From meng at cgl.ucsf.edu  Tue Sep  1 09:23:30 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 1 Sep 2015 09:23:30 -0700
Subject: [Chimera-users] Rapid residue identification near ligands
In-Reply-To: <1441074721508.66820@wabash.edu>
References: <1441074721508.66820@wabash.edu>
Message-ID: <DC5ACFFE-0B86-4493-B1BD-81B0B1318388@cgl.ucsf.edu>

Greetings Korbin,

That ?smart initial display? makes use of Chimera?s automatic initial classification of atoms into ligand, ions, solvent, and main.  The rules for identifying those groups are outlined here, but you can just make use of it in Chimera by specifying ?ligand? in various commands:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/surface.html#surfcats>

Note, however, that rules can only go so far, and ?ligand? will often include things like sulfate, phosphate, glycerol, etc. that may be included in the crystallization experiment, but are not necessarily biologically relevant.

As for contacts, the smart initial display is very similar to the ribbons preset described here
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#interactive>
? in that they show residues within 3.6 A of ?ligand? or ?ions?

You could choose to define contacts with a different cutoff, either a simple distance between atomic centers (as in command-line zone specifications) or amount of VDW overlap, which takes into account the different sizes of different atom types (as in the ?findclash? command).
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>

Examples:

select ligand z<4.5
writesel ~/Desktop/contacts1.txt
   ?select all residues with any atom within 4.5 A of ?ligand? (which includes ?ligand?), write list of selected residues to file

color red ligand z<4.5 & protein
   ?color red protein residues with any atom within 4.5 A of ?ligand?

findclash ligand test protein overlap -0.5 hb 0 select true log true
     ?select all ligand-protein atom pairs with VDW surfaces within 0.5 A of each other and write pair information to Reply Log

For scripting looping through several structures, see <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.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 Aug 31, 2015, at 7:31 PM, Korbin West <khwest16 at wabash.edu> wrote:
> 
> Greetings all,
> 
> We need to be able to easily assign ligands to a chain (or chains) and to rapidly ID the residues in contact with it. I believe Chimera processes the structures and immediately displays ligands and maybe contacts, so it "knows" this information somehow. Does anyone know of a way to identify these easily and quickly so we can analyze large numbers of files? Also, if the output could be in the form of a text file or such that would be beneficial as well. Thank you all for your help. 
> 
> Best,
> Korbin West
> Wabash College




From tiger5201989 at 126.com  Tue Sep  1 08:27:35 2015
From: tiger5201989 at 126.com (=?utf-8?B?5p2O5pm65rW3?=)
Date: Tue, 1 Sep 2015 23:27:35 +0800
Subject: [Chimera-users] make a movie showing the process from an ASU model
	to the complete model of virus
Message-ID: <A6C37CE2-08A7-4536-A14E-F0D7D15AD892@126.com>

Hi,
I just obtained an atomic model of the asymmetric unit of an icosahedral T=7 virus capsid , and I want to make a movie to play the whole process from the ASU model to the full capsid model by imposing its icosahedral symmetry.
Please show me some examples of the command lines to generate such kind of movies. Thanks!

Best regards!

Zhihai



From 21620101152414 at stu.xmu.edu.cn  Tue Sep  1 20:46:58 2015
From: 21620101152414 at stu.xmu.edu.cn (=?utf-8?B?5p2O5pm65rW3?=)
Date: Wed, 2 Sep 2015 11:46:58 +0800
Subject: [Chimera-users] make a movie showing the process from an ASU model
	to the complete model of virus
Message-ID: <8BAA0123-B37E-41DA-A2AC-19C39833C8BB@stu.xmu.edu.cn>

Hi,
I just obtained an atomic model of the asymmetric unit of an icosahedral T=7 virus capsid , and I want to make a movie to play the whole process from the ASU model to the full capsid model by imposing its icosahedral symmetry.
Please show me some examples of the command lines to generate such kind of movies. Thanks!

Best regards!

