> 
>> You could use the Chimera ?measure correlation? command with the rotationAxis and angleRange and plot options to measure the correlation value as one map is rotated relative to the other.  This doesn?t report the maximum correlation position but you could find the maximum in the tabulated values in the reply log.
>> 
>> 	http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/measure.html#correlation
>> 
>> Tom
>> 
>> 
>>> On Mar 19, 2015, at 9:44 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
>>> 
>>> Hi,
>>> 
>>> If I have two maps of the same symmetry (say C4), and I align them using fit in map, is there any way to force chimera to keep the rotation axes of the two maps aligned, and to only search rotation around (and translation along) that axis, rather than arbitrary rotations?
>>> 
>>> Cheers,
>>> Oliver.
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>> 
>> 
> 
> 

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From smith_liu123 at 163.com  Sat Mar 21 07:44:58 2015
From: smith_liu123 at 163.com (Smith Liu)
Date: Sat, 21 Mar 2015 22:44:58 +0800 (CST)
Subject: [Chimera-users] problem related to open the chimera file by Coot
In-Reply-To: <6FC75CC5-FED9-42EE-A384-AFA21DBB340C@cgl.ucsf.edu>
References: <25e5621d.62e0.14c30a71b2f.Coremail.smith_liu123@163.com>
	<6FC75CC5-FED9-42EE-A384-AFA21DBB340C@cgl.ucsf.edu>
Message-ID: <21f5251b.6e11.14c3ccb4d4e.Coremail.smith_liu123@163.com>

Dear Elaine,
 
It is diffrent from the previou post. In the previous shift, the map and pdb did not fit (caused by an accident) in Chimera, and thus they did not fit in Coot. In my situation, the PDB and map fit in Chimera, but did not fit in Coot.
 
Thus can you think out someway to have them fit in Coot?
 
Smith








At 2015-03-19 23:35:15, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:
>Dear Smith,
>It may be the same issue as discussed in this previous post -- if so, it is a Coot problem, but a workaround is described:
>
><http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-February/010736.html>
>
>I hope this helps,
>Elaine
>----------
>Elaine C. Meng, Ph.D. 
>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>Department of Pharmaceutical Chemistry
>University of California, San Francisco
>
>On Mar 18, 2015, at 11:10 PM, "Smith Liu" <smith_liu123 at 163.com> wrote:
>
>> Dear All,
>>  
>> I have fit a PDB file with a MRC by the Chimera. I saved both the fitted PDB file and the fitted MRC file by coot. When I open the fitted PDB file and the fitted MRC file  by Chimera at the same time, they still fit perfectly. However when I open the Chimera  fitted PDB file and the Chimera fitted MRC file by coot, the protein backbone (and the sidechains) does not fit the MRC file anymore.
>>  
>> Will you please tell me what should I do in order to have the Chimera fitted PDB file and the Chimera fitted MRC file still fit in Coot?
>>  
>> I am looking forward to getting your reply.
>>  
>> Smith
>
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From meng at cgl.ucsf.edu  Sun Mar 22 09:57:40 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sun, 22 Mar 2015 09:57:40 -0700
Subject: [Chimera-users] Query on morph command in Chimera
In-Reply-To: <F6926FE9-F3E0-454D-A0FA-37DC55F07159@mrc-lmb.cam.ac.uk>
References: <F6926FE9-F3E0-454D-A0FA-37DC55F07159@mrc-lmb.cam.ac.uk>
Message-ID: <2CBCC4C4-30B5-4FD4-8D7E-8B009528BD30@cgl.ucsf.edu>


On Mar 22, 2015, at 9:38 AM, vinothkumar <vkumar at mrc-lmb.cam.ac.uk> wrote:

> Dear Elaine,
> I have three different volumes/maps of the same protein but differing in conformation. I am able to use the command line - ?vop morph #0,1,2 constantVolume True model #3 frames 200? which then interpolates and I could produce a movie. However, by default the threshold for the volumes and level goes to 4. Is there a way to insert in the command line to tell that all the volumes be set to level (1) and a certain threshold.
> Thank you
> Regards
> Vinoth

Dear Vinoth,
You should adjust the threshold of the maps before the morphing.  This could be done with the ?volume? command if you are not using GUIs, e.g. command:

volume all level 1

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general>

Actually, my own experiments suggest it is only the threshold of the first input map that matters in setting the starting level of the morph.  If you use the ?constantVolume? morphing option, however, the threshold will be adjusted to keep the enclosed volume constant.  If you really wanted to keep it exactly at 1 through the whole morph, you would not use that option.

I hope this helps! For future questions, we recommend you send them to chimera-users at cgl.ucsf.edu (CC?d here) instead of to me or other individuals directly, unless you are including private data.  Thanks,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco






From mborgnia at helix.nih.gov  Sun Mar 22 10:41:54 2015
From: mborgnia at helix.nih.gov (Mario J. Borgnia)
Date: Sun, 22 Mar 2015 13:41:54 -0400
Subject: [Chimera-users] Sampling the density of a map in the vicinity of
	each atom in a model
Message-ID: <550EFEE2.40301@helix.nih.gov>

Hi,
I have a density map in mrc format and a model in pdb format. I would
like to calculate the average density within a 3D window centered at the
coordinates of each atom in the model and include the result as an
attribute for the atom. Despite some effort searching for the answer, I
cannot find out how to do this easily. I could try and go deep into
Python programming but, before I reinvent the wheel, I'd like to know
whether there already is a simpler way to do this in Chimera.

Thanks!

Mario


-- 
+---------------------------------+
| Mario J. Borgnia, Ph. D.        |
|                                 |
| Lab of Cell Biology             |
| NIH NCI/CCR                     |
| 50 South Drive Rm 4306 MSC 8008 |
| Bethesda MD 20892-8008          |
|                                 |
| Tel: (301) 594 0563             |
| mborgnia at nih.gov                |
+---------------------------------+



From mborgnia at helix.nih.gov  Sun Mar 22 13:36:32 2015
From: mborgnia at helix.nih.gov (Mario J. Borgnia)
Date: Sun, 22 Mar 2015 16:36:32 -0400
Subject: [Chimera-users] Query on morph command in Chimera
In-Reply-To: <2CBCC4C4-30B5-4FD4-8D7E-8B009528BD30@cgl.ucsf.edu>
References: <F6926FE9-F3E0-454D-A0FA-37DC55F07159@mrc-lmb.cam.ac.uk>
	<2CBCC4C4-30B5-4FD4-8D7E-8B009528BD30@cgl.ucsf.edu>
Message-ID: <550F27D0.7050509@helix.nih.gov>

Hi Vinoth and Elaine,
I stumbled upon the same problem. I think Vinoth is referring to "step"
rather than "level". If that is the case, the following command would do
the trick:

vop morph #0,1,2 constantVolume True model #3 frames 200; volume #3 step 1


Best,

Mario



On 03/22/2015 12:57 PM, Elaine Meng wrote:
> On Mar 22, 2015, at 9:38 AM, vinothkumar <vkumar at mrc-lmb.cam.ac.uk> wrote:
>
>> Dear Elaine,
>> I have three different volumes/maps of the same protein but differing in conformation. I am able to use the command line - ?vop morph #0,1,2 constantVolume True model #3 frames 200? which then interpolates and I could produce a movie. However, by default the threshold for the volumes and level goes to 4. Is there a way to insert in the command line to tell that all the volumes be set to level (1) and a certain threshold.
>> Thank you
>> Regards
>> Vinoth
> Dear Vinoth,
> You should adjust the threshold of the maps before the morphing.  This could be done with the ?volume? command if you are not using GUIs, e.g. command:
>
> volume all level 1
>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general>
>
> Actually, my own experiments suggest it is only the threshold of the first input map that matters in setting the starting level of the morph.  If you use the ?constantVolume? morphing option, however, the threshold will be adjusted to keep the enclosed volume constant.  If you really wanted to keep it exactly at 1 through the whole morph, you would not use that option.
>
> I hope this helps! For future questions, we recommend you send them to chimera-users at cgl.ucsf.edu (CC?d here) instead of to me or other individuals directly, unless you are including private data.  Thanks,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

-- 
+---------------------------------+
| Mario J. Borgnia, Ph. D.        |
|                                 |
| Lab of Cell Biology             |
| NIH NCI/CCR                     |
| 50 South Drive Rm 4306 MSC 8008 |
| Bethesda MD 20892-8008          |
|                                 |
| Tel: (301) 594 0563             |
| mborgnia at nih.gov                |
+---------------------------------+



From mborgnia at helix.nih.gov  Sun Mar 22 14:05:56 2015
From: mborgnia at helix.nih.gov (Mario J. Borgnia)
Date: Sun, 22 Mar 2015 17:05:56 -0400
Subject: [Chimera-users] Query on morph command in Chimera
In-Reply-To: <550F27D0.7050509@helix.nih.gov>
References: <F6926FE9-F3E0-454D-A0FA-37DC55F07159@mrc-lmb.cam.ac.uk>
	<2CBCC4C4-30B5-4FD4-8D7E-8B009528BD30@cgl.ucsf.edu>
	<550F27D0.7050509@helix.nih.gov>
Message-ID: <550F2EB4.5020000@helix.nih.gov>

Vinoth,

I forgot to mention that this command pair (separated by ;):

vop morph #0,1,2 constantVolume True model #3 frames 200; volume #3 step 1

behaves differently from:

vop morph #0,2 constantVolume True model #3 frames 200 step 1

In the latter, "step" refers to the binning of the data of the morphed
volume, which is done somewhere before the morph is displayed. This
issue is especially confusing for large volumes because the decision
regarding the step that will be used to display the data (the actual
step and not the binning) is done based on the size of the volume. Thus,
if you start with a volume that is large, Chimera will increase the step
and display the data as if binned, indicating the value of the binning
as a "step" in the "volume viewer". Thus, using "step 1" in the vop
command will not bin the morph map and the display will stay at step 4.
If, instead, you were to use:

vop morph #0,2 constantVolume True model #3 frames 200 step 4

The result will look the same, but now the actual data of the morph will
be binned by 4 and the "step box" on "volume viewer" will read "1". Now
if you notice the size of the volume indicated next to the name, it will
be binned. (e.g. 60^3 instead of 240^3).

I hope this helps understand what's going on.


Mario




On 03/22/2015 04:36 PM, Mario J. Borgnia wrote:
> Hi Vinoth and Elaine,
> I stumbled upon the same problem. I think Vinoth is referring to "step"
> rather than "level". If that is the case, the following command would do
> the trick:
>
> vop morph #0,1,2 constantVolume True model #3 frames 200; volume #3 step 1
>
>
> Best,
>
> Mario
>
>
>
> On 03/22/2015 12:57 PM, Elaine Meng wrote:
>> On Mar 22, 2015, at 9:38 AM, vinothkumar <vkumar at mrc-lmb.cam.ac.uk> wrote:
>>
>>> Dear Elaine,
>>> I have three different volumes/maps of the same protein but differing in conformation. I am able to use the command line - ?vop morph #0,1,2 constantVolume True model #3 frames 200? which then interpolates and I could produce a movie. However, by default the threshold for the volumes and level goes to 4. Is there a way to insert in the command line to tell that all the volumes be set to level (1) and a certain threshold.
>>> Thank you
>>> Regards
>>> Vinoth
>> Dear Vinoth,
>> You should adjust the threshold of the maps before the morphing.  This could be done with the ?volume? command if you are not using GUIs, e.g. command:
>>
>> volume all level 1
>>
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general>
>>
>> Actually, my own experiments suggest it is only the threshold of the first input map that matters in setting the starting level of the morph.  If you use the ?constantVolume? morphing option, however, the threshold will be adjusted to keep the enclosed volume constant.  If you really wanted to keep it exactly at 1 through the whole morph, you would not use that option.
>>
>> I hope this helps! For future questions, we recommend you send them to chimera-users at cgl.ucsf.edu (CC?d here) instead of to me or other individuals directly, unless you are including private data.  Thanks,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>>
>>
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

-- 
+---------------------------------+
| Mario J. Borgnia, Ph. D.        |
|                                 |
| Lab of Cell Biology             |
| NIH NCI/CCR                     |
| 50 South Drive Rm 4306 MSC 8008 |
| Bethesda MD 20892-8008          |
|                                 |
| Tel: (301) 594 0563             |
| mborgnia at nih.gov                |
+---------------------------------+



From goddard at sonic.net  Mon Mar 23 09:56:51 2015
From: goddard at sonic.net (Tom Goddard)
Date: Mon, 23 Mar 2015 09:56:51 -0700
Subject: [Chimera-users] Sampling the density of a map in the vicinity
	of each atom in a model
In-Reply-To: <550EFEE2.40301@helix.nih.gov>
References: <550EFEE2.40301@helix.nih.gov>
Message-ID: <4AD5FA23-8DAF-4FBA-B39B-15365A6CD64B@sonic.net>

Hi Mario,

  An approach to this is to simply Gaussian smooth the map (vop gaussian command), then use the Values at Atom Positions tool.  The Gaussian smoothing replaces the value at each grid point with a weighted average of nearby grid values with a Gaussian fall-off of weights with distance from the atom.  You said ?windowing? which usually means you make a hard cutoff, you use an unweighted average within a box centered at an atom, or within a sphere centered at an atom.  For most uses I think the soft cutoff of a Gaussian weighting with distance is better than hard cutoff.  If you really want the hard-cutoff and unweighted averaging it would require Python programming.

	Tom


> On Mar 22, 2015, at 10:41 AM, Mario J. Borgnia wrote:
> 
> Hi,
> I have a density map in mrc format and a model in pdb format. I would
> like to calculate the average density within a 3D window centered at the
> coordinates of each atom in the model and include the result as an
> attribute for the atom. Despite some effort searching for the answer, I
> cannot find out how to do this easily. I could try and go deep into
> Python programming but, before I reinvent the wheel, I'd like to know
> whether there already is a simpler way to do this in Chimera.
> 
> Thanks!
> 
> Mario
> 
> 
> -- 
> +---------------------------------+
> | Mario J. Borgnia, Ph. D.        |
> |                                 |
> | Lab of Cell Biology             |
> | NIH NCI/CCR                     |
> | 50 South Drive Rm 4306 MSC 8008 |
> | Bethesda MD 20892-8008          |
> |                                 |
> | Tel: (301) 594 0563             |
> | mborgnia at nih.gov                |
> +---------------------------------+
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From goddard at sonic.net  Mon Mar 23 10:00:03 2015
From: goddard at sonic.net (Tom Goddard)
Date: Mon, 23 Mar 2015 10:00:03 -0700
Subject: [Chimera-users] Sampling the density of a map in the vicinity
	of each atom in a model
In-Reply-To: <550EFEE2.40301@helix.nih.gov>
References: <550EFEE2.40301@helix.nih.gov>
Message-ID: <71695917-8A68-4561-AB6F-8DDC32A8C258@sonic.net>

Hi Mario,

  I just remembered I wrote a little Python to average map values in a sphere around atoms, called mapsum.py on the Chimera Python scripts web page:

	http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts>

  Tom


> On Mar 22, 2015, at 10:41 AM, Mario J. Borgnia <mborgnia at helix.nih.gov> wrote:
> 
> Hi,
> I have a density map in mrc format and a model in pdb format. I would
> like to calculate the average density within a 3D window centered at the
> coordinates of each atom in the model and include the result as an
> attribute for the atom. Despite some effort searching for the answer, I
> cannot find out how to do this easily. I could try and go deep into
> Python programming but, before I reinvent the wheel, I'd like to know
> whether there already is a simpler way to do this in Chimera.
> 
> Thanks!
> 
> Mario
> 
> 
> -- 
> +---------------------------------+
> | Mario J. Borgnia, Ph. D.        |
> |                                 |
> | Lab of Cell Biology             |
> | NIH NCI/CCR                     |
> | 50 South Drive Rm 4306 MSC 8008 |
> | Bethesda MD 20892-8008          |
> |                                 |
> | Tel: (301) 594 0563             |
> | mborgnia at nih.gov                |
> +---------------------------------+
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 

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From goddard at sonic.net  Mon Mar 23 10:03:15 2015
From: goddard at sonic.net (Tom Goddard)
Date: Mon, 23 Mar 2015 10:03:15 -0700
Subject: [Chimera-users] Query on morph command in Chimera
In-Reply-To: <550F2EB4.5020000@helix.nih.gov>
References: <F6926FE9-F3E0-454D-A0FA-37DC55F07159@mrc-lmb.cam.ac.uk>
	<2CBCC4C4-30B5-4FD4-8D7E-8B009528BD30@cgl.ucsf.edu>
	<550F27D0.7050509@helix.nih.gov> <550F2EB4.5020000@helix.nih.gov>
Message-ID: <2CAB9582-75BF-496E-8538-BB69396D3793@sonic.net>

Hi Vinoth,

  Chimera automatically chooses the map step size so your graphics doesn?t get too slow.  But you can have it always use step 1 by changing a setting in the Volume Viewer dialog, menu Features / Data Display Options, ?Adjust step to show at most N Mvoxels?.  Just uncheck that option and you will always get full resolution map display, ie. step 1.  You can save that setting if you like with Volume Viewer menu Features / Save Default Dialog Settings.