Zhihai Li

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From valerio.chiarini at helsinki.fi  Wed Sep  2 01:04:22 2015
From: valerio.chiarini at helsinki.fi (Valerio Chiarini)
Date: Wed, 02 Sep 2015 11:04:22 +0300
Subject: [Chimera-users] chimera visualization
In-Reply-To: <D76AF1D1-41B5-40A9-8531-6CD3BC6A219A@cgl.ucsf.edu>
References: <20150831151946.Horde.veC2pm66tK1EIa8LqZPL0Q2@webmail.helsinki.fi>
	<D76AF1D1-41B5-40A9-8531-6CD3BC6A219A@cgl.ucsf.edu>
Message-ID: <20150902110422.Horde.Aos-i02bA_biD003q0VgVg1@webmail.helsinki.fi>

Hi Elaine,

the problem is that the structures I superimpose with matchmaker  
belong to the same pdb file, which means that I can select one chain  
but when I am about to show a residue (eg. ser) in stick the previous  
selection disappears and the serines of all structures are shown.

Valerio

Quoting Elaine Meng <meng at cgl.ucsf.edu>:

> Dear Valerio,
> It should be no problem.  Just superimpose the structures and show  
> their backbones as sticks, in the same way as for crystal structures.
>
> You could superimpose with MatchMaker (in menu under Tools?  
> Structure Comparison) or with Ensemble Match (in menu under Tools?  
> MD/Ensemble Analysis).
> <www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
>
> There are examples of using these tools in various tutorials:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.html>
>
> You can show backbone sticks with the Actions menu or with commands,  
> for example:
>
> open 1g1p
> ~ribbon
> disp @n,ca,c,o
>
> 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 Aug 31, 2015, at 5:19 AM, Valerio Chiarini  
>> <valerio.chiarini at helsinki.fi> wrote:
>>
>> Dear Elaine,
>> I would like to produce images from chimera showing an NMR bundle  
>> structure (backbone only) with stick-represented residues each one  
>> belonging to different single structures. I know it?s possible to  
>> do it with pymol but unfortunately the structures superimposition  
>> is not as good as in chimera. Would it be possible?
>> Thank you in advance,
>> Valerio





From meng at cgl.ucsf.edu  Wed Sep  2 09:29:49 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 2 Sep 2015 09:29:49 -0700
Subject: [Chimera-users] chimera visualization
In-Reply-To: <20150902110422.Horde.Aos-i02bA_biD003q0VgVg1@webmail.helsinki.fi>
References: <20150831151946.Horde.veC2pm66tK1EIa8LqZPL0Q2@webmail.helsinki.fi>
	<D76AF1D1-41B5-40A9-8531-6CD3BC6A219A@cgl.ucsf.edu>
	<20150902110422.Horde.Aos-i02bA_biD003q0VgVg1@webmail.helsinki.fi>
Message-ID: <74CBE6F2-7862-40E1-8435-1A47B8BE6F7E@cgl.ucsf.edu>

Dear Valerio,
It should not matter, each is still a separate model.  If you open the PDB as model #0 but it contains an NMR ensemble, the members are models #0.1, #0.2, ? etc.

I don?t know what steps you are using, but you can control exactly which structure(s) in which to show a particular residue in several ways.  Here are just two ways:

Ctrl-click to select the ribbon segment of just one residue in one structure (this mainly works for where they are not too close together), menu: Actions? Atoms/Bonds? show

Use a command, for example to show residue 45 of chain A in the 5th ensemble member of model 0 only:

display #0.5:45.A

You can use the balloon information that pops up when you hold the mouse cursor over some part a of a structure to tell you which model number and which residue it is.

Again, it is just the same as if you have multiple non-NMR structures open.
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 Sep 2, 2015, at 1:04 AM, Valerio Chiarini <valerio.chiarini at helsinki.fi> wrote:

> Hi Elaine,
> the problem is that the structures I superimpose with matchmaker belong to the same pdb file, which means that I can select one chain but when I am about to show a residue (eg. ser) in stick the previous selection disappears and the serines of all structures are shown.
> Valerio
> 
> Quoting Elaine Meng <meng at cgl.ucsf.edu>:
> 
>> Dear Valerio,
>> It should be no problem.  Just superimpose the structures and show their backbones as sticks, in the same way as for crystal structures.
>> 
>> You could superimpose with MatchMaker (in menu under Tools? Structure Comparison) or with Ensemble Match (in menu under Tools? MD/Ensemble Analysis).
>> <www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
>> 
>> There are examples of using these tools in various tutorials:
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html>
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.html>
>> 
>> You can show backbone sticks with the Actions menu or with commands, for example:
>> 
>> open 1g1p
>> ~ribbon
>> disp @n,ca,c,o
>> 
>> 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 Aug 31, 2015, at 5:19 AM, Valerio Chiarini <valerio.chiarini at helsinki.fi> wrote:
>>> 
>>> Dear Elaine,
>>> I would like to produce images from chimera showing an NMR bundle structure (backbone only) with stick-represented residues each one belonging to different single structures. I know it?s possible to do it with pymol but unfortunately the structures superimposition is not as good as in chimera. Would it be possible?
>>> Thank you in advance,
>>> Valerio
> 