	Tom


> On Mar 22, 2015, at 2:05 PM, Mario J. Borgnia <mborgnia at helix.nih.gov> wrote:
> 
> Vinoth,
> 
> I forgot to mention that this command pair (separated by ;):
> 
> vop morph #0,1,2 constantVolume True model #3 frames 200; volume #3 step 1
> 
> behaves differently from:
> 
> vop morph #0,2 constantVolume True model #3 frames 200 step 1
> 
> In the latter, "step" refers to the binning of the data of the morphed
> volume, which is done somewhere before the morph is displayed. This
> issue is especially confusing for large volumes because the decision
> regarding the step that will be used to display the data (the actual
> step and not the binning) is done based on the size of the volume. Thus,
> if you start with a volume that is large, Chimera will increase the step
> and display the data as if binned, indicating the value of the binning
> as a "step" in the "volume viewer". Thus, using "step 1" in the vop
> command will not bin the morph map and the display will stay at step 4.
> If, instead, you were to use:
> 
> vop morph #0,2 constantVolume True model #3 frames 200 step 4
> 
> The result will look the same, but now the actual data of the morph will
> be binned by 4 and the "step box" on "volume viewer" will read "1". Now
> if you notice the size of the volume indicated next to the name, it will
> be binned. (e.g. 60^3 instead of 240^3).
> 
> I hope this helps understand what's going on.
> 
> 
> Mario
> 
> 
> 
> 
> On 03/22/2015 04:36 PM, Mario J. Borgnia wrote:
>> Hi Vinoth and Elaine,
>> I stumbled upon the same problem. I think Vinoth is referring to "step"
>> rather than "level". If that is the case, the following command would do
>> the trick:
>> 
>> vop morph #0,1,2 constantVolume True model #3 frames 200; volume #3 step 1
>> 
>> 
>> Best,
>> 
>> Mario
>> 
>> 
>> 
>> On 03/22/2015 12:57 PM, Elaine Meng wrote:
>>> On Mar 22, 2015, at 9:38 AM, vinothkumar <vkumar at mrc-lmb.cam.ac.uk> wrote:
>>> 
>>>> Dear Elaine,
>>>> I have three different volumes/maps of the same protein but differing in conformation. I am able to use the command line - ?vop morph #0,1,2 constantVolume True model #3 frames 200? which then interpolates and I could produce a movie. However, by default the threshold for the volumes and level goes to 4. Is there a way to insert in the command line to tell that all the volumes be set to level (1) and a certain threshold.
>>>> Thank you
>>>> Regards
>>>> Vinoth
>>> Dear Vinoth,
>>> You should adjust the threshold of the maps before the morphing.  This could be done with the ?volume? command if you are not using GUIs, e.g. command:
>>> 
>>> volume all level 1
>>> 
>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general>
>>> 
>>> Actually, my own experiments suggest it is only the threshold of the first input map that matters in setting the starting level of the morph.  If you use the ?constantVolume? morphing option, however, the threshold will be adjusted to keep the enclosed volume constant.  If you really wanted to keep it exactly at 1 through the whole morph, you would not use that option.
>>> 
>>> I hope this helps! For future questions, we recommend you send them to chimera-users at cgl.ucsf.edu (CC?d here) instead of to me or other individuals directly, unless you are including private data.  Thanks,
>>> Elaine
>>> -----
>>> Elaine C. Meng, Ph.D.                       
>>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> -- 
> +---------------------------------+
> | Mario J. Borgnia, Ph. D.        |
> |                                 |
> | Lab of Cell Biology             |
> | NIH NCI/CCR                     |
> | 50 South Drive Rm 4306 MSC 8008 |
> | Bethesda MD 20892-8008          |
> |                                 |
> | Tel: (301) 594 0563             |
> | mborgnia at nih.gov                |
> +---------------------------------+
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From vkumar at mrc-lmb.cam.ac.uk  Sun Mar 22 10:02:38 2015
From: vkumar at mrc-lmb.cam.ac.uk (vinothkumar)
Date: Sun, 22 Mar 2015 17:02:38 +0000
Subject: [Chimera-users] Query on morph command in Chimera
In-Reply-To: <2CBCC4C4-30B5-4FD4-8D7E-8B009528BD30@cgl.ucsf.edu>
References: <F6926FE9-F3E0-454D-A0FA-37DC55F07159@mrc-lmb.cam.ac.uk>
	<2CBCC4C4-30B5-4FD4-8D7E-8B009528BD30@cgl.ucsf.edu>
Message-ID: <F6594D08-6DA7-40B3-89EF-2FE671C24F96@mrc-lmb.cam.ac.uk>

Dear Elaine,
	Thanks for the quick reply. I have the volumes open and all of them are with same threshold but only when I type in command line then the morph starts different from the original volumes. I just figured a way round it. After it has created the morph map as a new model, then I change the levels and record the movie. 

Thanks again


Vinoth

On 22 Mar 2015, at 16:57, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 
> On Mar 22, 2015, at 9:38 AM, vinothkumar <vkumar at mrc-lmb.cam.ac.uk> wrote:
> 
>> Dear Elaine,
>> I have three different volumes/maps of the same protein but differing in conformation. I am able to use the command line - ?vop morph #0,1,2 constantVolume True model #3 frames 200? which then interpolates and I could produce a movie. However, by default the threshold for the volumes and level goes to 4. Is there a way to insert in the command line to tell that all the volumes be set to level (1) and a certain threshold.
>> Thank you
>> Regards
>> Vinoth
> 
> Dear Vinoth,
> You should adjust the threshold of the maps before the morphing.  This could be done with the ?volume? command if you are not using GUIs, e.g. command:
> 
> volume all level 1
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general>
> 
> Actually, my own experiments suggest it is only the threshold of the first input map that matters in setting the starting level of the morph.  If you use the ?constantVolume? morphing option, however, the threshold will be adjusted to keep the enclosed volume constant.  If you really wanted to keep it exactly at 1 through the whole morph, you would not use that option.
> 
> I hope this helps! For future questions, we recommend you send them to chimera-users at cgl.ucsf.edu (CC?d here) instead of to me or other individuals directly, unless you are including private data.  Thanks,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> 

Vinothkumar K.R.
Structural Studies Division
MRC-Laboratory of Molecular Biology
Francis Crick Avenue,
Cambridge
CB2 0QH

Tel: 44-(0)1223-267484





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From smith_liu123 at 163.com  Mon Mar 23 23:47:29 2015
From: smith_liu123 at 163.com (Smith Liu)
Date: Tue, 24 Mar 2015 14:47:29 +0800 (CST)
Subject: [Chimera-users] command related to the alignment of the ribbon form
 and the ball & stick form
Message-ID: <744f8945.1b1c6.14c4a8939f1.Coremail.smith_liu123@163.com>

Dear All,
 
If by Chimera we open a PDB and a corresponding mrc file, and we display the molecule by both ribbon format and ball & stick format, we can find there is a minor disalignment between the ribbon representation and the ball & stick representation.
 
I remember I have read somewhere by a ribbon related command the Chimera can align the ribbon representation and ball & stick presentation nicely, but I have forgotten where I read the tutorial or introduction.
 
Will you please tell me the command to have chimera to get good alignment of the ribbon representation and ball & stick presentation, or tell me the weblink of the corresponding tutorial or reference?
 
I am looking forward to getting your reply.
 
Smith
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From meng at cgl.ucsf.edu  Tue Mar 24 09:33:09 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 24 Mar 2015 09:33:09 -0700
Subject: [Chimera-users] command related to the alignment of the ribbon
	form and the ball & stick form
In-Reply-To: <744f8945.1b1c6.14c4a8939f1.Coremail.smith_liu123@163.com>
References: <744f8945.1b1c6.14c4a8939f1.Coremail.smith_liu123@163.com>
Message-ID: <B829F4F1-74BD-4B14-B11E-A2BA0713D0C9@cgl.ucsf.edu>

Dear Smith,
The default ribbon path is smoothed, which gives a nicer-looking ribbon but doesn't exactly match the positions of the backbone atoms.  I'm guessing this is what you meant.  

You can make the ribbon go exactly through the CA atom positions by using cardinal spline instead of the default B-spline, for example with command:

ribspline card

?as you can see, that gives a very wavy ribbon.  There are several command options for adjusting the parameters.  For example, I like to apply some compromise smoothing to just the beta-strands:

ribspline card smooth strand

See the manual page for explanations of the command options:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ribspline.html>

To go back to the default ribbon path, command:

ribspline b

Further details:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#offset>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 23, 2015, at 11:47 PM, "Smith Liu" <smith_liu123 at 163.com> wrote:

> Dear All,
>  
> If by Chimera we open a PDB and a corresponding mrc file, and we display the molecule by both ribbon format and ball & stick format, we can find there is a minor disalignment between the ribbon representation and the ball & stick representation.
>  
> I remember I have read somewhere by a ribbon related command the Chimera can align the ribbon representation and ball & stick presentation nicely, but I have forgotten where I read the tutorial or introduction.
>  
> Will you please tell me the command to have chimera to get good alignment of the ribbon representation and ball & stick presentation, or tell me the weblink of the corresponding tutorial or reference?
>  
> I am looking forward to getting your reply.
>  
> Smith




From phil.cruz at nih.gov  Tue Mar 24 14:07:19 2015
From: phil.cruz at nih.gov (Cruz, Phil (NIH/NIAID) [C])
Date: Tue, 24 Mar 2015 21:07:19 +0000
Subject: [Chimera-users] Creating MultiScale surface from a script
Message-ID: <D1374A45.97A9%cruzp2@mail.nih.gov>

Hello Chimera users,

I need to create a MultiScale surface from a Chimera python script when the model is of large structures such as virus particles.  On a Mac, the following lines work great:

import MultiScale
d = MultiScale.show_multiscale_model_dialog()
d.make_multimers_cb(molecules=None)

and produce the desired surface output.

Unfortunately, where I really need this to work is on a Linux server using the special version of Chimera that doesn't require a graphics head.  When I run the script there I get errors, presumably when the script tries to create the dialog:

Traceback (most recent call last):
  File "/opt/UCSF/Chimera64-1.10.1/share/chimeraInit.py", line 698, in init
    midas_text.doRunScript("runscript", script)
  File "/opt/UCSF/Chimera64-1.10.1/share/Midas/midas_text.py", line 2206, in doRunScript
    execfile(scriptPath, scriptGlobals)
  File "Chimera_Molecular.py", line 301, in <module>
    d = MultiScale.show_multiscale_model_dialog()
  File "/opt/UCSF/Chimera64-1.10.1/share/MultiScale/__init__.py", line 2296, in show_multiscale_model_dialog
    return dialogs.display(MultiScale_Model_Dialog.name)
  File "/opt/UCSF/Chimera64-1.10.1/share/chimera/dialogs.py", line 76, in display
    dialog = find(name, create=1)
  File "/opt/UCSF/Chimera64-1.10.1/share/chimera/dialogs.py", line 61, in find
    return d()
  File "/opt/UCSF/Chimera64-1.10.1/share/chimera/baseDialog.py", line 665, in __init__
    from tkgui import windowSystem
  File "/opt/UCSF/Chimera64-1.10.1/share/chimera/tkgui.py", line 73, in <module>
    import Togl
ImportError: No module named Togl

Is there a way to have the script create the multiscale surface without invoking the dialog (if that's what the issue is), or some other approach to get this to work in the required environment?

Thanks for any suggestions.

--
Phillip Cruz, Ph.D.
Contractor, Medical Science & Computing

Computational Structural Biologist
Computational Biology Section
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

31 Center Dr., Room 3B62
Bethesda, MD 20892-0485
Office:  301-451-1089
http://bioinformatics.niaid.nih.gov<http://bioinformatics.niaid.nih.gov/> (Within NIH)
http://exon.niaid.nih.gov<http://exon.niaid.nih.gov/> (Public)

Disclaimer:
The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.



From goddard at sonic.net  Tue Mar 24 15:56:53 2015
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 24 Mar 2015 15:56:53 -0700
Subject: [Chimera-users] Creating MultiScale surface from a script
In-Reply-To: <D1374A45.97A9%cruzp2@mail.nih.gov>
References: <D1374A45.97A9%cruzp2@mail.nih.gov>
Message-ID: <788B564E-0F6D-4631-A4D7-5FF6F55CF7A8@sonic.net>

Hi Phil,

  The Multiscale tool won?t work in headless Chimera.  Unfortunately that code was written in antiquity and only operates through a GUI interface.  But you can use the Chimera ?sym? command to get multiscale style surfaces of symmetric structures.  For example,

  open 2bbv
  sym #0 surf true

Check out the sym command documentation

	http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sym.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sym.html>

I believe it works in the headless Chimera, although I have not tested that.

	Tom



> On Mar 24, 2015, at 2:07 PM, Cruz, Phil (NIH/NIAID) [C] wrote:
> 
> Hello Chimera users,
> 
> I need to create a MultiScale surface from a Chimera python script when the model is of large structures such as virus particles.  On a Mac, the following lines work great:
> 
> import MultiScale
> d = MultiScale.show_multiscale_model_dialog()
> d.make_multimers_cb(molecules=None)
> 
> and produce the desired surface output.
> 
> Unfortunately, where I really need this to work is on a Linux server using the special version of Chimera that doesn't require a graphics head.  When I run the script there I get errors, presumably when the script tries to create the dialog:
> 
> Traceback (most recent call last):
>  File "/opt/UCSF/Chimera64-1.10.1/share/chimeraInit.py", line 698, in init
>    midas_text.doRunScript("runscript", script)
>  File "/opt/UCSF/Chimera64-1.10.1/share/Midas/midas_text.py", line 2206, in doRunScript
>    execfile(scriptPath, scriptGlobals)
>  File "Chimera_Molecular.py", line 301, in <module>
>    d = MultiScale.show_multiscale_model_dialog()
>  File "/opt/UCSF/Chimera64-1.10.1/share/MultiScale/__init__.py", line 2296, in show_multiscale_model_dialog
>    return dialogs.display(MultiScale_Model_Dialog.name)
>  File "/opt/UCSF/Chimera64-1.10.1/share/chimera/dialogs.py", line 76, in display
>    dialog = find(name, create=1)
>  File "/opt/UCSF/Chimera64-1.10.1/share/chimera/dialogs.py", line 61, in find
>    return d()
>  File "/opt/UCSF/Chimera64-1.10.1/share/chimera/baseDialog.py", line 665, in __init__
>    from tkgui import windowSystem
>  File "/opt/UCSF/Chimera64-1.10.1/share/chimera/tkgui.py", line 73, in <module>
>    import Togl
> ImportError: No module named Togl
> 
> Is there a way to have the script create the multiscale surface without invoking the dialog (if that's what the issue is), or some other approach to get this to work in the required environment?
> 
> Thanks for any suggestions.
> 
> --
> Phillip Cruz, Ph.D.
> Contractor, Medical Science & Computing
> 
> Computational Structural Biologist
> Computational Biology Section
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
> 
> 31 Center Dr., Room 3B62
> Bethesda, MD 20892-0485
> Office:  301-451-1089
> http://bioinformatics.niaid.nih.gov<http://bioinformatics.niaid.nih.gov/> (Within NIH)
> http://exon.niaid.nih.gov<http://exon.niaid.nih.gov/> (Public)
> 
> Disclaimer:
> The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 

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From sunyeping at aliyun.com  Wed Mar 25 03:11:44 2015
From: sunyeping at aliyun.com (sunyeping)
Date: Wed, 25 Mar 2015 18:11:44 +0800
Subject: [Chimera-users] =?utf-8?q?black_bar_in_saved_image?=
Message-ID: <24df7b34-98dc-4647-b219-869f2bd0e909@aliyun.com>

Dear all,I find in the saved volume image (png file), there are some black bar whick mask the image? Please see the following link:https://www.dropbox.com/s/nvy3douvafymqxd/image.png?dl=0Do you know how to get rid of them?Thank you very much!
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
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From dem at g.ucla.edu  Wed Mar 25 00:52:17 2015
From: dem at g.ucla.edu (Dan McNamara)
Date: Wed, 25 Mar 2015 00:52:17 -0700
Subject: [Chimera-users] Problems with reproducing 'write relative' output
Message-ID: <CAP5sn90MkJVMo=JxRVXMc-njZ_c3LU0DMYCDkak1HWn9pszzPw@mail.gmail.com>

Hi all,

I am encountering a strange inconsistency with the 'relative' option for
the "write" command. Searching for similar problems on the mailing list
came up short, so I thought I'd ask about it.

To put it briefly, I run chimera with --nogui and perform ~780,000 total
matches in which I write out new coordinates using 'relative.' My issue
lies in automating this process with .com scripts, which creates different
results from typing out the exact same commands into the command line of
the GUI. This has been plaguing me for a year or so, and most recently I
can cite using version 1.10.1 (build 40427).

Below is a small example to illustrate my operations. The "B-new_#.pdb"
output files will contain different coordinates if they originate from
automated runs or manual execution.

This problem is sporadic and I cannot narrow down the source of the
discrepancy. From best I can tell, there are occasionally output files from
automation (e.g. B-new_#.pdb) that are in the correct coordinate reference
frame. However, many (most?) are not and it is a big obstacle.

I hope that someone may have some insight on this problem.

/////////// example ///////////
open A.pdb
open B.pdb
open C.pdb

##write out selection from #0 [this file is always consistent]
select #0:...
write selected relative 0 #0 A-new.pdb

##move #2 onto #0
match #2:... #0:...
##move #1 onto #2
match #1:... #2:...

##write out selection from #1 and save it in its new position relative to
#0 [inconsistent]
select #1:...
write selected relative 0 #1 B-new_1.pdb
~select all

##move #1 slightly
match #1:... #2:...+1

##write out selection from #1 and save it in its new position relative to
#0 [inconsistent]
select #1:...
write selected relative 0 #1 B-new_2.pdb
~select all

##move #1 slightly more
match #1:... #2:...+2

##write out selection from #1 and save it in its new position relative to
#0 [inconsistent]
select #1:...
write selected relative 0 #1 B-new_3.pdb
/////////// example ///////////

Best,
Dan McNamara
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From gregc at cgl.ucsf.edu  Wed Mar 25 12:40:49 2015
From: gregc at cgl.ucsf.edu (gregc at cgl.ucsf.edu)
Date: Wed, 25 Mar 2015 19:40:49 +0000
Subject: [Chimera-users] black bar in saved image
In-Reply-To: <24df7b34-98dc-4647-b219-869f2bd0e909@aliyun.com>
References: <24df7b34-98dc-4647-b219-869f2bd0e909@aliyun.com>
Message-ID: <ec491f3736f9e09089f0b0b6535de5d8@mail.cgl.ucsf.edu>

For Chimera bugs, please use Chimera's Help / Report a Bug dialog.? That will tell us more about your computer that will let us see if the bug is related to your setup.? Specially, it tells us the version of Chimera, which operating system is being used, the graphics card, and the graphics driver version.

That said, I haven't seen this bug for many years.? So if you're not using a current version of Chimera, it's time to update.? The other common fix is to update your graphics driver (or install one, if you haven't already).

??? HTH,

??? Greg

March 25 2015 3:47 AM, "sunyeping"  wrote:
Dear all,I find in the saved volume image (png file), there are some black bar whick mask the image? Please see the following link:https://www.dropbox.com/s/nvy3douvafymqxd/image.png?dl=0 (https://www.dropbox.com/s/nvy3douvafymqxd/image.png?dl=0)Do you know how to get rid of them?Thank you very much!
	Yeping Sun

	Institute of Microbiology, Chinese Academy of Sciences
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From goddard at sonic.net  Wed Mar 25 17:06:06 2015
From: goddard at sonic.net (Tom Goddard)
Date: Wed, 25 Mar 2015 17:06:06 -0700
Subject: [Chimera-users] Problems with reproducing 'write relative'
	output
In-Reply-To: <CAP5sn90MkJVMo=JxRVXMc-njZ_c3LU0DMYCDkak1HWn9pszzPw@mail.gmail.com>
References: <CAP5sn90MkJVMo=JxRVXMc-njZ_c3LU0DMYCDkak1HWn9pszzPw@mail.gmail.com>
Message-ID: <617D5901-8610-4042-9D5E-D0238C3C26EA@sonic.net>

Hi Dan,

  That?s mysterious and sounds like a bug.  I?m sure we could get to the bottom of it if you submitted a bug report with Chimera menu Help / Report a Bug? and attach a zip file containing the 3 input PDB files A.pdb, B.pdb and C.pdb and the incorrect PDB output files that result and the exact script.  That would let us reproduce the problem and fix it.

	Tom


> On Mar 25, 2015, at 12:52 AM, Dan McNamara wrote:
> 
> Hi all,
> 
> I am encountering a strange inconsistency with the 'relative' option for the "write" command. Searching for similar problems on the mailing list came up short, so I thought I'd ask about it.
> 
> To put it briefly, I run chimera with --nogui and perform ~780,000 total matches in which I write out new coordinates using 'relative.' My issue lies in automating this process with .com scripts, which creates different results from typing out the exact same commands into the command line of the GUI. This has been plaguing me for a year or so, and most recently I can cite using version 1.10.1 (build 40427).
> 
> Below is a small example to illustrate my operations. The "B-new_#.pdb" output files will contain different coordinates if they originate from automated runs or manual execution. 
> 
> This problem is sporadic and I cannot narrow down the source of the discrepancy. From best I can tell, there are occasionally output files from automation (e.g. B-new_#.pdb) that are in the correct coordinate reference frame. However, many (most?) are not and it is a big obstacle.
> 
> I hope that someone may have some insight on this problem.
> 
> /////////// example ///////////
> open A.pdb
> open B.pdb
> open C.pdb
> 
> ##write out selection from #0 [this file is always consistent]
> select #0:...
> write selected relative 0 #0 A-new.pdb
> 
> ##move #2 onto #0
> match #2:... #0:...
> ##move #1 onto #2
> match #1:... #2:...
> 
> ##write out selection from #1 and save it in its new position relative to #0 [inconsistent]
> select #1:...
> write selected relative 0 #1 B-new_1.pdb
> ~select all
> 
> ##move #1 slightly 
> match #1:... #2:...+1
> 
> ##write out selection from #1 and save it in its new position relative to #0 [inconsistent]
> select #1:...
> write selected relative 0 #1 B-new_2.pdb
> ~select all
> 
> ##move #1 slightly more
> match #1:... #2:...+2
> 
> ##write out selection from #1 and save it in its new position relative to #0 [inconsistent]
> select #1:...
> write selected relative 0 #1 B-new_3.pdb
> /////////// example ///////////
> 
> Best,
> Dan McNamara
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From olibclarke at gmail.com  Thu Mar 26 10:03:06 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Thu, 26 Mar 2015 13:03:06 -0400
Subject: [Chimera-users] Toggle active vs displayed for checkboxes at bottom
	of screen?
Message-ID: <48232DA5-E1AE-4194-A275-B42D00A223A3@gmail.com>

Hi, this is more of a feature suggestion than anything, and I guess it is unlikely to be implemented before Chimera 2, but thought I?d put it out there anyway. 

Currently the checkboxes at the bottom of the main display control whether or not a model is active - this is very handy when reorienting models with respect to one another. 

I would love a similar means to toggle the display of individual models without going to the model panel. One way would be to alter the ?Active models? text label (circled in screenshot) to ?Displayed models?, and change the behaviour/meaning of the checkboxes accordingly, similar to the A/I/R/S selection mode changer at the bottom right of the main display. 

So you would click ?Active models?, and the text would switch to ?Displayed models?, and the configuration of the checkboxes  would change so that the displayed models (rather than the active models) are checked. 

Is this something that would be possible in a future version?

Best,
Oliver.
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From meng at cgl.ucsf.edu  Thu Mar 26 10:28:00 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 26 Mar 2015 10:28:00 -0700
Subject: [Chimera-users] Toggle active vs displayed for checkboxes at
	bottom of screen?
In-Reply-To: <48232DA5-E1AE-4194-A275-B42D00A223A3@gmail.com>
References: <48232DA5-E1AE-4194-A275-B42D00A223A3@gmail.com>
Message-ID: <39A36A1D-66E3-4B56-9E53-EFCE5695CD3D@cgl.ucsf.edu>

Hi Oliver,
I personally would rather just have checkboxes for model-display instead of model-active!  The current model-active checkboxes are somewhat of a legacy from the previous-generation program, MidasPlus.  Your idea to switch between the two is also reasonable.  However, I can only "lobby" for changes, since I'm the token non-programmer on the team?. unless you count fortran (most people don't, and not to worry, my fortran programs aren't going into Chimera).

Possible yes? the difficult thing is to manage and prioritize requests and our own plans without letting things fall through the cracks between when they are suggested and when they can be implemented.  This is always an issue, whether Chimera 1 or 2...

Consider also that Chimera2 will have certain major differences that may make some suggested changes less applicable or less needed.

Thanks for your ideas!  Sincerely,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 26, 2015, at 10:03 AM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Hi, this is more of a feature suggestion than anything, and I guess it is unlikely to be implemented before Chimera 2, but thought I?d put it out there anyway. 
> 
> Currently the checkboxes at the bottom of the main display control whether or not a model is active - this is very handy when reorienting models with respect to one another. 
> 
> I would love a similar means to toggle the display of individual models without going to the model panel. One way would be to alter the ?Active models? text label (circled in screenshot) to ?Displayed models?, and change the behaviour/meaning of the checkboxes accordingly, similar to the A/I/R/S selection mode changer at the bottom right of the main display. 
> 
> So you would click ?Active models?, and the text would switch to ?Displayed models?, and the configuration of the checkboxes  would change so that the displayed models (rather than the active models) are checked. 
> 
> Is this something that would be possible in a future version?
> 
> Best,
> Oliver.




From olibclarke at gmail.com  Thu Mar 26 14:03:54 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Thu, 26 Mar 2015 17:03:54 -0400
Subject: [Chimera-users] Rename models from command line
Message-ID: <C23CFCD2-E425-4A41-A1D6-94C5C3876C12@gmail.com>

Hi all,

Is there any way to rename models from the command line? I can do so using the model panel, but I have a script that generates a bunch of different models, and I would like to give them descriptive names apart from the model id in the script.

Oliver.


From meng at cgl.ucsf.edu  Thu Mar 26 14:51:03 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 26 Mar 2015 14:51:03 -0700
Subject: [Chimera-users] Rename models from command line
In-Reply-To: <C23CFCD2-E425-4A41-A1D6-94C5C3876C12@gmail.com>
References: <C23CFCD2-E425-4A41-A1D6-94C5C3876C12@gmail.com>
Message-ID: <39403E98-BFAB-4D12-9DB1-11CD3D86163F@cgl.ucsf.edu>

Hi Oliver,
Not exactly, at least with commands, but you may be able to accomplish essentially what you desire by using "alias" (string substitution into commands) and/or named selections.

See
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/namesel.html>

I'm fond of aliases, which don't require you to go through selection.
I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


On Mar 26, 2015, at 2:03 PM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Hi all,
> 
> Is there any way to rename models from the command line? I can do so using the model panel, but I have a script that generates a bunch of different models, and I would like to give them descriptive names apart from the model id in the script.
> 
> Oliver.
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From olibclarke at gmail.com  Thu Mar 26 14:58:56 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Thu, 26 Mar 2015 17:58:56 -0400
Subject: [Chimera-users] Rename models from command line
In-Reply-To: <39403E98-BFAB-4D12-9DB1-11CD3D86163F@cgl.ucsf.edu>
References: <C23CFCD2-E425-4A41-A1D6-94C5C3876C12@gmail.com>
	<39403E98-BFAB-4D12-9DB1-11CD3D86163F@cgl.ucsf.edu>
Message-ID: <04D02A4B-6961-40CE-BEB3-641B94AA739D@gmail.com>

Thanks Elaine - I use both of those commands frequently, but unfortunately in this case I actually do want to change the model name. 

I?m using a long alias with many molmap calls on different selections to generate and color low resolution blobs corresponding to each domain of my protein, and I would like to change the names of the output model as I do so so that I know that model #1.20 corresponds to ?domain xyz? without switching it on and off in the model panel.

Cheers,
Oli.
> On Mar 26, 2015, at 5:51 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Oliver,
> Not exactly, at least with commands, but you may be able to accomplish essentially what you desire by using "alias" (string substitution into commands) and/or named selections.
> 
> See
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/namesel.html>
> 
> I'm fond of aliases, which don't require you to go through selection.
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> On Mar 26, 2015, at 2:03 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
>> Hi all,
>> 
>> Is there any way to rename models from the command line? I can do so using the model panel, but I have a script that generates a bunch of different models, and I would like to give them descriptive names apart from the model id in the script.
>> 
>> Oliver.
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From bobby.barnett at gmail.com  Fri Mar 27 07:01:23 2015
From: bobby.barnett at gmail.com (Bobby Barnett)
Date: Fri, 27 Mar 2015 10:01:23 -0400
Subject: [Chimera-users] Tutorials
In-Reply-To: <ACDFA2D2-00D0-406A-9064-44B6DD08729B@cgl.ucsf.edu>
References: <CAG3+mPnn=eNMNSDxFvoNauxheJWCJ9vBwmsBTtZJ1JZt9OZkzw@mail.gmail.com>
	<ACDFA2D2-00D0-406A-9064-44B6DD08729B@cgl.ucsf.edu>
Message-ID: <CAG3+mPmN7h6assf+jdgHY-gzPvFKPNsbEMEi7Zy00kXy_w3+Dg@mail.gmail.com>

Dear Elaine,

I meant to thank you earlier for the many tutorials you provided, but I got
distracted.

I did have another question and i will post it on the regular way if it is
needed, but is there a tutorial using the Autodock Vina under the tools
Surface Binding Analysis option?  I have tried several times to perform
this with one of the autodock tutorials and can't get it to work under
chimera.

Thanks again for your help.  I really appreciate all of the tutorials and
the videos that you and your group provide.

Bobby Barnett, semi-retired crystallographer

On Thu, Feb 26, 2015 at 1:09 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Bobby,
> We have quite a few Chimera tutorials, but the main issue for you is
> probably whether they are suitable for undergraduates.  Maybe other
> undergraduate educators will have better suggestions or materials that they
> can send you; the tutorials that we provide do presuppose some knowledge of
> protein structure and organic chemistry, but you can take a look and see
> what you think...
>
> The User's Guide (included with Chimera download but also shown on our
> website) includes several tutorials, including "getting started" for
> Chimera beginners.  You can get to the copies included in your download
> from the Chimera Help menu.  The copies at our website are here, but if you
> stick with the downloaded ones (menu: Help? Tutorials) they are
> version-synchronized with the software.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html>
>
> While "getting started" may be simplest in terms of Chimera, some of the
> others in the User's Guide that are more basic in terms of the science are
> the Surface Properties image tutorial and the Structure Analysis and
> Comparison tutorial.  I usually suggest the latter for graduate students
> learning Chimera because it includes several common protein analysis tasks.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
>
> There are also a bunch of tutorials on the website only, listed here:
> <http://www.rbvi.ucsf.edu/chimera/tutorials.html>
>
> The most basic of these Chimera-wise is the expanded "getting started"
> tutorial:
> <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>
>
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Feb 26, 2015, at 9:32 AM, Bobby Barnett <bobby.barnett at gmail.com>
> wrote:
>
> > I was wondering if anyone had interactive tutorial session(s) that can
> be used to educate a small class of undergraduate students.
> >
> > Bobby Barnett
> >
> > Department of Chemistry
> > University of Chemistry
>
>
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From meng at cgl.ucsf.edu  Fri Mar 27 10:07:17 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 27 Mar 2015 10:07:17 -0700
Subject: [Chimera-users] Tutorials
In-Reply-To: <CAG3+mPmN7h6assf+jdgHY-gzPvFKPNsbEMEi7Zy00kXy_w3+Dg@mail.gmail.com>
References: <CAG3+mPnn=eNMNSDxFvoNauxheJWCJ9vBwmsBTtZJ1JZt9OZkzw@mail.gmail.com>
	<ACDFA2D2-00D0-406A-9064-44B6DD08729B@cgl.ucsf.edu>
	<CAG3+mPmN7h6assf+jdgHY-gzPvFKPNsbEMEi7Zy00kXy_w3+Dg@mail.gmail.com>
Message-ID: <F38A9ECE-32EC-4471-8B67-79B4B643C7F6@cgl.ucsf.edu>

Dear Bobby,
You?re welcome.  

We don?t have a tutorial for the Autodock Vina interface, but there is a manual page.  It should be reasonably friendly if you open the ligand and receptor as two separate models (from two separate input PDB files) and just fill in the required fields in Chimera?s Autodock Vina dialog, including drawing a box with the mouse in the main window to define a search area.

See the manual page for explanations of the fields in the dialog:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>

Looking at other (non-Chimera) tutorials might be confusing because they are not describing using this interface in Chimera.  They might be useful for explaining what the advanced parameters mean, but you wouldn?t want to try to follow them step by step.  Also keep in mind that Autodock is a different program from Autodock Vina.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 27, 2015, at 7:01 AM, Bobby Barnett <bobby.barnett at gmail.com> wrote:

> Dear Elaine,
> 
> I meant to thank you earlier for the many tutorials you provided, but I got distracted.
> 
> I did have another question and i will post it on the regular way if it is needed, but is there a tutorial using the Autodock Vina under the tools Surface Binding Analysis option?  I have tried several times to perform this with one of the autodock tutorials and can't get it to work under chimera.
> 
> Thanks again for your help.  I really appreciate all of the tutorials and the videos that you and your group provide.
> 
> Bobby Barnett, semi-retired crystallographer
> 




From chiendarret at gmail.com  Sat Mar 28 06:34:17 2015
From: chiendarret at gmail.com (Francesco Pietra)
Date: Sat, 28 Mar 2015 14:34:17 +0100
Subject: [Chimera-users] segname
Message-ID: <CAEv0nmuLw9wX+_mGd_Hd_fo8ECLqNxrd7GDJM+dN+H+SgsQs=w@mail.gmail.com>

Hello:

May I ask whether there is till a problem in having CHIMERA understanding
segname? For those working with XPLOR (NAMD, for example) and multichain
proteins, rendering results with CHIMERA becomes very tedious (having to
use atom indexes)

Thanks
francesco pietra
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From bobby.barnett at gmail.com  Sat Mar 28 11:25:07 2015
From: bobby.barnett at gmail.com (Bobby Barnett)
Date: Sat, 28 Mar 2015 14:25:07 -0400
Subject: [Chimera-users] Tutorials
In-Reply-To: <F38A9ECE-32EC-4471-8B67-79B4B643C7F6@cgl.ucsf.edu>
References: <CAG3+mPnn=eNMNSDxFvoNauxheJWCJ9vBwmsBTtZJ1JZt9OZkzw@mail.gmail.com>
	<ACDFA2D2-00D0-406A-9064-44B6DD08729B@cgl.ucsf.edu>
	<CAG3+mPmN7h6assf+jdgHY-gzPvFKPNsbEMEi7Zy00kXy_w3+Dg@mail.gmail.com>
	<F38A9ECE-32EC-4471-8B67-79B4B643C7F6@cgl.ucsf.edu>
Message-ID: <CAG3+mPkmbH1nvOs53+Xm+oRVK=e4LM+VvF_ozK-9Kx3+Zaya2w@mail.gmail.com>

Dear Elaine,

Thanks for the advice about using the Autodock Vina option under
Surface/Binding Analysis.  I have run this with both the web based option
and the local option and get  the same error "[Errno 13] Permission denied:
'trial.receptor.pdb'"  I don't see a way around this error.  Do I need to
run the program as Administrator?

Thanks again for your help.

Bobby Barnett



On Fri, Mar 27, 2015 at 1:07 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Bobby,
> You?re welcome.
>
> We don?t have a tutorial for the Autodock Vina interface, but there is a
> manual page.  It should be reasonably friendly if you open the ligand and
> receptor as two separate models (from two separate input PDB files) and
> just fill in the required fields in Chimera?s Autodock Vina dialog,
> including drawing a box with the mouse in the main window to define a
> search area.
>
> See the manual page for explanations of the fields in the dialog:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
>
> Looking at other (non-Chimera) tutorials might be confusing because they
> are not describing using this interface in Chimera.  They might be useful
> for explaining what the advanced parameters mean, but you wouldn?t want to
> try to follow them step by step.  Also keep in mind that Autodock is a
> different program from Autodock Vina.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Mar 27, 2015, at 7:01 AM, Bobby Barnett <bobby.barnett at gmail.com>
> wrote:
>
> > Dear Elaine,
> >
> > I meant to thank you earlier for the many tutorials you provided, but I
> got distracted.
> >
> > I did have another question and i will post it on the regular way if it
> is needed, but is there a tutorial using the Autodock Vina under the tools
> Surface Binding Analysis option?  I have tried several times to perform
> this with one of the autodock tutorials and can't get it to work under
> chimera.
> >
> > Thanks again for your help.  I really appreciate all of the tutorials
> and the videos that you and your group provide.
> >
> > Bobby Barnett, semi-retired crystallographer
> >
>
>
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From meng at cgl.ucsf.edu  Sat Mar 28 15:43:53 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sat, 28 Mar 2015 15:43:53 -0700
Subject: [Chimera-users] Tutorials
In-Reply-To: <CAG3+mPkmbH1nvOs53+Xm+oRVK=e4LM+VvF_ozK-9Kx3+Zaya2w@mail.gmail.com>
References: <CAG3+mPnn=eNMNSDxFvoNauxheJWCJ9vBwmsBTtZJ1JZt9OZkzw@mail.gmail.com>
	<ACDFA2D2-00D0-406A-9064-44B6DD08729B@cgl.ucsf.edu>
	<CAG3+mPmN7h6assf+jdgHY-gzPvFKPNsbEMEi7Zy00kXy_w3+Dg@mail.gmail.com>
	<F38A9ECE-32EC-4471-8B67-79B4B643C7F6@cgl.ucsf.edu>
	<CAG3+mPkmbH1nvOs53+Xm+oRVK=e4LM+VvF_ozK-9Kx3+Zaya2w@mail.gmail.com>
Message-ID: <77844DF8-C075-43B0-8EA3-6A9E879F379A@cgl.ucsf.edu>

Dear Bobby,
It sounds like you need to make sure to specify an output location where you have permission to read and write files.  For example, my directory (Mac) is /Users/meng and I can specify output as /Users/meng/test (or /Users/meng/Desktop/test , etc.) to create several files with filenames that start with ?test?? but of course you would need to specify a different pathname according to however your computer is set up.
Elaine

On Mar 28, 2015, at 11:25 AM, Bobby Barnett wrote:

> Dear Elaine,
> 
> Thanks for the advice about using the Autodock Vina option under Surface/Binding Analysis.  I have run this with both the web based option and the local option and get  the same error "[Errno 13] Permission denied: 'trial.receptor.pdb'"  I don't see a way around this error.  Do I need to run the program as Administrator?
> 
> Thanks again for your help.
> 
> Bobby Barnett
> 
> 
> 
> On Fri, Mar 27, 2015 at 1:07 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Dear Bobby,
> You?re welcome.
> 
> We don?t have a tutorial for the Autodock Vina interface, but there is a manual page.  It should be reasonably friendly if you open the ligand and receptor as two separate models (from two separate input PDB files) and just fill in the required fields in Chimera?s Autodock Vina dialog, including drawing a box with the mouse in the main window to define a search area.
> 
> See the manual page for explanations of the fields in the dialog:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
> 
> Looking at other (non-Chimera) tutorials might be confusing because they are not describing using this interface in Chimera.  They might be useful for explaining what the advanced parameters mean, but you wouldn?t want to try to follow them step by step.  Also keep in mind that Autodock is a different program from Autodock Vina.
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Mar 27, 2015, at 7:01 AM, Bobby Barnett <bobby.barnett at gmail.com> wrote:
> 
> > Dear Elaine,
> >
> > I meant to thank you earlier for the many tutorials you provided, but I got distracted.
> >
> > I did have another question and i will post it on the regular way if it is needed, but is there a tutorial using the Autodock Vina under the tools Surface Binding Analysis option?  I have tried several times to perform this with one of the autodock tutorials and can't get it to work under chimera.
> >
> > Thanks again for your help.  I really appreciate all of the tutorials and the videos that you and your group provide.
> >
> > Bobby Barnett, semi-retired crystallographer
> >



From darrellh at niaid.nih.gov  Sun Mar 29 12:10:51 2015
From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E])
Date: Sun, 29 Mar 2015 19:10:51 +0000
Subject: [Chimera-users] Running graphical Chimera from remote server
Message-ID: <D13DFEB5.32C4B%darrellh@niaid.nih.gov>

Hi Chimera friends,

I want to run a graphics-enabled Chimera from a remote Ubuntu server. The Ubuntu server is quite beefy (and not virtualized), but it has a stock video card. When I run "glxgears", I can see the gears and get about 60 fps (reported), but the gears don't move and aren't interactive.