From meng at cgl.ucsf.edu  Wed Sep  2 09:51:49 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 2 Sep 2015 09:51:49 -0700
Subject: [Chimera-users] make a movie showing the process from an ASU
	model to the complete model of virus
In-Reply-To: <8BAA0123-B37E-41DA-A2AC-19C39833C8BB@stu.xmu.edu.cn>
References: <8BAA0123-B37E-41DA-A2AC-19C39833C8BB@stu.xmu.edu.cn>
Message-ID: <46ACB536-0E4C-459C-918B-60B7C3D64756@cgl.ucsf.edu>

Hi Zhihai,
First figure out the commands to do what you want to show in Chimera.  After that?s done, then you can add commands for making it into a movie.

There are several example command files for movies, but they are showing different things than you want to show.  However, they will be useful for understanding general things like movement, controlling color and display, adding title text, and the movie-recording process.  See the ?making movies? page including discussion of content and links to example files:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#content>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples>

For what you want to do, it sounds like you just need to open your asymmetric unit structure and then use the ?sym? command to apply the symmetry.  However, I don?t know if your structure already includes the needed symmetry matrix information in it.  If not, you may need to specify it manually in the command.  See ?sym? manpage:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>

Also be aware that you wouldn?t always do everything within the movie script.  You might just save a Chimera session that has all the pre-made structures and text labels.  You could then restore the session and just use the script to show, hide, and move things at the appropriate times within the movie instead of re-making everything every time.

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 Sep 1, 2015, at 8:46 PM, ??? <21620101152414 at stu.xmu.edu.cn> wrote:

> Hi,
> I just obtained an atomic model of the asymmetric unit of an icosahedral T=7 virus capsid , and I want to make a movie to play the whole process from the ASU model to the full capsid model by imposing its icosahedral symmetry.
> Please show me some examples of the command lines to generate such kind of movies. Thanks!
> Best regards!
> Zhihai Li




From gtzotzos at me.com  Thu Sep  3 07:53:56 2015
From: gtzotzos at me.com (George Tzotzos)
Date: Thu, 03 Sep 2015 16:53:56 +0200
Subject: [Chimera-users] Distance in pi-interactions
Message-ID: <4E9733CD-2FA4-4F38-B74C-D6EDE4F9A72A@me.com>

I?m trying to work out the distance between two arene rings involved in pi-interactions. Is there a way of measuring the distance centre-to-centre of each arene ring? Or any other sensible way? I?m attaching a snapshot for easy reference.

Thanks in advance for any suggestions.

Regards

George
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From meng at cgl.ucsf.edu  Thu Sep  3 09:40:25 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 3 Sep 2015 09:40:25 -0700
Subject: [Chimera-users] Distance in pi-interactions
In-Reply-To: <4E9733CD-2FA4-4F38-B74C-D6EDE4F9A72A@me.com>
References: <4E9733CD-2FA4-4F38-B74C-D6EDE4F9A72A@me.com>
Message-ID: <0FC548EA-73AC-49A5-A9FE-E46BE940421F@cgl.ucsf.edu>

Hi George,
You can define a centroid for each ring and then measure the centroid-centroid distance.  This could be done with the Axes/Planes/Centroids graphical interface (in menu under Tools? Structure Analysis) or with the commands ?define? and ?distance?.

With the graphical tool you?d click the ?Define centroid?? button.  You?d need to select the first set of atoms in the main window (the usual way, Ctrl-click the first, Shift-Ctrl-click  to keep adding more atoms to the selection) before apply/OK..  Then you?d need to select the second set of atoms and define centroid again.  Then the dialog will list two centroids, and you can just choose both rows with the mouse to have the distance reported near the bottom of that same dialog.  Details:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>

With ?define centroid? you?d have to either select the atoms and use ?sel? or specify them directly by residue number and atom names, and you?d need to use ?define" twice to define the two different centroids.  Then you could use the ?distance? command with the IDs of the two centroids.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.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 Sep 3, 2015, at 7:53 AM, George Tzotzos <gtzotzos at me.com> wrote:
> 
> I?m trying to work out the distance between two arene rings involved in pi-interactions. Is there a way of measuring the distance centre-to-centre of each arene ring? Or any other sensible way? I?m attaching a snapshot for easy reference.
> Thanks in advance for any suggestions.
> Regards
> George




From gtzotzos at me.com  Thu Sep  3 09:44:10 2015
From: gtzotzos at me.com (George Tzotzos)
Date: Thu, 03 Sep 2015 18:44:10 +0200
Subject: [Chimera-users] Distance in pi-interactions
In-Reply-To: <0FC548EA-73AC-49A5-A9FE-E46BE940421F@cgl.ucsf.edu>
References: <4E9733CD-2FA4-4F38-B74C-D6EDE4F9A72A@me.com>
	<0FC548EA-73AC-49A5-A9FE-E46BE940421F@cgl.ucsf.edu>
Message-ID: <E179B4D6-6B84-4C68-B36B-92F30BE2CC45@me.com>

Thank you Elaine. Grateful as ever

George

> On 03 Sep 2015, at 18:40, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi George,
> You can define a centroid for each ring and then measure the centroid-centroid distance.  This could be done with the Axes/Planes/Centroids graphical interface (in menu under Tools? Structure Analysis) or with the commands ?define? and ?distance?.
> 
> With the graphical tool you?d click the ?Define centroid?? button.  You?d need to select the first set of atoms in the main window (the usual way, Ctrl-click the first, Shift-Ctrl-click  to keep adding more atoms to the selection) before apply/OK..  Then you?d need to select the second set of atoms and define centroid again.  Then the dialog will list two centroids, and you can just choose both rows with the mouse to have the distance reported near the bottom of that same dialog.  Details:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>
> 
> With ?define centroid? you?d have to either select the atoms and use ?sel? or specify them directly by residue number and atom names, and you?d need to use ?define" twice to define the two different centroids.  Then you could use the ?distance? command with the IDs of the two centroids.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.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 Sep 3, 2015, at 7:53 AM, George Tzotzos <gtzotzos at me.com> wrote:
>> 
>> I?m trying to work out the distance between two arene rings involved in pi-interactions. Is there a way of measuring the distance centre-to-centre of each arene ring? Or any other sensible way? I?m attaching a snapshot for easy reference.
>> Thanks in advance for any suggestions.
>> Regards
>> George
> 




From gtzotzos at me.com  Thu Sep  3 11:51:25 2015
From: gtzotzos at me.com (George Tzotzos)
Date: Thu, 03 Sep 2015 20:51:25 +0200
Subject: [Chimera-users] Distance in pi-interactions
In-Reply-To: <0FC548EA-73AC-49A5-A9FE-E46BE940421F@cgl.ucsf.edu>
References: <4E9733CD-2FA4-4F38-B74C-D6EDE4F9A72A@me.com>
	<0FC548EA-73AC-49A5-A9FE-E46BE940421F@cgl.ucsf.edu>
Message-ID: <095E2673-C446-4467-AE4A-DF22F99A2592@me.com>

Hi Elaine,

It just occurred to me. I used your advice and managed to determine the distance between the two centroids.

However, I would like to depict it graphically. Having created the two centroids, c1 and c2, I selected them both by Ctrl-click and Shift-Ctrl-click. In the control panel distance c1 c2 gives me the distance as expected. However, I have not manage to generate a distance line by using the Structure Measurements/Distance tool. I think, it?s because it does not recognise the centroids as atoms. I?m attaching a snapshot of this just in case it helps.