I found this message from the listserv a few years ago that recommends the use of VirtualGL:
http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-September/007953.html

My X windowing system is Xquartz on a Mac. Is my problem related to software GL or to the poor graphics card?

Related question: what X windowing system do you recommend on a Windows system? CYGWIN?

Thanks,
Darrell

--
Darrell Hurt, Ph.D.
Acting Chief
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

5601 Fishers Lane, 4A31
North Bethesda, MD 20852
Office: 240-669-2741
Mobile: 301-758-3559
Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>
Twitter: @niaidbioit<https://twitter.com/niaidbioit> , @NIH3Dprint<https://twitter.com/nih3dprint>

Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.



From darrellh at niaid.nih.gov  Sun Mar 29 15:55:27 2015
From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E])
Date: Sun, 29 Mar 2015 22:55:27 +0000
Subject: [Chimera-users] Running graphical Chimera from remote server
Message-ID: <D13E3077.32C50%darrellh@niaid.nih.gov>

Hello again,

I still have to try VirtualGL (as suggested on a previous thread).
However, I want to share the following information:

I learned that the 60 fps I was getting on glxgears is likely due to
Ubuntu having "sync" enabled by default, which means that glxgears always
runs at about 60 fps. So let's ignore that bit of information.
http://askubuntu.com/questions/31488/how-to-test-if-my-video-card-has-3d-su
pport

My glxinfo (see below at "OpenGL renderer string") suggests that I have an
NVIDIA graphics card installed. But "lspci -vnn | grep -i VGA" suggests
that I have a simple Matrox graphics card:


<output of lspci>

01:00.1 VGA compatible controller [0300]: Matrox Electronics Systems Ltd.
MGA G200EH [102b:0533] (rev 01) (prog-if 00 [VGA controller])



<output of glxinfo>

name of display: localhost:11.0
display: localhost:11  screen: 0
direct rendering: No (If you want to find out why, try setting
LIBGL_DEBUG=verbose)
server glx vendor string: SGI
server glx version string: 1.4
server glx extensions:
    GLX_ARB_create_context, GLX_ARB_create_context_profile,
    GLX_ARB_multisample, GLX_EXT_import_context, GLX_EXT_visual_info,
    GLX_EXT_visual_rating, GLX_OML_swap_method, GLX_SGIS_multisample,
    GLX_SGIX_fbconfig
client glx vendor string: Mesa Project and SGI
client glx version string: 1.4
client glx extensions:
    GLX_ARB_create_context, GLX_ARB_create_context_profile,
    GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_import_context,
    GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_EXT_framebuffer_sRGB,
    GLX_EXT_create_context_es2_profile, GLX_MESA_copy_sub_buffer,
    GLX_MESA_multithread_makecurrent, GLX_MESA_swap_control,
    GLX_OML_swap_method, GLX_OML_sync_control, GLX_SGI_make_current_read,
    GLX_SGI_swap_control, GLX_SGI_video_sync, GLX_SGIS_multisample,
    GLX_SGIX_fbconfig, GLX_SGIX_pbuffer, GLX_SGIX_visual_select_group,
    GLX_EXT_texture_from_pixmap, GLX_INTEL_swap_event
GLX version: 1.4
GLX extensions:
    GLX_ARB_create_context, GLX_ARB_create_context_profile,
    GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_import_context,
    GLX_EXT_visual_info, GLX_EXT_visual_rating,
    GLX_MESA_multithread_makecurrent, GLX_OML_swap_method,
    GLX_SGI_make_current_read, GLX_SGIS_multisample, GLX_SGIX_fbconfig,
    GLX_SGIX_pbuffer
OpenGL vendor string: NVIDIA Corporation
OpenGL renderer string: NVIDIA GeForce 9400M OpenGL Engine
OpenGL version string: 1.4 (2.1 NVIDIA-8.16.81 310.40.00.20f04)
OpenGL extensions:
    GL_ARB_depth_texture, GL_ARB_draw_buffers, GL_ARB_fragment_program,
    GL_ARB_fragment_program_shadow, GL_ARB_imaging, GL_ARB_multisample,
    GL_ARB_multitexture, GL_ARB_occlusion_query, GL_ARB_point_parameters,
    GL_ARB_point_sprite, GL_ARB_shadow, GL_ARB_texture_border_clamp,
    GL_ARB_texture_compression, GL_ARB_texture_cube_map,
    GL_ARB_texture_env_add, GL_ARB_texture_env_combine,
    GL_ARB_texture_env_crossbar, GL_ARB_texture_env_dot3,
    GL_ARB_texture_mirrored_repeat, GL_ARB_texture_non_power_of_two,
    GL_ARB_texture_rectangle, GL_ARB_transpose_matrix,
GL_ARB_vertex_program,
    GL_ARB_window_pos, GL_EXT_abgr, GL_EXT_bgra, GL_EXT_blend_color,
    GL_EXT_blend_equation_separate, GL_EXT_blend_func_separate,
    GL_EXT_blend_minmax, GL_EXT_blend_subtract, GL_EXT_clip_volume_hint,
    GL_EXT_draw_range_elements, GL_EXT_fog_coord,
GL_EXT_framebuffer_object,
    GL_EXT_multi_draw_arrays, GL_EXT_point_parameters,
GL_EXT_rescale_normal,
    GL_EXT_secondary_color, GL_EXT_separate_specular_color,
    GL_EXT_shadow_funcs, GL_EXT_stencil_two_side, GL_EXT_stencil_wrap,
    GL_EXT_texture_compression_dxt1, GL_EXT_texture_compression_s3tc,
    GL_EXT_texture_edge_clamp, GL_EXT_texture_env_add,
    GL_EXT_texture_filter_anisotropic, GL_EXT_texture_lod_bias,
    GL_EXT_texture_mirror_clamp, GL_EXT_texture_rectangle,
    GL_APPLE_packed_pixels, GL_ATI_draw_buffers,
GL_ATI_texture_env_combine3,
    GL_ATI_texture_mirror_once, GL_ATIX_texture_env_combine3,
    GL_IBM_texture_mirrored_repeat, GL_INGR_blend_func_separate,
    GL_NV_blend_square, GL_NV_depth_clamp, GL_NV_fog_distance,
    GL_NV_fragment_program_option, GL_NV_fragment_program2,
    GL_NV_light_max_exponent, GL_NV_multisample_filter_hint,
    GL_NV_point_sprite, GL_NV_texgen_reflection, GL_NV_texture_rectangle,
    GL_NV_vertex_program2_option, GL_NV_vertex_program3,
    GL_SGIS_generate_mipmap, GL_SGIS_texture_border_clamp,
    GL_SGIS_texture_edge_clamp, GL_SGIS_texture_lod,
GL_SUN_multi_draw_arrays







-- 
Darrell Hurt, Ph.D.
Acting Chief
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH
 
5601 Fishers Lane, 4A31
North Bethesda, MD 20852
Office: 240-669-2741
Mobile: 301-758-3559Web: BCBB Home Page
<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb
.aspx#niaid_inlineNav_Anchor>
Twitter: @niaidbioit <https://twitter.com/niaidbioit> , @NIH3Dprint
<https://twitter.com/nih3dprint>


Disclaimer: The information in this e-mail and any of its attachments is
confidential and may contain sensitive information. It should not be used
by anyone who is not the original intended recipient. If you have received
this e-mail in error please inform the sender and delete it from your
mailbox or any other storage devices. National Institute of Allergy and
Infectious Diseases shall not accept liability for any statements made
that are sender's own and not expressly made on behalf of the NIAID by one
of its representatives.






On 3/29/15 7:10 PM, "Hurt, Darrell (NIH/NIAID) [E]"
<darrellh at niaid.nih.gov> wrote:

>Hi Chimera friends,
>
>I want to run a graphics-enabled Chimera from a remote Ubuntu server. The
>Ubuntu server is quite beefy (and not virtualized), but it has a stock
>video card. When I run "glxgears", I can see the gears and get about 60
>fps (reported), but the gears don't move and aren't interactive.
>
>I found this message from the listserv a few years ago that recommends
>the use of VirtualGL:
>http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-September/007953.ht
>ml
>
>My X windowing system is Xquartz on a Mac. Is my problem related to
>software GL or to the poor graphics card?
>
>Related question: what X windowing system do you recommend on a Windows
>system? CYGWIN?
>
>Thanks,
>Darrell
>
>--
>Darrell Hurt, Ph.D.
>Acting Chief
>Bioinformatics and Computational Biosciences Branch (BCBB)
>OCICB/OSMO/OD/NIAID/NIH
>
>5601 Fishers Lane, 4A31
>North Bethesda, MD 20852
>Office: 240-669-2741
>Mobile: 301-758-3559
>Web: BCBB Home 
>Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages
>/bcbb.aspx#niaid_inlineNav_Anchor>
>Twitter: @niaidbioit<https://twitter.com/niaidbioit> ,
>@NIH3Dprint<https://twitter.com/nih3dprint>
>
>Disclaimer: The information in this e-mail and any of its attachments is
>confidential and may contain sensitive information. It should not be used
>by anyone who is not the original intended recipient. If you have
>received this e-mail in error please inform the sender and delete it from
>your mailbox or any other storage devices. National Institute of Allergy
>and Infectious Diseases shall not accept liability for any statements
>made that are sender's own and not expressly made on behalf of the NIAID
>by one of its representatives.
>
>_______________________________________________
>Chimera-users mailing list
>Chimera-users at cgl.ucsf.edu
>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From smith_liu123 at 163.com  Sun Mar 29 20:44:58 2015
From: smith_liu123 at 163.com (Smith Liu)
Date: Mon, 30 Mar 2015 11:44:58 +0800 (CST)
Subject: [Chimera-users] on the section command
Message-ID: <1201373.cd3d.14c68c84845.Coremail.smith_liu123@163.com>

Dear All,
 
Wil you please tell me how can I stop or pause the movie playing as a specific point which I want to watch carefully when the section command is in the execution?
 
Smith
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From meng at cgl.ucsf.edu  Mon Mar 30 08:25:09 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 30 Mar 2015 08:25:09 -0700
Subject: [Chimera-users] on the section command
In-Reply-To: <1201373.cd3d.14c68c84845.Coremail.smith_liu123@163.com>
References: <1201373.cd3d.14c68c84845.Coremail.smith_liu123@163.com>
Message-ID: <AF33FB6C-FA92-4B0D-9746-56E8284283F4@cgl.ucsf.edu>

Dear Smith,
I would recommend using "section" yourself manually in the command line with small distance values.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/section.html>

In other words, you could run a script that has all the commands before that point.  Then, in the command line keep entering "section" with short distance values.

Although there is a "pause" command that you can put into a script to easily escape or resume execution, it cannot be in the middle of some other command, only before or after it.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/pause.html>

Movie-related commands:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco



On Mar 29, 2015, at 8:44 PM, "Smith Liu" <smith_liu123 at 163.com> wrote:

> Dear All,
>  
> Wil you please tell me how can I stop or pause the movie playing as a specific point which I want to watch carefully when the section command is in the execution?
>  
> Smith




From meng at cgl.ucsf.edu  Mon Mar 30 08:41:10 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 30 Mar 2015 08:41:10 -0700
Subject: [Chimera-users] on the section command
In-Reply-To: <AF33FB6C-FA92-4B0D-9746-56E8284283F4@cgl.ucsf.edu>
References: <1201373.cd3d.14c68c84845.Coremail.smith_liu123@163.com>
	<AF33FB6C-FA92-4B0D-9746-56E8284283F4@cgl.ucsf.edu>
Message-ID: <90151C2B-AA5D-4EA1-9B85-6F1356995B23@cgl.ucsf.edu>

Another tip:
I would also save a position (see "savepos" command) right before you start sectioning.  Then you can easily return to that point over and over, with "reset" to the saved position.  I often use this general process when I'm developing a command script for movie content.
Elaine

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html>


On Mar 30, 2015, at 8:25 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Smith,
> I would recommend using "section" yourself manually in the command line with small distance values.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/section.html>
> 
> In other words, you could run a script that has all the commands before that point.  Then, in the command line keep entering "section" with short distance values.
> 
> Although there is a "pause" command that you can put into a script to easily escape or resume execution, it cannot be in the middle of some other command, only before or after it.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/pause.html>
> 
> Movie-related commands:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands>
> 
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> 
> On Mar 29, 2015, at 8:44 PM, "Smith Liu" <smith_liu123 at 163.com> wrote:
> 
>> Dear All,
>> 
>> Wil you please tell me how can I stop or pause the movie playing as a specific point which I want to watch carefully when the section command is in the execution?
>> 
>> Smith
> 




From tchesnok at ualberta.ca  Thu Mar 26 13:59:21 2015
From: tchesnok at ualberta.ca (Egor Tchesnokov)
Date: Thu, 26 Mar 2015 14:59:21 -0600
Subject: [Chimera-users] MatchMaker-vs-MatchAlign
Message-ID: <CAPAU3wcQgdVvWbTP1JJyrWv=wLkKPp9f08PBzTgJ+X8jumW-PQ@mail.gmail.com>

Hello,

1.
I used MatchMaker to align two structures, worked well and I got an
alignment file-1.
Then I clicked on MatchAlign and got alignment file-2.

The alignment-1 is different from alignment-2.

Could you please let me know what is the differnce between MatchMaker and
MatchAlign?

2.
In the same function I can't find RR distance map. Is it applicable to
MatchMaker/MatchAlign?

Thank you
Egor
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From goddard at sonic.net  Mon Mar 30 10:33:07 2015
From: goddard at sonic.net (Tom Goddard)
Date: Mon, 30 Mar 2015 10:33:07 -0700
Subject: [Chimera-users] Running graphical Chimera from remote server
In-Reply-To: <D13E3077.32C50%darrellh@niaid.nih.gov>
References: <D13E3077.32C50%darrellh@niaid.nih.gov>
Message-ID: <52CCA567-3FB0-4DE0-B737-7B76B0A7D519@sonic.net>

Hi Darrell,

  You are trying to remote display Chimera from a Linux machine to a Mac using the XQuartz X11 window server.  As you?ve found out this doesn?t work very well.  Unfortunately X remote display hasn?t worked very well with OpenGL for a decade or more.  Basically the X client on your Linux machine isn?t compatible with the X server on your Mac, even though there are standards and they should work.  The graphics card on your Linux server is not relevant ? it is not used.  The Linux machine will send OpenGL to your Mac and its graphics card and the Mac graphics driver will be used.  The output of glxinfo run on the Linux machine indicates you have a NVIDIA GeForce 9400M graphics card on the Mac and the Linux machine is using Mesa for its OpenGL.  It looks like your Linux Mesa (which is the software OpenGL library) is version 1.4 which is archaic.  The Mac graphics driver is willing to run OpenGL 2.1.  (The Mac is the ?server? and the Linux machine is the ?client? ? the server actually renders the graphics on its screen).

  The only chance of success with this setup is to update your Linux Mesa to a modern version.  I don?t think it is likely to work, but there is a chance.  Usually remote display from one linux machine to another will work, and probably from Mac to Mac will also work.  But once you get different X/OpenGL implementations on the client and server some bugs cause them to be incompatible with each other.

  None of what I said pertains to VirtualGL ? I don?t know what that is or whether it could help.

	Tom



> On Mar 29, 2015, at 3:55 PM, Hurt, Darrell (NIH/NIAID) [E] wrote:
> 
> Hello again,
> 
> I still have to try VirtualGL (as suggested on a previous thread).
> However, I want to share the following information:
> 
> I learned that the 60 fps I was getting on glxgears is likely due to
> Ubuntu having "sync" enabled by default, which means that glxgears always
> runs at about 60 fps. So let's ignore that bit of information.
> http://askubuntu.com/questions/31488/how-to-test-if-my-video-card-has-3d-su
> pport
> 
> My glxinfo (see below at "OpenGL renderer string") suggests that I have an
> NVIDIA graphics card installed. But "lspci -vnn | grep -i VGA" suggests
> that I have a simple Matrox graphics card:
> 
> 
> <output of lspci>
> 
> 01:00.1 VGA compatible controller [0300]: Matrox Electronics Systems Ltd.
> MGA G200EH [102b:0533] (rev 01) (prog-if 00 [VGA controller])
> 
> 
> 
> <output of glxinfo>
> 
> name of display: localhost:11.0
> display: localhost:11  screen: 0
> direct rendering: No (If you want to find out why, try setting
> LIBGL_DEBUG=verbose)
> server glx vendor string: SGI
> server glx version string: 1.4
> server glx extensions:
>    GLX_ARB_create_context, GLX_ARB_create_context_profile,
>    GLX_ARB_multisample, GLX_EXT_import_context, GLX_EXT_visual_info,
>    GLX_EXT_visual_rating, GLX_OML_swap_method, GLX_SGIS_multisample,
>    GLX_SGIX_fbconfig
> client glx vendor string: Mesa Project and SGI
> client glx version string: 1.4
> client glx extensions:
>    GLX_ARB_create_context, GLX_ARB_create_context_profile,
>    GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_import_context,
>    GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_EXT_framebuffer_sRGB,
>    GLX_EXT_create_context_es2_profile, GLX_MESA_copy_sub_buffer,
>    GLX_MESA_multithread_makecurrent, GLX_MESA_swap_control,
>    GLX_OML_swap_method, GLX_OML_sync_control, GLX_SGI_make_current_read,
>    GLX_SGI_swap_control, GLX_SGI_video_sync, GLX_SGIS_multisample,
>    GLX_SGIX_fbconfig, GLX_SGIX_pbuffer, GLX_SGIX_visual_select_group,
>    GLX_EXT_texture_from_pixmap, GLX_INTEL_swap_event
> GLX version: 1.4
> GLX extensions:
>    GLX_ARB_create_context, GLX_ARB_create_context_profile,
>    GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_import_context,
>    GLX_EXT_visual_info, GLX_EXT_visual_rating,
>    GLX_MESA_multithread_makecurrent, GLX_OML_swap_method,
>    GLX_SGI_make_current_read, GLX_SGIS_multisample, GLX_SGIX_fbconfig,
>    GLX_SGIX_pbuffer
> OpenGL vendor string: NVIDIA Corporation
> OpenGL renderer string: NVIDIA GeForce 9400M OpenGL Engine
> OpenGL version string: 1.4 (2.1 NVIDIA-8.16.81 310.40.00.20f04)
> OpenGL extensions:
>    GL_ARB_depth_texture, GL_ARB_draw_buffers, GL_ARB_fragment_program,
>    GL_ARB_fragment_program_shadow, GL_ARB_imaging, GL_ARB_multisample,
>    GL_ARB_multitexture, GL_ARB_occlusion_query, GL_ARB_point_parameters,
>    GL_ARB_point_sprite, GL_ARB_shadow, GL_ARB_texture_border_clamp,
>    GL_ARB_texture_compression, GL_ARB_texture_cube_map,
>    GL_ARB_texture_env_add, GL_ARB_texture_env_combine,
>    GL_ARB_texture_env_crossbar, GL_ARB_texture_env_dot3,
>    GL_ARB_texture_mirrored_repeat, GL_ARB_texture_non_power_of_two,
>    GL_ARB_texture_rectangle, GL_ARB_transpose_matrix,
> GL_ARB_vertex_program,
>    GL_ARB_window_pos, GL_EXT_abgr, GL_EXT_bgra, GL_EXT_blend_color,
>    GL_EXT_blend_equation_separate, GL_EXT_blend_func_separate,
>    GL_EXT_blend_minmax, GL_EXT_blend_subtract, GL_EXT_clip_volume_hint,
>    GL_EXT_draw_range_elements, GL_EXT_fog_coord,
> GL_EXT_framebuffer_object,
>    GL_EXT_multi_draw_arrays, GL_EXT_point_parameters,
> GL_EXT_rescale_normal,
>    GL_EXT_secondary_color, GL_EXT_separate_specular_color,
>    GL_EXT_shadow_funcs, GL_EXT_stencil_two_side, GL_EXT_stencil_wrap,
>    GL_EXT_texture_compression_dxt1, GL_EXT_texture_compression_s3tc,
>    GL_EXT_texture_edge_clamp, GL_EXT_texture_env_add,
>    GL_EXT_texture_filter_anisotropic, GL_EXT_texture_lod_bias,
>    GL_EXT_texture_mirror_clamp, GL_EXT_texture_rectangle,
>    GL_APPLE_packed_pixels, GL_ATI_draw_buffers,
> GL_ATI_texture_env_combine3,
>    GL_ATI_texture_mirror_once, GL_ATIX_texture_env_combine3,
>    GL_IBM_texture_mirrored_repeat, GL_INGR_blend_func_separate,
>    GL_NV_blend_square, GL_NV_depth_clamp, GL_NV_fog_distance,
>    GL_NV_fragment_program_option, GL_NV_fragment_program2,
>    GL_NV_light_max_exponent, GL_NV_multisample_filter_hint,
>    GL_NV_point_sprite, GL_NV_texgen_reflection, GL_NV_texture_rectangle,
>    GL_NV_vertex_program2_option, GL_NV_vertex_program3,
>    GL_SGIS_generate_mipmap, GL_SGIS_texture_border_clamp,
>    GL_SGIS_texture_edge_clamp, GL_SGIS_texture_lod,
> GL_SUN_multi_draw_arrays
> 
> 
> 
> 
> 
> 
> 
> -- 
> Darrell Hurt, Ph.D.
> Acting Chief
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
> 
> 5601 Fishers Lane, 4A31
> North Bethesda, MD 20852
> Office: 240-669-2741
> Mobile: 301-758-3559Web: BCBB Home Page
> <http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb
> .aspx#niaid_inlineNav_Anchor>
> Twitter: @niaidbioit <https://twitter.com/niaidbioit> , @NIH3Dprint
> <https://twitter.com/nih3dprint>
> 
> 
> Disclaimer: The information in this e-mail and any of its attachments is
> confidential and may contain sensitive information. It should not be used
> by anyone who is not the original intended recipient. If you have received
> this e-mail in error please inform the sender and delete it from your
> mailbox or any other storage devices. National Institute of Allergy and
> Infectious Diseases shall not accept liability for any statements made
> that are sender's own and not expressly made on behalf of the NIAID by one
> of its representatives.
> 
> 
> 
> 
> 
> 
> On 3/29/15 7:10 PM, "Hurt, Darrell (NIH/NIAID) [E]"
> wrote:
> 
>> Hi Chimera friends,
>> 
>> I want to run a graphics-enabled Chimera from a remote Ubuntu server. The
>> Ubuntu server is quite beefy (and not virtualized), but it has a stock
>> video card. When I run "glxgears", I can see the gears and get about 60
>> fps (reported), but the gears don't move and aren't interactive.
>> 
>> I found this message from the listserv a few years ago that recommends
>> the use of VirtualGL:
>> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-September/007953.ht
>> ml
>> 
>> My X windowing system is Xquartz on a Mac. Is my problem related to
>> software GL or to the poor graphics card?
>> 
>> Related question: what X windowing system do you recommend on a Windows
>> system? CYGWIN?
>> 
>> Thanks,
>> Darrell
>> 
>> --
>> Darrell Hurt, Ph.D.
>> Acting Chief
>> Bioinformatics and Computational Biosciences Branch (BCBB)
>> OCICB/OSMO/OD/NIAID/NIH
>> 
>> 5601 Fishers Lane, 4A31
>> North Bethesda, MD 20852
>> Office: 240-669-2741
>> Mobile: 301-758-3559
>> Web: BCBB Home 
>> Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages
>> /bcbb.aspx#niaid_inlineNav_Anchor>
>> Twitter: @niaidbioit<https://twitter.com/niaidbioit> ,
>> @NIH3Dprint<https://twitter.com/nih3dprint>
>> 
>> Disclaimer: The information in this e-mail and any of its attachments is
>> confidential and may contain sensitive information. It should not be used
>> by anyone who is not the original intended recipient. If you have
>> received this e-mail in error please inform the sender and delete it from
>> your mailbox or any other storage devices. National Institute of Allergy
>> and Infectious Diseases shall not accept liability for any statements
>> made that are sender's own and not expressly made on behalf of the NIAID
>> by one of its representatives.
>> 
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From meng at cgl.ucsf.edu  Mon Mar 30 10:50:25 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 30 Mar 2015 10:50:25 -0700
Subject: [Chimera-users] MatchMaker-vs-MatchAlign
In-Reply-To: <CAPAU3wcQgdVvWbTP1JJyrWv=wLkKPp9f08PBzTgJ+X8jumW-PQ@mail.gmail.com>
References: <CAPAU3wcQgdVvWbTP1JJyrWv=wLkKPp9f08PBzTgJ+X8jumW-PQ@mail.gmail.com>
Message-ID: <1121A1FA-A27F-4B15-8CE9-DECFE5EE99D1@cgl.ucsf.edu>

Hello Egor,
The differences are discussed in several places, for example in the MatchMaker manual page:

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html#final>

and details of each are also in their manual pages and our 2006 publication which is linked to the above.  I recommend looking at those for a full understanding, but I will try to summarize as briefly as possible here?

Matchmaker only makes pairwise sequence alignments, and it uses some combination of sequence and secondary structure information.  If the sequences are dissimilar (distantly related proteins) it might be that only small parts of the pairwise alignment are correct, but even so, because of the fit iteration, it can make a good superposition.  If the sequences are fairly similar, however, the Matchmaker pairwise alignments may all be completely correct.  The main purpose of Matchmaker is to superimpose structures, however.  The sequence alignment is just a by-product.

Match->Align then uses only the 3D superposition information: which alpha-carbons are near to which other alpha-carbons. It doesn't pay any attention to the actual sequences.  If the 3D superposition looks good to you, it may be that the Match->Align result will have more correct columns than the Matchmaker result, especially when the sequences are distantly related.  Also, Matchmaker only gives you pairwise, whereas if you have a multiple superposition (>2 structures), Match->Align can give you a multiple alignment (>2 sequences).

Note also you can try using MUSCLE or Clustal Omega web services to realign all the sequences if you want to use only sequence and not structure information in calculating a multiple alignment (from the alignment window menu: Edit? Realign Sequences).

I don't understand your question about RR distance maps.  It makes a distance map, which is a different purpose than Matchmaker (main purpose is superposition) and Match->Align (purpose is to create a sequence alignment from your existing superposition).  In the case of using RR distance maps to compare multiple related structures, it does happen to make a sequence alignment, but currently you can't control any of the sequence alignment parameters, so I wouldn't use it for the purpose of making a sequence alignment.

Also, if you meant you couldn't find the RR distance maps tool at all, if you have Chimera 1.10 or greater it is in the Tools menu under Structure Comparison.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rrdistmaps/rrdistmaps.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 26, 2015, at 1:59 PM, Egor Tchesnokov <tchesnok at ualberta.ca> wrote:

> Hello,
> 1.
> I used MatchMaker to align two structures, worked well and I got an alignment file-1.
> Then I clicked on MatchAlign and got alignment file-2. 
> 
> The alignment-1 is different from alignment-2.
> 
> Could you please let me know what is the differnce between MatchMaker and MatchAlign?
> 
> 2.
> In the same function I can't find RR distance map. Is it applicable to MatchMaker/MatchAlign?
> Thank you
> Egor




From tchesnok at ualberta.ca  Mon Mar 30 11:38:36 2015
From: tchesnok at ualberta.ca (Egor Tchesnokov)
Date: Mon, 30 Mar 2015 12:38:36 -0600
Subject: [Chimera-users] MatchMaker-vs-MatchAlign
In-Reply-To: <1121A1FA-A27F-4B15-8CE9-DECFE5EE99D1@cgl.ucsf.edu>
References: <CAPAU3wcQgdVvWbTP1JJyrWv=wLkKPp9f08PBzTgJ+X8jumW-PQ@mail.gmail.com>
	<1121A1FA-A27F-4B15-8CE9-DECFE5EE99D1@cgl.ucsf.edu>
Message-ID: <CAPAU3wcdxbAJxt-gkk6s3k_LSiAVYvYhwrnJ26VcRRTmbWE8uw@mail.gmail.com>

Dear Elaine,

Thank you so much for the explanations! Yes, it helps a lot.

Best
Egor

On Mon, Mar 30, 2015 at 11:50 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hello Egor,
> The differences are discussed in several places, for example in the
> MatchMaker manual page:
>
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html#final
> >
>
> and details of each are also in their manual pages and our 2006
> publication which is linked to the above.  I recommend looking at those for
> a full understanding, but I will try to summarize as briefly as possible
> here?
>
> Matchmaker only makes pairwise sequence alignments, and it uses some
> combination of sequence and secondary structure information.  If the
> sequences are dissimilar (distantly related proteins) it might be that only
> small parts of the pairwise alignment are correct, but even so, because of
> the fit iteration, it can make a good superposition.  If the sequences are
> fairly similar, however, the Matchmaker pairwise alignments may all be
> completely correct.  The main purpose of Matchmaker is to superimpose
> structures, however.  The sequence alignment is just a by-product.
>
> Match->Align then uses only the 3D superposition information: which
> alpha-carbons are near to which other alpha-carbons. It doesn't pay any
> attention to the actual sequences.  If the 3D superposition looks good to
> you, it may be that the Match->Align result will have more correct columns
> than the Matchmaker result, especially when the sequences are distantly
> related.  Also, Matchmaker only gives you pairwise, whereas if you have a
> multiple superposition (>2 structures), Match->Align can give you a
> multiple alignment (>2 sequences).
>
> Note also you can try using MUSCLE or Clustal Omega web services to
> realign all the sequences if you want to use only sequence and not
> structure information in calculating a multiple alignment (from the
> alignment window menu: Edit? Realign Sequences).
>
> I don't understand your question about RR distance maps.  It makes a
> distance map, which is a different purpose than Matchmaker (main purpose is
> superposition) and Match->Align (purpose is to create a sequence alignment
> from your existing superposition).  In the case of using RR distance maps
> to compare multiple related structures, it does happen to make a sequence
> alignment, but currently you can't control any of the sequence alignment
> parameters, so I wouldn't use it for the purpose of making a sequence
> alignment.
>
> Also, if you meant you couldn't find the RR distance maps tool at all, if
> you have Chimera 1.10 or greater it is in the Tools menu under Structure
> Comparison.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rrdistmaps/rrdistmaps.html
> >
>
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Mar 26, 2015, at 1:59 PM, Egor Tchesnokov <tchesnok at ualberta.ca> wrote:
>
> > Hello,
> > 1.
> > I used MatchMaker to align two structures, worked well and I got an
> alignment file-1.
> > Then I clicked on MatchAlign and got alignment file-2.
> >
> > The alignment-1 is different from alignment-2.
> >
> > Could you please let me know what is the differnce between MatchMaker
> and MatchAlign?
> >
> > 2.
> > In the same function I can't find RR distance map. Is it applicable to
> MatchMaker/MatchAlign?
> > Thank you
> > Egor
>
>
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From pett at cgl.ucsf.edu  Mon Mar 30 14:32:35 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 30 Mar 2015 14:32:35 -0700
Subject: [Chimera-users] segname
In-Reply-To: <CAEv0nmuLw9wX+_mGd_Hd_fo8ECLqNxrd7GDJM+dN+H+SgsQs=w@mail.gmail.com>
References: <CAEv0nmuLw9wX+_mGd_Hd_fo8ECLqNxrd7GDJM+dN+H+SgsQs=w@mail.gmail.com>
Message-ID: <F3B9ED17-0CEF-4BD0-AF23-4F0EAF416264@cgl.ucsf.edu>

Hi Francesco,
	It should be available as the atom attribute pdbSegment, e.g. "color red @/pdbSegment=XY2".  If that doesn't work, please let me know and attach a PDB file with segment info in it that I can use for testing.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Mar 28, 2015, at 6:34 AM, Francesco Pietra <chiendarret at gmail.com> wrote:

> Hello:
> 
> May I ask whether there is till a problem in having CHIMERA understanding segname? For those working with XPLOR (NAMD, for example) and multichain proteins, rendering results with CHIMERA becomes very tedious (having to use atom indexes)
> 
> Thanks
> francesco pietra
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




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From pett at cgl.ucsf.edu  Mon Mar 30 14:40:19 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 30 Mar 2015 14:40:19 -0700
Subject: [Chimera-users] Rename models from command line
In-Reply-To: <04D02A4B-6961-40CE-BEB3-641B94AA739D@gmail.com>
References: <C23CFCD2-E425-4A41-A1D6-94C5C3876C12@gmail.com>
	<39403E98-BFAB-4D12-9DB1-11CD3D86163F@cgl.ucsf.edu>
	<04D02A4B-6961-40CE-BEB3-641B94AA739D@gmail.com>
Message-ID: <D99C141F-F726-4CE3-A173-D506EA54FFB1@cgl.ucsf.edu>

You can change the name with "setattr m name new_name".

--Eric

On Mar 26, 2015, at 2:58 PM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Thanks Elaine - I use both of those commands frequently, but unfortunately in this case I actually do want to change the model name. 
> 
> I?m using a long alias with many molmap calls on different selections to generate and color low resolution blobs corresponding to each domain of my protein, and I would like to change the names of the output model as I do so so that I know that model #1.20 corresponds to ?domain xyz? without switching it on and off in the model panel.
> 
> Cheers,
> Oli.
>> On Mar 26, 2015, at 5:51 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Hi Oliver,
>> Not exactly, at least with commands, but you may be able to accomplish essentially what you desire by using "alias" (string substitution into commands) and/or named selections.
>> 
>> See
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/namesel.html>
>> 
>> I'm fond of aliases, which don't require you to go through selection.
>> I hope this helps,
>> Elaine
>> ----------
>> Elaine C. Meng, Ph.D. 
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> 
>> On Mar 26, 2015, at 2:03 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
>> 
>>> Hi all,
>>> 
>>> Is there any way to rename models from the command line? I can do so using the model panel, but I have a script that generates a bunch of different models, and I would like to give them descriptive names apart from the model id in the script.
>>> 
>>> Oliver.
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From pett at cgl.ucsf.edu  Mon Mar 30 14:41:40 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 30 Mar 2015 14:41:40 -0700
Subject: [Chimera-users] Rename models from command line
In-Reply-To: <D99C141F-F726-4CE3-A173-D506EA54FFB1@cgl.ucsf.edu>
References: <C23CFCD2-E425-4A41-A1D6-94C5C3876C12@gmail.com>
	<39403E98-BFAB-4D12-9DB1-11CD3D86163F@cgl.ucsf.edu>
	<04D02A4B-6961-40CE-BEB3-641B94AA739D@gmail.com>
	<D99C141F-F726-4CE3-A173-D506EA54FFB1@cgl.ucsf.edu>
Message-ID: <AB9A8326-6CF0-42DC-BA77-2B3CE904BB05@cgl.ucsf.edu>

Oops, that will change all models' names of course.  Add "#1" to the end of that to change just model 1.

--Eric

On Mar 30, 2015, at 2:40 PM, Eric Pettersen <pett at cgl.ucsf.EDU> wrote:

> You can change the name with "setattr m name new_name".
> 
> --Eric
> 
> On Mar 26, 2015, at 2:58 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
>> Thanks Elaine - I use both of those commands frequently, but unfortunately in this case I actually do want to change the model name. 
>> 
>> I?m using a long alias with many molmap calls on different selections to generate and color low resolution blobs corresponding to each domain of my protein, and I would like to change the names of the output model as I do so so that I know that model #1.20 corresponds to ?domain xyz? without switching it on and off in the model panel.
>> 
>> Cheers,
>> Oli.
>>> On Mar 26, 2015, at 5:51 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>> 
>>> Hi Oliver,
>>> Not exactly, at least with commands, but you may be able to accomplish essentially what you desire by using "alias" (string substitution into commands) and/or named selections.
>>> 
>>> See
>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/namesel.html>
>>> 
>>> I'm fond of aliases, which don't require you to go through selection.
>>> I hope this helps,
>>> Elaine
>>> ----------
>>> Elaine C. Meng, Ph.D. 
>>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>> 
>>> 
>>> On Mar 26, 2015, at 2:03 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
>>> 
>>>> Hi all,
>>>> 
>>>> Is there any way to rename models from the command line? I can do so using the model panel, but I have a script that generates a bunch of different models, and I would like to give them descriptive names apart from the model id in the script.
>>>> 
>>>> Oliver.
>>>> _______________________________________________
>>>> Chimera-users mailing list
>>>> Chimera-users at cgl.ucsf.edu
>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>> 
>> 
>> 
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
> 




From darrellh at niaid.nih.gov  Mon Mar 30 15:40:02 2015
From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E])
Date: Mon, 30 Mar 2015 22:40:02 +0000
Subject: [Chimera-users] Running graphical Chimera from remote server
In-Reply-To: <52CCA567-3FB0-4DE0-B737-7B76B0A7D519@sonic.net>
References: <D13E3077.32C50%darrellh@niaid.nih.gov>
	<52CCA567-3FB0-4DE0-B737-7B76B0A7D519@sonic.net>
Message-ID: <D13F8074.33101%darrellh@niaid.nih.gov>

Hi Tom,

Thank you for this wonderfully erudite explanation! And thanks for
suggesting a path forward.