Best regards

George

 
> On 03 Sep 2015, at 18:40, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi George,
> You can define a centroid for each ring and then measure the centroid-centroid distance.  This could be done with the Axes/Planes/Centroids graphical interface (in menu under Tools? Structure Analysis) or with the commands ?define? and ?distance?.
> 
> With the graphical tool you?d click the ?Define centroid?? button.  You?d need to select the first set of atoms in the main window (the usual way, Ctrl-click the first, Shift-Ctrl-click  to keep adding more atoms to the selection) before apply/OK..  Then you?d need to select the second set of atoms and define centroid again.  Then the dialog will list two centroids, and you can just choose both rows with the mouse to have the distance reported near the bottom of that same dialog.  Details:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>
> 
> With ?define centroid? you?d have to either select the atoms and use ?sel? or specify them directly by residue number and atom names, and you?d need to use ?define" twice to define the two different centroids.  Then you could use the ?distance? command with the IDs of the two centroids.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.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 Sep 3, 2015, at 7:53 AM, George Tzotzos <gtzotzos at me.com> wrote:
>> 
>> I?m trying to work out the distance between two arene rings involved in pi-interactions. Is there a way of measuring the distance centre-to-centre of each arene ring? Or any other sensible way? I?m attaching a snapshot for easy reference.
>> Thanks in advance for any suggestions.
>> Regards
>> George
> 

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From meng at cgl.ucsf.edu  Thu Sep  3 12:03:02 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 3 Sep 2015 12:03:02 -0700
Subject: [Chimera-users] Distance in pi-interactions
In-Reply-To: <095E2673-C446-4467-AE4A-DF22F99A2592@me.com>
References: <4E9733CD-2FA4-4F38-B74C-D6EDE4F9A72A@me.com>
	<0FC548EA-73AC-49A5-A9FE-E46BE940421F@cgl.ucsf.edu>
	<095E2673-C446-4467-AE4A-DF22F99A2592@me.com>
Message-ID: <6AE0F026-1A95-4707-9232-18C79359FDB8@cgl.ucsf.edu>

Hi George,
That?s right, you cannot show a distance line between centroid objects.

If you want to do that, you have to use a different method to put a fake atom at each centroid, and then measure the distance between the two fake atoms.

The other method is described in this previous post:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-October/010383.html>

You would probably want to delete the centroid objects first, or just start over without centroid objects, so they won?t get in the way.
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 Sep 3, 2015, at 11:51 AM, George Tzotzos <gtzotzos at me.com> wrote:
> 
> Hi Elaine,
> It just occurred to me. I used your advice and managed to determine the distance between the two centroids.
> However, I would like to depict it graphically. Having created the two centroids, c1 and c2, I selected them both by Ctrl-click and Shift-Ctrl-click. In the control panel distance c1 c2 gives me the distance as expected. However, I have not manage to generate a distance line by using the Structure Measurements/Distance tool. I think, it?s because it does not recognise the centroids as atoms. I?m attaching a snapshot of this just in case it helps.
> Best regards
> George




From gtzotzos at me.com  Thu Sep  3 12:18:56 2015
From: gtzotzos at me.com (George Tzotzos)
Date: Thu, 03 Sep 2015 21:18:56 +0200
Subject: [Chimera-users] Distance in pi-interactions
In-Reply-To: <6AE0F026-1A95-4707-9232-18C79359FDB8@cgl.ucsf.edu>
References: <4E9733CD-2FA4-4F38-B74C-D6EDE4F9A72A@me.com>
	<0FC548EA-73AC-49A5-A9FE-E46BE940421F@cgl.ucsf.edu>
	<095E2673-C446-4467-AE4A-DF22F99A2592@me.com>
	<6AE0F026-1A95-4707-9232-18C79359FDB8@cgl.ucsf.edu>
Message-ID: <D71F42EB-D187-492C-B471-1BA649266ABE@me.com>

Grateful

George

> On 03 Sep 2015, at 21:03, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi George,
> That?s right, you cannot show a distance line between centroid objects.
> 
> If you want to do that, you have to use a different method to put a fake atom at each centroid, and then measure the distance between the two fake atoms.
> 
> The other method is described in this previous post:
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-October/010383.html>
> 
> You would probably want to delete the centroid objects first, or just start over without centroid objects, so they won?t get in the way.
> 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 Sep 3, 2015, at 11:51 AM, George Tzotzos <gtzotzos at me.com> wrote:
>> 
>> Hi Elaine,
>> It just occurred to me. I used your advice and managed to determine the distance between the two centroids.
>> However, I would like to depict it graphically. Having created the two centroids, c1 and c2, I selected them both by Ctrl-click and Shift-Ctrl-click. In the control panel distance c1 c2 gives me the distance as expected. However, I have not manage to generate a distance line by using the Structure Measurements/Distance tool. I think, it?s because it does not recognise the centroids as atoms. I?m attaching a snapshot of this just in case it helps.
>> Best regards
>> George
> 




From peggyschsu at gate.sinica.edu.tw  Mon Sep  7 17:08:41 2015
From: peggyschsu at gate.sinica.edu.tw (=?big5?B?s1yy0Kdn?=)
Date: Tue, 8 Sep 2015 08:08:41 +0800
Subject: [Chimera-users] Align and average intensity images in Chimera
Message-ID: <002001d0e9ca$8515d310$8f417930$@gate.sinica.edu.tw>

To whom it may concern,

 

I am willing to use Chimera for aligning several images from the structure
illumination microscope (SIM).

Here is the surface maps generated by Chimera from two images. 

cid:image005.jpg at 01D0E986.2CF5F370

 

After alignment by the tool ?Fit in Map?, they are aligned very well.

cid:image006.jpg at 01D0E986.2CF5F370

 

My next step is to average the intensity from two aligned images and
generate a new map which will be used to fit other images.

Can anyone tell me how to do it in Chimera? 

By the way, please also tell me what the values mean in the reply log. 

cid:image007.jpg at 01D0E986.2CF5F370

 

It helps me to use another software to complete the mission, if I can get
the rotation, voxel shift, or even scaling values from the alignment.

Thank you!

 

 

 

 

 

All Best,

Peggy Hsu, PhD

Institute of Cellular and Organismic Biology, Academia Sinica

128 Academia Rd Sec 2, Nankang, 

Taipei 11529, Taiwan

Tel: 886-2-2787-1531 (O)

email: peggyschsu at gate.sinica.edu.tw

 

 

 

 

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From goddard at sonic.net  Mon Sep  7 18:27:34 2015
From: goddard at sonic.net (Tom Goddard)
Date: Mon, 7 Sep 2015 18:27:34 -0700
Subject: [Chimera-users] Align and average intensity images in Chimera
In-Reply-To: <002001d0e9ca$8515d310$8f417930$@gate.sinica.edu.tw>
References: <002001d0e9ca$8515d310$8f417930$@gate.sinica.edu.tw>
Message-ID: <CAF3E882-CC04-4E9F-913C-51B0C5383A89@sonic.net>

Hi Peggy,

  To average two aligned 3d maps use the Chimera "vop add" command:

	vop add #0,1 scaleFactors 0.5,0.5

which will create a new map.  If the two maps have different intensity normalization than you probably want to normalize them to have the same intensities in getting the average.  For instance if the intensity values for map #1 are 10 times greater than map #0 I would instead use

	vop add #0,1 scaleFactors 0.5,0.05

to reduce the map #1 intensity by a factor of 10.  More info on vop add is in the Chimera manual

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

  The numbers in the reply log after using Fit Map give the motion required for the alignment.  The 3 row, 4 column matrix gives the 3x3 rotation matrix in the first 3 columns and the translation in the 4th column.  In your screen image, the translation is 0.92, 6.14, -0.04 so about 6 units in y.  Since your maps are from TIF images, Chimera may not know the pixel size (unless it is an OMETIFF), and will take it to be 1, so the shift of 6 units would be 6 pixels.  If Chimera does know the pixel size, say it is 0.2 microns, then it would have reported the shift as 1.2 in the reply log, since those numbers use physical units.  With light microscopy your z-spacing is usually different from x and y.  So you may want to set the correct numbers.  This is done in the Volume Viewer dialog, menu Features / Coordinates, the voxel size field.  For instance for x,y,z grid spacings 0.2, 0.2 and 0.3 microns enter 0.2 0.2 0.3.  This will be important if Fit Map rotates the image in doing the alignment.  More info on fitmap is in the Chimera manual.

	http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/fitmaps/fitmaps.html <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/fitmaps/fitmaps.html>

Chimera does not optimize scaling, so if your images have different magnification you will have to figure out a way to get them to the same magnification.