I have a somewhat related question, but I think I'll ask it on a new
thread.

Thanks again,
Darrell

-- 
Darrell Hurt, Ph.D.
Acting Chief
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH
 
5601 Fishers Lane, 4A31
North Bethesda, MD 20852
Office: 240-669-2741
Mobile: 301-758-3559Web: BCBB Home Page
<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb
.aspx#niaid_inlineNav_Anchor>
Twitter: @niaidbioit <https://twitter.com/niaidbioit> , @NIH3Dprint
<https://twitter.com/nih3dprint>


Disclaimer: The information in this e-mail and any of its attachments is
confidential and may contain sensitive information. It should not be used
by anyone who is not the original intended recipient. If you have received
this e-mail in error please inform the sender and delete it from your
mailbox or any other storage devices. National Institute of Allergy and
Infectious Diseases shall not accept liability for any statements made
that are sender's own and not expressly made on behalf of the NIAID by one
of its representatives.






On 3/30/15 5:33 PM, "Tom Goddard" <goddard at sonic.net> wrote:

>Hi Darrell,
>
>  You are trying to remote display Chimera from a Linux machine to a Mac
>using the XQuartz X11 window server.  As you?ve found out this doesn?t
>work very well.  Unfortunately X remote display hasn?t worked very well
>with OpenGL for a decade or more.  Basically the X client on your Linux
>machine isn?t compatible with the X server on your Mac, even though there
>are standards and they should work.  The graphics card on your Linux
>server is not relevant ? it is not used.  The Linux machine will send
>OpenGL to your Mac and its graphics card and the Mac graphics driver will
>be used.  The output of glxinfo run on the Linux machine indicates you
>have a NVIDIA GeForce 9400M graphics card on the Mac and the Linux
>machine is using Mesa for its OpenGL.  It looks like your Linux Mesa
>(which is the software OpenGL library) is version 1.4 which is archaic.
>The Mac graphics driver is willing to run OpenGL 2.1.  (The Mac is the
>?server? and the Linux machine is the ?client? ? the server actually
>renders the graphics on its screen).
>
>  The only chance of success with this setup is to update your Linux Mesa
>to a modern version.  I don?t think it is likely to work, but there is a
>chance.  Usually remote display from one linux machine to another will
>work, and probably from Mac to Mac will also work.  But once you get
>different X/OpenGL implementations on the client and server some bugs
>cause them to be incompatible with each other.
>
>  None of what I said pertains to VirtualGL ? I don?t know what that is
>or whether it could help.
>
>	Tom
>
>
>
>> On Mar 29, 2015, at 3:55 PM, Hurt, Darrell (NIH/NIAID) [E] wrote:
>> 
>> Hello again,
>> 
>> I still have to try VirtualGL (as suggested on a previous thread).
>> However, I want to share the following information:
>> 
>> I learned that the 60 fps I was getting on glxgears is likely due to
>> Ubuntu having "sync" enabled by default, which means that glxgears
>>always
>> runs at about 60 fps. So let's ignore that bit of information.
>> 
>>http://askubuntu.com/questions/31488/how-to-test-if-my-video-card-has-3d-
>>su
>> pport
>> 
>> My glxinfo (see below at "OpenGL renderer string") suggests that I have
>>an
>> NVIDIA graphics card installed. But "lspci -vnn | grep -i VGA" suggests
>> that I have a simple Matrox graphics card:
>> 
>> 
>> <output of lspci>
>> 
>> 01:00.1 VGA compatible controller [0300]: Matrox Electronics Systems
>>Ltd.
>> MGA G200EH [102b:0533] (rev 01) (prog-if 00 [VGA controller])
>> 
>> 
>> 
>> <output of glxinfo>
>> 
>> name of display: localhost:11.0
>> display: localhost:11  screen: 0
>> direct rendering: No (If you want to find out why, try setting
>> LIBGL_DEBUG=verbose)
>> server glx vendor string: SGI
>> server glx version string: 1.4
>> server glx extensions:
>>    GLX_ARB_create_context, GLX_ARB_create_context_profile,
>>    GLX_ARB_multisample, GLX_EXT_import_context, GLX_EXT_visual_info,
>>    GLX_EXT_visual_rating, GLX_OML_swap_method, GLX_SGIS_multisample,
>>    GLX_SGIX_fbconfig
>> client glx vendor string: Mesa Project and SGI
>> client glx version string: 1.4
>> client glx extensions:
>>    GLX_ARB_create_context, GLX_ARB_create_context_profile,
>>    GLX_ARB_get_proc_address, GLX_ARB_multisample,
>>GLX_EXT_import_context,
>>    GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_EXT_framebuffer_sRGB,
>>    GLX_EXT_create_context_es2_profile, GLX_MESA_copy_sub_buffer,
>>    GLX_MESA_multithread_makecurrent, GLX_MESA_swap_control,
>>    GLX_OML_swap_method, GLX_OML_sync_control, GLX_SGI_make_current_read,
>>    GLX_SGI_swap_control, GLX_SGI_video_sync, GLX_SGIS_multisample,
>>    GLX_SGIX_fbconfig, GLX_SGIX_pbuffer, GLX_SGIX_visual_select_group,
>>    GLX_EXT_texture_from_pixmap, GLX_INTEL_swap_event
>> GLX version: 1.4
>> GLX extensions:
>>    GLX_ARB_create_context, GLX_ARB_create_context_profile,
>>    GLX_ARB_get_proc_address, GLX_ARB_multisample,
>>GLX_EXT_import_context,
>>    GLX_EXT_visual_info, GLX_EXT_visual_rating,
>>    GLX_MESA_multithread_makecurrent, GLX_OML_swap_method,
>>    GLX_SGI_make_current_read, GLX_SGIS_multisample, GLX_SGIX_fbconfig,
>>    GLX_SGIX_pbuffer
>> OpenGL vendor string: NVIDIA Corporation
>> OpenGL renderer string: NVIDIA GeForce 9400M OpenGL Engine
>> OpenGL version string: 1.4 (2.1 NVIDIA-8.16.81 310.40.00.20f04)
>> OpenGL extensions:
>>    GL_ARB_depth_texture, GL_ARB_draw_buffers, GL_ARB_fragment_program,
>>    GL_ARB_fragment_program_shadow, GL_ARB_imaging, GL_ARB_multisample,
>>    GL_ARB_multitexture, GL_ARB_occlusion_query, GL_ARB_point_parameters,
>>    GL_ARB_point_sprite, GL_ARB_shadow, GL_ARB_texture_border_clamp,
>>    GL_ARB_texture_compression, GL_ARB_texture_cube_map,
>>    GL_ARB_texture_env_add, GL_ARB_texture_env_combine,
>>    GL_ARB_texture_env_crossbar, GL_ARB_texture_env_dot3,
>>    GL_ARB_texture_mirrored_repeat, GL_ARB_texture_non_power_of_two,
>>    GL_ARB_texture_rectangle, GL_ARB_transpose_matrix,
>> GL_ARB_vertex_program,
>>    GL_ARB_window_pos, GL_EXT_abgr, GL_EXT_bgra, GL_EXT_blend_color,
>>    GL_EXT_blend_equation_separate, GL_EXT_blend_func_separate,
>>    GL_EXT_blend_minmax, GL_EXT_blend_subtract, GL_EXT_clip_volume_hint,
>>    GL_EXT_draw_range_elements, GL_EXT_fog_coord,
>> GL_EXT_framebuffer_object,
>>    GL_EXT_multi_draw_arrays, GL_EXT_point_parameters,
>> GL_EXT_rescale_normal,
>>    GL_EXT_secondary_color, GL_EXT_separate_specular_color,
>>    GL_EXT_shadow_funcs, GL_EXT_stencil_two_side, GL_EXT_stencil_wrap,
>>    GL_EXT_texture_compression_dxt1, GL_EXT_texture_compression_s3tc,
>>    GL_EXT_texture_edge_clamp, GL_EXT_texture_env_add,
>>    GL_EXT_texture_filter_anisotropic, GL_EXT_texture_lod_bias,
>>    GL_EXT_texture_mirror_clamp, GL_EXT_texture_rectangle,
>>    GL_APPLE_packed_pixels, GL_ATI_draw_buffers,
>> GL_ATI_texture_env_combine3,
>>    GL_ATI_texture_mirror_once, GL_ATIX_texture_env_combine3,
>>    GL_IBM_texture_mirrored_repeat, GL_INGR_blend_func_separate,
>>    GL_NV_blend_square, GL_NV_depth_clamp, GL_NV_fog_distance,
>>    GL_NV_fragment_program_option, GL_NV_fragment_program2,
>>    GL_NV_light_max_exponent, GL_NV_multisample_filter_hint,
>>    GL_NV_point_sprite, GL_NV_texgen_reflection, GL_NV_texture_rectangle,
>>    GL_NV_vertex_program2_option, GL_NV_vertex_program3,
>>    GL_SGIS_generate_mipmap, GL_SGIS_texture_border_clamp,
>>    GL_SGIS_texture_edge_clamp, GL_SGIS_texture_lod,
>> GL_SUN_multi_draw_arrays
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> -- 
>> Darrell Hurt, Ph.D.
>> Acting Chief
>> Bioinformatics and Computational Biosciences Branch (BCBB)
>> OCICB/OSMO/OD/NIAID/NIH
>> 
>> 5601 Fishers Lane, 4A31
>> North Bethesda, MD 20852
>> Office: 240-669-2741
>> Mobile: 301-758-3559Web: BCBB Home Page
>> 
>><http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bc
>>bb
>> .aspx#niaid_inlineNav_Anchor>
>> Twitter: @niaidbioit <https://twitter.com/niaidbioit> , @NIH3Dprint
>> <https://twitter.com/nih3dprint>
>> 
>> 
>> Disclaimer: The information in this e-mail and any of its attachments is
>> confidential and may contain sensitive information. It should not be
>>used
>> by anyone who is not the original intended recipient. If you have
>>received
>> this e-mail in error please inform the sender and delete it from your
>> mailbox or any other storage devices. National Institute of Allergy and
>> Infectious Diseases shall not accept liability for any statements made
>> that are sender's own and not expressly made on behalf of the NIAID by
>>one
>> of its representatives.
>> 
>> 
>> 
>> 
>> 
>> 
>> On 3/29/15 7:10 PM, "Hurt, Darrell (NIH/NIAID) [E]"
>> wrote:
>> 
>>> Hi Chimera friends,
>>> 
>>> I want to run a graphics-enabled Chimera from a remote Ubuntu server.
>>>The
>>> Ubuntu server is quite beefy (and not virtualized), but it has a stock
>>> video card. When I run "glxgears", I can see the gears and get about 60
>>> fps (reported), but the gears don't move and aren't interactive.
>>> 
>>> I found this message from the listserv a few years ago that recommends
>>> the use of VirtualGL:
>>> 
>>>http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-September/007953.
>>>ht
>>> ml
>>> 
>>> My X windowing system is Xquartz on a Mac. Is my problem related to
>>> software GL or to the poor graphics card?
>>> 
>>> Related question: what X windowing system do you recommend on a Windows
>>> system? CYGWIN?
>>> 
>>> Thanks,
>>> Darrell
>>> 
>>> --
>>> Darrell Hurt, Ph.D.
>>> Acting Chief
>>> Bioinformatics and Computational Biosciences Branch (BCBB)
>>> OCICB/OSMO/OD/NIAID/NIH
>>> 
>>> 5601 Fishers Lane, 4A31
>>> North Bethesda, MD 20852
>>> Office: 240-669-2741
>>> Mobile: 301-758-3559
>>> Web: BCBB Home 
>>> 
>>>Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pag
>>>es
>>> /bcbb.aspx#niaid_inlineNav_Anchor>
>>> Twitter: @niaidbioit<https://twitter.com/niaidbioit> ,
>>> @NIH3Dprint<https://twitter.com/nih3dprint>
>>> 
>>> Disclaimer: The information in this e-mail and any of its attachments
>>>is
>>> confidential and may contain sensitive information. It should not be
>>>used
>>> by anyone who is not the original intended recipient. If you have
>>> received this e-mail in error please inform the sender and delete it
>>>from
>>> your mailbox or any other storage devices. National Institute of
>>>Allergy
>>> and Infectious Diseases shall not accept liability for any statements
>>> made that are sender's own and not expressly made on behalf of the
>>>NIAID
>>> by one of its representatives.
>>> 
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
>> 
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
>




From darrellh at niaid.nih.gov  Mon Mar 30 15:50:18 2015
From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E])
Date: Mon, 30 Mar 2015 22:50:18 +0000
Subject: [Chimera-users] Picking not working in RDS
Message-ID: <D13F83A3.3311F%darrellh@niaid.nih.gov>

Hi Chimera friends,

I'm using the Microsoft Remote Desktop Mac client to connect to a Microsoft Remote Desktop Server (an "RDS" running Windows Server 2012 R2). That RDS is serving out a Windows 8 environment and I'm running the latest Chimera release in it very successfully. Except that selection by picking (Ctrl-mouse_button_1) and centering (Ctrl-mouse_button_3) does NOT work. When I try to select by picking, the cursor changes from the arrow to hand momentarily. I also get this behavior when connecting to the RDS via any other client. Any thoughts on what might be happening and how to fix it?

Thanks,
Darrell

--
Darrell Hurt, Ph.D.
Acting Chief
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

5601 Fishers Lane, 4A31
North Bethesda, MD 20852
Office: 240-669-2741
Mobile: 301-758-3559
Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>
Twitter: @niaidbioit<https://twitter.com/niaidbioit> , @NIH3Dprint<https://twitter.com/nih3dprint>

Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.



From goddard at sonic.net  Mon Mar 30 16:25:53 2015
From: goddard at sonic.net (Tom Goddard)
Date: Mon, 30 Mar 2015 16:25:53 -0700
Subject: [Chimera-users] Toggle active vs displayed for checkboxes at
	bottom of screen?
In-Reply-To: <39A36A1D-66E3-4B56-9E53-EFCE5695CD3D@cgl.ucsf.edu>
References: <48232DA5-E1AE-4194-A275-B42D00A223A3@gmail.com>
	<39A36A1D-66E3-4B56-9E53-EFCE5695CD3D@cgl.ucsf.edu>
Message-ID: <E3CE7A84-0975-42CC-AB28-17265CCD5E4B@sonic.net>

Hi Oliver,

  I added a preference setting to show ?model displayed? checkbuttons below the command-line.  Also there is a preference setting to undisplay the ?model active? checkbuttons.  Or you can show no checkbuttons or show both active and displayed.  The preference setting can be saved so Chimera always starts with your desired setting.  The settings are under the ?Command-Line? category in the Preferences dialog in tonight?s daily build.

	Tom



> On Mar 26, 2015, at 10:28 AM, Elaine Meng wrote:
> 
> Hi Oliver,
> I personally would rather just have checkboxes for model-display instead of model-active!  The current model-active checkboxes are somewhat of a legacy from the previous-generation program, MidasPlus.  Your idea to switch between the two is also reasonable.  However, I can only "lobby" for changes, since I'm the token non-programmer on the team?. unless you count fortran (most people don't, and not to worry, my fortran programs aren't going into Chimera).
> 
> Possible yes? the difficult thing is to manage and prioritize requests and our own plans without letting things fall through the cracks between when they are suggested and when they can be implemented.  This is always an issue, whether Chimera 1 or 2...
> 
> Consider also that Chimera2 will have certain major differences that may make some suggested changes less applicable or less needed.
> 
> Thanks for your ideas!  Sincerely,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Mar 26, 2015, at 10:03 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
>> Hi, this is more of a feature suggestion than anything, and I guess it is unlikely to be implemented before Chimera 2, but thought I?d put it out there anyway. 
>> 
>> Currently the checkboxes at the bottom of the main display control whether or not a model is active - this is very handy when reorienting models with respect to one another. 
>> 
>> I would love a similar means to toggle the display of individual models without going to the model panel. One way would be to alter the ?Active models? text label (circled in screenshot) to ?Displayed models?, and change the behaviour/meaning of the checkboxes accordingly, similar to the A/I/R/S selection mode changer at the bottom right of the main display. 
>> 
>> So you would click ?Active models?, and the text would switch to ?Displayed models?, and the configuration of the checkboxes  would change so that the displayed models (rather than the active models) are checked. 
>> 
>> Is this something that would be possible in a future version?
>> 
>> Best,
>> Oliver.
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From olibclarke at gmail.com  Mon Mar 30 16:39:44 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Mon, 30 Mar 2015 19:39:44 -0400
Subject: [Chimera-users] Toggle active vs displayed for checkboxes at
	bottom of screen?
In-Reply-To: <E3CE7A84-0975-42CC-AB28-17265CCD5E4B@sonic.net>
References: <48232DA5-E1AE-4194-A275-B42D00A223A3@gmail.com>
	<39A36A1D-66E3-4B56-9E53-EFCE5695CD3D@cgl.ucsf.edu>
	<E3CE7A84-0975-42CC-AB28-17265CCD5E4B@sonic.net>
Message-ID: <52ABC6F0-9029-4E62-B784-6C2E6045E0BF@gmail.com>

Fantastic, thank you Tom! I?ll check it out as soon as it?s available.

Oliver.
> On Mar 30, 2015, at 7:25 PM, Tom Goddard <goddard at sonic.net> wrote:
> 
> Hi Oliver,
> 
>  I added a preference setting to show ?model displayed? checkbuttons below the command-line.  Also there is a preference setting to undisplay the ?model active? checkbuttons.  Or you can show no checkbuttons or show both active and displayed.  The preference setting can be saved so Chimera always starts with your desired setting.  The settings are under the ?Command-Line? category in the Preferences dialog in tonight?s daily build.
> 
> 	Tom
> 
> 
> 
>> On Mar 26, 2015, at 10:28 AM, Elaine Meng wrote:
>> 
>> Hi Oliver,
>> I personally would rather just have checkboxes for model-display instead of model-active!  The current model-active checkboxes are somewhat of a legacy from the previous-generation program, MidasPlus.  Your idea to switch between the two is also reasonable.  However, I can only "lobby" for changes, since I'm the token non-programmer on the team?. unless you count fortran (most people don't, and not to worry, my fortran programs aren't going into Chimera).
>> 
>> Possible yes? the difficult thing is to manage and prioritize requests and our own plans without letting things fall through the cracks between when they are suggested and when they can be implemented.  This is always an issue, whether Chimera 1 or 2...
>> 
>> Consider also that Chimera2 will have certain major differences that may make some suggested changes less applicable or less needed.
>> 
>> Thanks for your ideas!  Sincerely,
>> Elaine
>> ----------
>> Elaine C. Meng, Ph.D. 
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> On Mar 26, 2015, at 10:03 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
>> 
>>> Hi, this is more of a feature suggestion than anything, and I guess it is unlikely to be implemented before Chimera 2, but thought I?d put it out there anyway. 
>>> 
>>> Currently the checkboxes at the bottom of the main display control whether or not a model is active - this is very handy when reorienting models with respect to one another. 
>>> 
>>> I would love a similar means to toggle the display of individual models without going to the model panel. One way would be to alter the ?Active models? text label (circled in screenshot) to ?Displayed models?, and change the behaviour/meaning of the checkboxes accordingly, similar to the A/I/R/S selection mode changer at the bottom right of the main display. 
>>> 
>>> So you would click ?Active models?, and the text would switch to ?Displayed models?, and the configuration of the checkboxes  would change so that the displayed models (rather than the active models) are checked. 
>>> 
>>> Is this something that would be possible in a future version?
>>> 
>>> Best,
>>> Oliver.
>> 
>> 
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
> 




From goddard at sonic.net  Mon Mar 30 16:51:43 2015
From: goddard at sonic.net (Tom Goddard)
Date: Mon, 30 Mar 2015 16:51:43 -0700
Subject: [Chimera-users] Picking not working in RDS
In-Reply-To: <D13F83A3.3311F%darrellh@niaid.nih.gov>
References: <D13F83A3.3311F%darrellh@niaid.nih.gov>
Message-ID: <4EDC67D5-E9F7-4F13-A3F3-4418FE771AC1@sonic.net>

Hi Darrell,

  When you ctrl-left-click in Chimera the mouse pointer changes to a hand with the index finger pointing to the left while you hold the mouse down.  I guess that is what you mean when you say you see the cursor change to the hand.  That would indicate that Chimera does get the ctrl-click mouse event.  So one idea is that Chimera gets the ctrl-click but the x,y coordinates of the click reported to Chimera are wrong so it doesn?t select anything.  As a test of this you could select everything (Select / Select All) then try a ctrl-click to select something and see if that deselects everything, as if the click was on the background.  It seems unlikely the mouse pointer position could be reported wrong since that would probably make pressing on menus and buttons not work as well.  Another test, when you ctrl-left-drag Chimera draws a green outline box ? does that appear?  Another idea is that Chimera gets the ctrl-click but in never gets the mouse release when it actually does the selection.  Have you tested that ctrl-click select actually works on the Windows machine?  If Windows falls back to the archaic Microsoft GDI graphics driver, then I believe ctrl-click does not work.  You can find out what driver Chimera is using with Chimera menu entry Help / Report a Bug? under ?Gathered Information?.  One last thing to check.  When you hover the mouse over and atom, a popup window shows the name of the atom.  That uses the same Chimera code as ctrl-click selection to figure out what atom the pointer is over.  Does that work?

	Tom


> On Mar 30, 2015, at 3:50 PM, Hurt, Darrell (NIH/NIAID) [E]  wrote:
> 
> Hi Chimera friends,
> 
> I'm using the Microsoft Remote Desktop Mac client to connect to a Microsoft Remote Desktop Server (an "RDS" running Windows Server 2012 R2). That RDS is serving out a Windows 8 environment and I'm running the latest Chimera release in it very successfully. Except that selection by picking (Ctrl-mouse_button_1) and centering (Ctrl-mouse_button_3) does NOT work. When I try to select by picking, the cursor changes from the arrow to hand momentarily. I also get this behavior when connecting to the RDS via any other client. Any thoughts on what might be happening and how to fix it?
> 
> Thanks,
> Darrell
> 
> --
> Darrell Hurt, Ph.D.
> Acting Chief
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
> 
> 5601 Fishers Lane, 4A31
> North Bethesda, MD 20852
> Office: 240-669-2741
> Mobile: 301-758-3559
> Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>
> Twitter: @niaidbioit<https://twitter.com/niaidbioit> , @NIH3Dprint<https://twitter.com/nih3dprint>
> 
> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From darrellh at niaid.nih.gov  Mon Mar 30 18:04:13 2015
From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E])
Date: Tue, 31 Mar 2015 01:04:13 +0000
Subject: [Chimera-users] Picking not working in RDS
In-Reply-To: <4EDC67D5-E9F7-4F13-A3F3-4418FE771AC1@sonic.net>
References: <D13F83A3.3311F%darrellh@niaid.nih.gov>
	<4EDC67D5-E9F7-4F13-A3F3-4418FE771AC1@sonic.net>
Message-ID: <D13F9D62.331DF%darrellh@niaid.nih.gov>

Hi Tom,

Thanks again for this great troubleshooting.

I've tested as you described and here are my results:

(1) Ctrl-click to deselect after a "Select All": this works as expected

(2) Ctrl-left-drag does present a box and does select whatever is enclosed
in the selection box

(3) I don't have access to the actual Windows machine -- the RDS machine
is itself a virtual machine.

(4) The results in the "Gathered Information" box reveal the problem: it
is using the GDI renderer! (Full details at the bottom of the email.)

(5) Hover does not reveal any information.

This then begs the question: how to fix the problem? Do we just install a
better OpenGL renderer on the virtual RDS? Are the following articles on
the right track?
https://www.vmware.com/support/ws55/doc/ws_vidsound_d3d_enabling_host.html
http://www.phoronix.com/scan.php?page=article&item=vmware_vmwgfx_g3d&num=1

Thanks!
Darrell



OpenGL Vendor: Microsoft Corporation
OpenGL Renderer: GDI Generic
OpenGL Version: 1.1.0
Manufacturer: VMware, Inc.
Model: VMware Virtual Platform
TotalPhysicalMemory: 17179398144

????????????????????
Multisampling: False
Shadows: False
Shadow texture size: 2048
Silhouettes: False
Depth cue: True
Subdivision quality: 1.50
Single-layer transparency: True
Transparent background: False
Shaders supported: False
Using shader: False
Window size: 535 474
Camera mode: mono
Orthographic projection: False
Center of rotation: front center
Near/far clipping: False
Key light: True
Fill light: True
Back light: False
Ambient light: 0.20
Specular sharpness: 30.00
Specular reflectivity: 1.00

????????????????????
AntialiasLines: native
AntialiasPoints: native
BlendEquation: not supported
BlendFuncSeparate: not supported
BrokenAttribLocation: native, disabled
ChoosePixelFormat: not supported
ColorTable: extension
CompileAndExecute: native
CompiledVertexArray: not supported
CubeMap: not supported
CullVertex: not supported
DrawElementsInstanced: not supported, disabled
DrawRangeElements: not supported
FBConfig: not supported
FBOShadows: native
FastMultisampling: not supported, disabled
FramebufferMultisample: not supported
FramebufferObject: not supported
LimitVertexAttribDivisor: native, disabled
Multisample: not supported
Multitexture: not supported
PackedDepthStencil: not supported
PalettedTexture: not supported
PointParameters: not supported
SeamlessCubeMap: not supported
SeparateSpecularColor: not supported
Shading: not supported
Shadows: not supported
StereoMultisample: not supported
StereoRubberBanding: native
Texture3D: not supported
TextureColorTable: not supported
TextureEdgeClamp: not supported
TrustColorLogicBlend: native
TrustNormals: native
VertexArray: native
VertexAttrib: not supported
VertexAttribDivisor: not supported
VertexBufferObject: not supported
WindowPos: not supported










-- 
Darrell Hurt, Ph.D.
Acting Chief
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH
 
5601 Fishers Lane, 4A31
North Bethesda, MD 20852
Office: 240-669-2741
Mobile: 301-758-3559Web: BCBB Home Page
<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb
.aspx#niaid_inlineNav_Anchor>
Twitter: @niaidbioit <https://twitter.com/niaidbioit> , @NIH3Dprint
<https://twitter.com/nih3dprint>


Disclaimer: The information in this e-mail and any of its attachments is
confidential and may contain sensitive information. It should not be used
by anyone who is not the original intended recipient. If you have received
this e-mail in error please inform the sender and delete it from your
mailbox or any other storage devices. National Institute of Allergy and
Infectious Diseases shall not accept liability for any statements made
that are sender's own and not expressly made on behalf of the NIAID by one
of its representatives.






On 3/30/15 11:51 PM, "Tom Goddard" <goddard at sonic.net> wrote:

>Hi Darrell,
>
>  When you ctrl-left-click in Chimera the mouse pointer changes to a hand
>with the index finger pointing to the left while you hold the mouse down.
> I guess that is what you mean when you say you see the cursor change to
>the hand.  That would indicate that Chimera does get the ctrl-click mouse
>event.  So one idea is that Chimera gets the ctrl-click but the x,y
>coordinates of the click reported to Chimera are wrong so it doesn?t
>select anything.  As a test of this you could select everything (Select /
>Select All) then try a ctrl-click to select something and see if that
>deselects everything, as if the click was on the background.  It seems
>unlikely the mouse pointer position could be reported wrong since that
>would probably make pressing on menus and buttons not work as well.
>Another test, when you ctrl-left-drag Chimera draws a green outline box ?
>does that appear?  Another idea is that Chimera gets the ctrl-click but
>in never gets the mouse release when it actually does the selection.
>Have you tested that ctrl-click select actually works on the Windows
>machine?  If Windows falls back to the archaic Microsoft GDI graphics
>driver, then I believe ctrl-click does not work.  You can find out what
>driver Chimera is using with Chimera menu entry Help / Report a Bug?
>under ?Gathered Information?.  One last thing to check.  When you hover
>the mouse over and atom, a popup window shows the name of the atom.  That
>uses the same Chimera code as ctrl-click selection to figure out what
>atom the pointer is over.  Does that work?
>
>	Tom
>
>
>> On Mar 30, 2015, at 3:50 PM, Hurt, Darrell (NIH/NIAID) [E]  wrote:
>> 
>> Hi Chimera friends,
>> 
>> I'm using the Microsoft Remote Desktop Mac client to connect to a
>>Microsoft Remote Desktop Server (an "RDS" running Windows Server 2012
>>R2). That RDS is serving out a Windows 8 environment and I'm running the
>>latest Chimera release in it very successfully. Except that selection by
>>picking (Ctrl-mouse_button_1) and centering (Ctrl-mouse_button_3) does
>>NOT work. When I try to select by picking, the cursor changes from the
>>arrow to hand momentarily. I also get this behavior when connecting to
>>the RDS via any other client. Any thoughts on what might be happening
>>and how to fix it?
>> 
>> Thanks,
>> Darrell
>> 
>> --
>> Darrell Hurt, Ph.D.
>> Acting Chief
>> Bioinformatics and Computational Biosciences Branch (BCBB)
>> OCICB/OSMO/OD/NIAID/NIH
>> 
>> 5601 Fishers Lane, 4A31
>> North Bethesda, MD 20852
>> Office: 240-669-2741
>> Mobile: 301-758-3559
>> Web: BCBB Home 
>>Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Page
>>s/bcbb.aspx#niaid_inlineNav_Anchor>
>> Twitter: @niaidbioit<https://twitter.com/niaidbioit> ,
>>@NIH3Dprint<https://twitter.com/nih3dprint>
>> 
>> Disclaimer: The information in this e-mail and any of its attachments
>>is confidential and may contain sensitive information. It should not be
>>used by anyone who is not the original intended recipient. If you have
>>received this e-mail in error please inform the sender and delete it
>>from your mailbox or any other storage devices. National Institute of
>>Allergy and Infectious Diseases shall not accept liability for any
>>statements made that are sender's own and not expressly made on behalf
>>of the NIAID by one of its representatives.
>> 
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
>




From goddard at sonic.net  Mon Mar 30 18:36:44 2015
From: goddard at sonic.net (Tom Goddard)
Date: Mon, 30 Mar 2015 18:36:44 -0700
Subject: [Chimera-users] Picking not working in RDS
In-Reply-To: <D13F9D62.331DF%darrellh@niaid.nih.gov>
References: <D13F83A3.3311F%darrellh@niaid.nih.gov>
	<4EDC67D5-E9F7-4F13-A3F3-4418FE771AC1@sonic.net>
	<D13F9D62.331DF%darrellh@niaid.nih.gov>
Message-ID: <4A7F05A4-7D1E-4C13-9A44-C576C78ABBB7@sonic.net>

Hi Darrell,

  Ok, that explains it. The virtual Windows machine is using the Microsoft GDI driver which is OpenGL 1.1 (the graphics standard from 1997). I have quite a few bug reports that ctrl-click selection does not work with the GDI driver. This driver is used when Windows does not support whatever (usually ancient) graphics hardware you have, so all rendering will be without hardware acceleration, so it will be extremely slow.  Also no modern OpenGL (like shader programs) can be used. I believe old Chimera versions worked with the GDI driver, but I?m not sure how old ? maybe Chimera 1.6 or 1.5 before we started using GPU shader programs.  It is possible that I can fix ctrl-click selection to work with the GDI driver.  But I will have to think about whether it makes sense to work on it, since I think supporting long obsolete computers and poor virtual machines will take away time from doing interesting new things in Chimera for people who have suitable computer setups for doing graphics.  There is no way around the broken selection when using the GDI driver that I know of other than using a very old Chimera version.

  Thinking ahead, we are working on Chimera 2, and it will require at least OpenGL 3.3 ? it will not show or do anything on GDI graphics.  So we are going to be setting some minimum graphics requirements for Chimera 2 that not all computers will meet.

	Tom



> On Mar 30, 2015, at 6:04 PM, Hurt, Darrell (NIH/NIAID) [E] wrote:
> 
> Hi Tom,
> 
> Thanks again for this great troubleshooting.
> 
> I've tested as you described and here are my results:
> 
> (1) Ctrl-click to deselect after a "Select All": this works as expected
> 
> (2) Ctrl-left-drag does present a box and does select whatever is enclosed
> in the selection box
> 
> (3) I don't have access to the actual Windows machine -- the RDS machine
> is itself a virtual machine.
> 
> (4) The results in the "Gathered Information" box reveal the problem: it
> is using the GDI renderer! (Full details at the bottom of the email.)
> 
> (5) Hover does not reveal any information.
> 
> This then begs the question: how to fix the problem? Do we just install a
> better OpenGL renderer on the virtual RDS? Are the following articles on
> the right track?
> https://www.vmware.com/support/ws55/doc/ws_vidsound_d3d_enabling_host.html
> http://www.phoronix.com/scan.php?page=article&item=vmware_vmwgfx_g3d&num=1
> 
> Thanks!
> Darrell
> 
> 
> 
> OpenGL Vendor: Microsoft Corporation
> OpenGL Renderer: GDI Generic
> OpenGL Version: 1.1.0
> Manufacturer: VMware, Inc.
> Model: VMware Virtual Platform
> TotalPhysicalMemory: 17179398144
> 
> ????????????????????
> Multisampling: False
> Shadows: False
> Shadow texture size: 2048
> Silhouettes: False
> Depth cue: True
> Subdivision quality: 1.50
> Single-layer transparency: True
> Transparent background: False
> Shaders supported: False
> Using shader: False
> Window size: 535 474
> Camera mode: mono
> Orthographic projection: False
> Center of rotation: front center
> Near/far clipping: False
> Key light: True
> Fill light: True
> Back light: False
> Ambient light: 0.20
> Specular sharpness: 30.00
> Specular reflectivity: 1.00
> 
> ????????????????????
> AntialiasLines: native
> AntialiasPoints: native
> BlendEquation: not supported
> BlendFuncSeparate: not supported
> BrokenAttribLocation: native, disabled
> ChoosePixelFormat: not supported
> ColorTable: extension
> CompileAndExecute: native
> CompiledVertexArray: not supported
> CubeMap: not supported
> CullVertex: not supported
> DrawElementsInstanced: not supported, disabled
> DrawRangeElements: not supported
> FBConfig: not supported
> FBOShadows: native
> FastMultisampling: not supported, disabled
> FramebufferMultisample: not supported
> FramebufferObject: not supported
> LimitVertexAttribDivisor: native, disabled
> Multisample: not supported
> Multitexture: not supported
> PackedDepthStencil: not supported
> PalettedTexture: not supported
> PointParameters: not supported
> SeamlessCubeMap: not supported
> SeparateSpecularColor: not supported
> Shading: not supported
> Shadows: not supported
> StereoMultisample: not supported
> StereoRubberBanding: native
> Texture3D: not supported
> TextureColorTable: not supported
> TextureEdgeClamp: not supported
> TrustColorLogicBlend: native
> TrustNormals: native
> VertexArray: native
> VertexAttrib: not supported
> VertexAttribDivisor: not supported
> VertexBufferObject: not supported
> WindowPos: not supported
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> -- 
> Darrell Hurt, Ph.D.
> Acting Chief
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
> 
> 5601 Fishers Lane, 4A31
> North Bethesda, MD 20852
> Office: 240-669-2741
> Mobile: 301-758-3559Web: BCBB Home Page
> <http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb
> .aspx#niaid_inlineNav_Anchor>
> Twitter: @niaidbioit <https://twitter.com/niaidbioit> , @NIH3Dprint
> <https://twitter.com/nih3dprint>
> 
> 
> Disclaimer: The information in this e-mail and any of its attachments is
> confidential and may contain sensitive information. It should not be used
> by anyone who is not the original intended recipient. If you have received
> this e-mail in error please inform the sender and delete it from your
> mailbox or any other storage devices. National Institute of Allergy and
> Infectious Diseases shall not accept liability for any statements made
> that are sender's own and not expressly made on behalf of the NIAID by one
> of its representatives.
> 
> 
> 
> 
> 
> 
> On 3/30/15 11:51 PM, "Tom Goddard" <goddard at sonic.net> wrote:
> 
>> Hi Darrell,
>> 
>> When you ctrl-left-click in Chimera the mouse pointer changes to a hand
>> with the index finger pointing to the left while you hold the mouse down.
>> I guess that is what you mean when you say you see the cursor change to
>> the hand.  That would indicate that Chimera does get the ctrl-click mouse
>> event.  So one idea is that Chimera gets the ctrl-click but the x,y
>> coordinates of the click reported to Chimera are wrong so it doesn?t
>> select anything.  As a test of this you could select everything (Select /
>> Select All) then try a ctrl-click to select something and see if that
>> deselects everything, as if the click was on the background.  It seems
>> unlikely the mouse pointer position could be reported wrong since that
>> would probably make pressing on menus and buttons not work as well.
>> Another test, when you ctrl-left-drag Chimera draws a green outline box ?
>> does that appear?  Another idea is that Chimera gets the ctrl-click but
>> in never gets the mouse release when it actually does the selection.
>> Have you tested that ctrl-click select actually works on the Windows
>> machine?  If Windows falls back to the archaic Microsoft GDI graphics
>> driver, then I believe ctrl-click does not work.  You can find out what
>> driver Chimera is using with Chimera menu entry Help / Report a Bug?
>> under ?Gathered Information?.  One last thing to check.  When you hover
>> the mouse over and atom, a popup window shows the name of the atom.  That
>> uses the same Chimera code as ctrl-click selection to figure out what
>> atom the pointer is over.  Does that work?
>> 
>> 	Tom
>> 
>> 
>>> On Mar 30, 2015, at 3:50 PM, Hurt, Darrell (NIH/NIAID) [E]  wrote:
>>> 
>>> Hi Chimera friends,
>>> 
>>> I'm using the Microsoft Remote Desktop Mac client to connect to a
>>> Microsoft Remote Desktop Server (an "RDS" running Windows Server 2012
>>> R2). That RDS is serving out a Windows 8 environment and I'm running the
>>> latest Chimera release in it very successfully. Except that selection by
>>> picking (Ctrl-mouse_button_1) and centering (Ctrl-mouse_button_3) does
>>> NOT work. When I try to select by picking, the cursor changes from the
>>> arrow to hand momentarily. I also get this behavior when connecting to
>>> the RDS via any other client. Any thoughts on what might be happening
>>> and how to fix it?
>>> 
>>> Thanks,
>>> Darrell
>>> 
>>> --
>>> Darrell Hurt, Ph.D.
>>> Acting Chief
>>> Bioinformatics and Computational Biosciences Branch (BCBB)
>>> OCICB/OSMO/OD/NIAID/NIH
>>> 
>>> 5601 Fishers Lane, 4A31
>>> North Bethesda, MD 20852
>>> Office: 240-669-2741
>>> Mobile: 301-758-3559
>>> Web: BCBB Home 
>>> Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Page
>>> s/bcbb.aspx#niaid_inlineNav_Anchor>
>>> Twitter: @niaidbioit<https://twitter.com/niaidbioit> ,
>>> @NIH3Dprint<https://twitter.com/nih3dprint>
>>> 
>>> Disclaimer: The information in this e-mail and any of its attachments
>>> is confidential and may contain sensitive information. It should not be
>>> used by anyone who is not the original intended recipient. If you have
>>> received this e-mail in error please inform the sender and delete it
>>> from your mailbox or any other storage devices. National Institute of
>>> Allergy and Infectious Diseases shall not accept liability for any
>>> statements made that are sender's own and not expressly made on behalf
>>> of the NIAID by one of its representatives.
>>> 
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>> 
>> 
> 
> 




From darrellh at niaid.nih.gov  Tue Mar 31 00:56:38 2015
From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E])
Date: Tue, 31 Mar 2015 07:56:38 +0000
Subject: [Chimera-users] Picking not working in RDS
In-Reply-To: <4A7F05A4-7D1E-4C13-9A44-C576C78ABBB7@sonic.net>
References: <D13F83A3.3311F%darrellh@niaid.nih.gov>
	<4EDC67D5-E9F7-4F13-A3F3-4418FE771AC1@sonic.net>
	<D13F9D62.331DF%darrellh@niaid.nih.gov>,
	<4A7F05A4-7D1E-4C13-9A44-C576C78ABBB7@sonic.net>
Message-ID: <9D5FAD8B-801F-479D-90CB-B00F1DAB041E@niaid.nih.gov>

Hi Tom,

No need to work on anything on your side. The problem is ours and with your help, we have a path forward. We'll explore our options on the virtual server.

Thanks,
Darrell

Sent from my iPhone

> On Mar 31, 2015, at 1:36 AM, Tom Goddard <goddard at sonic.net> wrote:
> 
> Hi Darrell,
> 
>  Ok, that explains it. The virtual Windows machine is using the Microsoft GDI driver which is OpenGL 1.1 (the graphics standard from 1997). I have quite a few bug reports that ctrl-click selection does not work with the GDI driver. This driver is used when Windows does not support whatever (usually ancient) graphics hardware you have, so all rendering will be without hardware acceleration, so it will be extremely slow.  Also no modern OpenGL (like shader programs) can be used. I believe old Chimera versions worked with the GDI driver, but I?m not sure how old ? maybe Chimera 1.6 or 1.5 before we started using GPU shader programs.  It is possible that I can fix ctrl-click selection to work with the GDI driver.  But I will have to think about whether it makes sense to work on it, since I think supporting long obsolete computers and poor virtual machines will take away time from doing interesting new things in Chimera for people who have suitable computer setups for doing graphics.  There is no way around the broken selection when using the GDI driver that I know of other than using a very old Chimera version.
> 
>  Thinking ahead, we are working on Chimera 2, and it will require at least OpenGL 3.3 ? it will not show or do anything on GDI graphics.  So we are going to be setting some minimum graphics requirements for Chimera 2 that not all computers will meet.
> 
>    Tom
> 
> 
> 
>> On Mar 30, 2015, at 6:04 PM, Hurt, Darrell (NIH/NIAID) [E] wrote:
>> 
>> Hi Tom,
>> 
>> Thanks again for this great troubleshooting.
>> 
>> I've tested as you described and here are my results:
>> 
>> (1) Ctrl-click to deselect after a "Select All": this works as expected
>> 
>> (2) Ctrl-left-drag does present a box and does select whatever is enclosed
>> in the selection box
>> 
>> (3) I don't have access to the actual Windows machine -- the RDS machine
>> is itself a virtual machine.
>> 
>> (4) The results in the "Gathered Information" box reveal the problem: it
>> is using the GDI renderer! (Full details at the bottom of the email.)
>> 
>> (5) Hover does not reveal any information.
>> 
>> This then begs the question: how to fix the problem? Do we just install a
>> better OpenGL renderer on the virtual RDS? Are the following articles on
>> the right track?
>> https://www.vmware.com/support/ws55/doc/ws_vidsound_d3d_enabling_host.html
>> http://www.phoronix.com/scan.php?page=article&item=vmware_vmwgfx_g3d&num=1
>> 
>> Thanks!
>> Darrell
>> 
>> 
>> 
>> OpenGL Vendor: Microsoft Corporation
>> OpenGL Renderer: GDI Generic
>> OpenGL Version: 1.1.0
>> Manufacturer: VMware, Inc.
>> Model: VMware Virtual Platform
>> TotalPhysicalMemory: 17179398144
>> 
>> ????????????????????
>> Multisampling: False
>> Shadows: False
>> Shadow texture size: 2048
>> Silhouettes: False
>> Depth cue: True
>> Subdivision quality: 1.50
>> Single-layer transparency: True
>> Transparent background: False
>> Shaders supported: False
>> Using shader: False
>> Window size: 535 474
>> Camera mode: mono
>> Orthographic projection: False
>> Center of rotation: front center
>> Near/far clipping: False
>> Key light: True
>> Fill light: True
>> Back light: False
>> Ambient light: 0.20
>> Specular sharpness: 30.00
>> Specular reflectivity: 1.00
>> 
>> ????????????????????
>> AntialiasLines: native
>> AntialiasPoints: native
>> BlendEquation: not supported
>> BlendFuncSeparate: not supported
>> BrokenAttribLocation: native, disabled
>> ChoosePixelFormat: not supported
>> ColorTable: extension
>> CompileAndExecute: native
>> CompiledVertexArray: not supported
>> CubeMap: not supported
>> CullVertex: not supported
>> DrawElementsInstanced: not supported, disabled
>> DrawRangeElements: not supported
>> FBConfig: not supported
>> FBOShadows: native
>> FastMultisampling: not supported, disabled
>> FramebufferMultisample: not supported
>> FramebufferObject: not supported
>> LimitVertexAttribDivisor: native, disabled
>> Multisample: not supported
>> Multitexture: not supported
>> PackedDepthStencil: not supported
>> PalettedTexture: not supported
>> PointParameters: not supported
>> SeamlessCubeMap: not supported
>> SeparateSpecularColor: not supported
>> Shading: not supported
>> Shadows: not supported
>> StereoMultisample: not supported
>> StereoRubberBanding: native
>> Texture3D: not supported
>> TextureColorTable: not supported
>> TextureEdgeClamp: not supported
>> TrustColorLogicBlend: native
>> TrustNormals: native
>> VertexArray: native
>> VertexAttrib: not supported
>> VertexAttribDivisor: not supported
>> VertexBufferObject: not supported
>> WindowPos: not supported
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> -- 
>> Darrell Hurt, Ph.D.
>> Acting Chief
>> Bioinformatics and Computational Biosciences Branch (BCBB)
>> OCICB/OSMO/OD/NIAID/NIH
>> 
>> 5601 Fishers Lane, 4A31
>> North Bethesda, MD 20852
>> Office: 240-669-2741
>> Mobile: 301-758-3559Web: BCBB Home Page
>> <http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb
>> .aspx#niaid_inlineNav_Anchor>
>> Twitter: @niaidbioit <https://twitter.com/niaidbioit> , @NIH3Dprint
>> <https://twitter.com/nih3dprint>
>> 
>> 
>> Disclaimer: The information in this e-mail and any of its attachments is
>> confidential and may contain sensitive information. It should not be used
>> by anyone who is not the original intended recipient. If you have received
>> this e-mail in error please inform the sender and delete it from your
>> mailbox or any other storage devices. National Institute of Allergy and
>> Infectious Diseases shall not accept liability for any statements made
>> that are sender's own and not expressly made on behalf of the NIAID by one
>> of its representatives.
>> 
>> 
>> 
>> 
>> 
>> 
>>> On 3/30/15 11:51 PM, "Tom Goddard" <goddard at sonic.net> wrote:
>>> 
>>> Hi Darrell,
>>> 
>>> When you ctrl-left-click in Chimera the mouse pointer changes to a hand
>>> with the index finger pointing to the left while you hold the mouse down.
>>> I guess that is what you mean when you say you see the cursor change to
>>> the hand.  That would indicate that Chimera does get the ctrl-click mouse
>>> event.  So one idea is that Chimera gets the ctrl-click but the x,y
>>> coordinates of the click reported to Chimera are wrong so it doesn?t
>>> select anything.  As a test of this you could select everything (Select /
>>> Select All) then try a ctrl-click to select something and see if that
>>> deselects everything, as if the click was on the background.  It seems
>>> unlikely the mouse pointer position could be reported wrong since that
>>> would probably make pressing on menus and buttons not work as well.
>>> Another test, when you ctrl-left-drag Chimera draws a green outline box ?
>>> does that appear?  Another idea is that Chimera gets the ctrl-click but
>>> in never gets the mouse release when it actually does the selection.
>>> Have you tested that ctrl-click select actually works on the Windows
>>> machine?  If Windows falls back to the archaic Microsoft GDI graphics
>>> driver, then I believe ctrl-click does not work.  You can find out what
>>> driver Chimera is using with Chimera menu entry Help / Report a Bug?
>>> under ?Gathered Information?.  One last thing to check.  When you hover
>>> the mouse over and atom, a popup window shows the name of the atom.  That
>>> uses the same Chimera code as ctrl-click selection to figure out what
>>> atom the pointer is over.  Does that work?
>>> 
>>>    Tom
>>> 
>>> 
>>>> On Mar 30, 2015, at 3:50 PM, Hurt, Darrell (NIH/NIAID) [E]  wrote:
>>>> 
>>>> Hi Chimera friends,
>>>> 
>>>> I'm using the Microsoft Remote Desktop Mac client to connect to a
>>>> Microsoft Remote Desktop Server (an "RDS" running Windows Server 2012
>>>> R2). That RDS is serving out a Windows 8 environment and I'm running the
>>>> latest Chimera release in it very successfully. Except that selection by
>>>> picking (Ctrl-mouse_button_1) and centering (Ctrl-mouse_button_3) does
>>>> NOT work. When I try to select by picking, the cursor changes from the
>>>> arrow to hand momentarily. I also get this behavior when connecting to
>>>> the RDS via any other client. Any thoughts on what might be happening
>>>> and how to fix it?
>>>> 
>>>> Thanks,
>>>> Darrell
>>>> 
>>>> --
>>>> Darrell Hurt, Ph.D.
>>>> Acting Chief
>>>> Bioinformatics and Computational Biosciences Branch (BCBB)
>>>> OCICB/OSMO/OD/NIAID/NIH
>>>> 
>>>> 5601 Fishers Lane, 4A31
>>>> North Bethesda, MD 20852
>>>> Office: 240-669-2741
>>>> Mobile: 301-758-3559
>>>> Web: BCBB Home 
>>>> Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Page
>>>> s/bcbb.aspx#niaid_inlineNav_Anchor>
>>>> Twitter: @niaidbioit<https://twitter.com/niaidbioit> ,
>>>> @NIH3Dprint<https://twitter.com/nih3dprint>
>>>> 
>>>> Disclaimer: The information in this e-mail and any of its attachments
>>>> is confidential and may contain sensitive information. It should not be
>>>> used by anyone who is not the original intended recipient. If you have
>>>> received this e-mail in error please inform the sender and delete it
>>>> from your mailbox or any other storage devices. National Institute of
>>>> Allergy and Infectious Diseases shall not accept liability for any
>>>> statements made that are sender's own and not expressly made on behalf
>>>> of the NIAID by one of its representatives.
>>>> 
>>>> _______________________________________________
>>>> Chimera-users mailing list
>>>> Chimera-users at cgl.ucsf.edu
>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 



From jram at pusan.ac.kr  Tue Mar 31 07:04:11 2015
From: jram at pusan.ac.kr (Jayaraman T)
Date: Tue, 31 Mar 2015 23:04:11 +0900 (GMT)
Subject: [Chimera-users] Request for axes measurements
Message-ID: <1427810651292.7044.183.00.1.jram@pusan.ac.kr>

Hi, 
I'm Jayaraman, pursuing PhD in Protein Engineering at Pusan National University. 
I just want to calculate the Axes for specific set of helical residue CA atoms and then to calculate the angle between them. 
Is it possible with Chimera and if so, please do help me out that how to do it. 
It would be grateful and looking forward to hear at your earliest convenience. 
Thank you. 
- - 
      With warm regards
 
  Jram | 201493155
  PhD Scholar
  jram at pusan.ac.kr
  Bio molecular Engineering Lab
  Dept of Chemical Engineering
  Pusan National University
  Busan, South Korea
  +8210 9906 3680
-------------- next part --------------
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From meng at cgl.ucsf.edu  Tue Mar 31 08:24:39 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 31 Mar 2015 08:24:39 -0700
Subject: [Chimera-users] Request for axes measurements
In-Reply-To: <1427810651292.7044.183.00.1.jram@pusan.ac.kr>
References: <1427810651292.7044.183.00.1.jram@pusan.ac.kr>
Message-ID: <AC6C6B31-87F0-4940-AFC1-3913F7B228AC@cgl.ucsf.edu>

Hi Jram,
Yes, you can do it in Chimera. Example image:
<http://www.rbvi.ucsf.edu/chimera/features.html#axesplanes>

Please see the Axes/Planes/Centroids tool (in menu under Tools? Structure Analysis).  Click the Help button to see its manual page, or view the same page on our website here:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>

As explained on that page, if you choose Define axes, "each helix" option it will use backbone atoms N,CA,C.  I would recommend using that for helices instead of only CA atoms, which you could do, but it would be a lot more work: you would have to do each helix one by one, select only its CA atoms, and choose the "selected atoms" option instead of "each helix" and give the axis a name, each time.

Also as explained in more detail on that page, after you define the helix axes, it is easy to measure the angle between any two:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#objectlist>

The axis definition and measurement could also be done with commands instead of the GUIs, with commands "define" and "angle" respectively.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>

Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 31, 2015, at 7:04 AM, Jayaraman T <jram at pusan.ac.kr> wrote:

> Hi, 
> I'm Jayaraman, pursuing PhD in Protein Engineering at Pusan National University. 
> I just want to calculate the Axes for specific set of helical residue CA atoms and then to calculate the angle between them. 
> Is it possible with Chimera and if so, please do help me out that how to do it. 
> It would be grateful and looking forward to hear at your earliest convenience. 
> Thank you. 
> 




From meng at cgl.ucsf.edu  Tue Mar 31 18:48:56 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 31 Mar 2015 18:48:56 -0700
Subject: [Chimera-users] Request for axes measurements
In-Reply-To: <1427851577262.7044.88.00.1.jram@pusan.ac.kr>
References: <1427810651292.7044.183.00.1.jram@pusan.ac.kr>,
	<AC6C6B31-87F0-4940-AFC1-3913F7B228AC@cgl.ucsf.edu>
	<1427851577262.7044.88.00.1.jram@pusan.ac.kr>
Message-ID: <5EA5B993-E189-4FE2-9D24-B4FEE1DDDF90@cgl.ucsf.edu>

Hi,
You?re welcome, but I don?t have any further details than what is already given in the manual:

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>

It?s recommended you send Chimera questions to chimera-users at cgl.ucsf.edu instead of me directly, in case others may be able to provide better answers!
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 31, 2015, at 6:26 PM, Jayaraman T <jram at pusan.ac.kr> wrote:

> 
> Hi Elaine Meng, 
> Yes i could figure now the axes as well as angle measurements between them and thanks for your timely help.
> 
> I would be happy if you could tell me the principle on which these axes are calculated. I have noticed that it's from Eigen vector values that are calculated for the coordinates of the set of atoms. 
> 
> I'm really interested on the backend for this calculation particularly, might help a bit progressing more for my research. 
> 
> Thanks again. 




From jram at pusan.ac.kr  Tue Mar 31 19:21:15 2015
From: jram at pusan.ac.kr (Jayaraman T)
Date: Wed, 1 Apr 2015 11:21:15 +0900 (GMT)
Subject: [Chimera-users] Request for axes measurements
In-Reply-To: <5EA5B993-E189-4FE2-9D24-B4FEE1DDDF90@cgl.ucsf.edu>
References: <1427810651292.7044.183.00.1.jram@pusan.ac.kr>,
	<AC6C6B31-87F0-4940-AFC1-3913F7B228AC@cgl.ucsf.edu>
	<1427851577262.7044.88.00.1.jram@pusan.ac.kr>,
	<5EA5B993-E189-4FE2-9D24-B4FEE1DDDF90@cgl.ucsf.edu>
Message-ID: <1427854875281.7044.22.00.1.jram@pusan.ac.kr>


 Hi ..

 Thats fine and i'll do that. 

 Thank you. 

-&nbsp;-&nbsp;
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;With&nbsp;warm&nbsp;regards
&nbsp;
&nbsp;&nbsp;Jram&nbsp;|&nbsp;201493155
&nbsp;&nbsp;PhD&nbsp;Scholar
&nbsp;&nbsp;jram at pusan.ac.kr
&nbsp;&nbsp;Bio&nbsp;molecular&nbsp;Engineering&nbsp;Lab
&nbsp;&nbsp;Dept&nbsp;of&nbsp;Chemical&nbsp;Engineering
&nbsp;&nbsp;Pusan&nbsp;National&nbsp;University
&nbsp;&nbsp;Busan,&nbsp;South&nbsp;Korea
&nbsp;&nbsp;+8210&nbsp;9906&nbsp;3680