	Tom


> On Sep 7, 2015, at 5:08 PM, ??? wrote:
> 
> To whom it may concern,
>  
> I am willing to use Chimera for aligning several images from the structure illumination microscope (SIM).
> Here is the surface maps generated by Chimera from two images. 
> <image001.jpg>
>  
> After alignment by the tool ?Fit in Map?, they are aligned very well.
> <image002.jpg>
>  
> My next step is to average the intensity from two aligned images and generate a new map which will be used to fit other images.
> Can anyone tell me how to do it in Chimera? 
> By the way, please also tell me what the values mean in the reply log. 
> <image003.jpg>
>  
> It helps me to use another software to complete the mission, if I can get the rotation, voxel shift, or even scaling values from the alignment.
> Thank you!
>  
>  
>  
>  
>  
> All Best,
> Peggy Hsu, PhD
> Institute of Cellular and Organismic Biology, Academia Sinica
> 128 Academia Rd Sec 2, Nankang, 
> Taipei 11529, Taiwan
> Tel: 886-2-2787-1531 (O)
> email: peggyschsu at gate.sinica.edu.tw <mailto:peggyschsu at gate.sinica.edu.tw>
>  
>  
>  
>  
> _______________________________________________
> 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 <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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From mohan.pradhan at ymail.com  Tue Sep  8 01:52:07 2015
From: mohan.pradhan at ymail.com (Mohan Pradhan)
Date: Tue, 8 Sep 2015 08:52:07 +0000 (UTC)
Subject: [Chimera-users] setting solvent density threshold at 2.5 times of
 the bulk solvent density
Message-ID: <889203903.2902719.1441702327597.JavaMail.yahoo@mail.yahoo.com>

Dear Chimera users,
I am using the Volume Viewer application in Chimera to visualize the solvent density around protein at a threshold value of 2.5 times of the bulk solvent density.
My understanding is that the iso value corresponding to the bulk solvent density is marked by the peak in the plot of the volume viewer. I am then multiplying the iso value of the peak by 2.5Is this the right way of identifying regions in protein that have a solvent density of 2.5 times of the bulk solvent density?
Kindly suggest.
Thanks,Mohan
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From meng at cgl.ucsf.edu  Tue Sep  8 09:14:30 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 8 Sep 2015 09:14:30 -0700
Subject: [Chimera-users] setting solvent density threshold at 2.5 times
	of the bulk solvent density
In-Reply-To: <889203903.2902719.1441702327597.JavaMail.yahoo@mail.yahoo.com>
References: <889203903.2902719.1441702327597.JavaMail.yahoo@mail.yahoo.com>
Message-ID: <F9D78D3A-5F54-49DA-BA32-6397EAFE2AC1@cgl.ucsf.edu>

Dear Mohan,
This sounds like a general issue with EM, independent of Chimera, and may depend on the specific data set, experimental conditions, resolution, etc.

Unfortunately I don?t have an answer? perhaps some users who are expert in EM may be able to respond.
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 Sep 8, 2015, at 1:52 AM, Mohan Pradhan <mohan.pradhan at ymail.com> wrote:
> 
> Dear Chimera users,
> I am using the Volume Viewer application in Chimera to visualize the solvent density around protein at a threshold value of 2.5 times of the bulk solvent density.
> 
> My understanding is that the iso value corresponding to the bulk solvent density is marked by the peak in the plot of the volume viewer. I am then multiplying the iso value of the peak by 2.5
> Is this the right way of identifying regions in protein that have a solvent density of 2.5 times of the bulk solvent density?
> 
> Kindly suggest.
> Thanks,
> Mohan




From goddard at sonic.net  Tue Sep  8 13:07:17 2015
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 8 Sep 2015 13:07:17 -0700
Subject: [Chimera-users] setting solvent density threshold at 2.5 times
	of the bulk solvent density
In-Reply-To: <889203903.2902719.1441702327597.JavaMail.yahoo@mail.yahoo.com>
References: <889203903.2902719.1441702327597.JavaMail.yahoo@mail.yahoo.com>
Message-ID: <08D59423-56CE-46CB-A99B-DC082DF98AA6@sonic.net>

Hi Mohan,

  What you suggest is not correct.  I don't know if your map is from x-ray crystallography or electron microscopy but in both cases the map values are not literally "density" (ie mass per unit volume).  The processing of the maps often introduces negative values, and often puts the most common map value (peak histogram) at zero or even a negative value.  As Elaine, suggested you would need to ask someone expert in the processing of maps.  Chimera only uses the numeric values in the map file, it knows nothing about how those values relate to physical properties.  I have never seen an attempt to quantify mass density with x-ray or EM of biological samples.  X-ray researchers instead usually look at a iso-contour 1 or 1.5 or 2 standard deviations above the mean map value.

	Tom

> On Sep 8, 2015, at 1:52 AM, Mohan Pradhan wrote:
> 
> Dear Chimera users,
> 
> I am using the Volume Viewer application in Chimera to visualize the solvent density around protein at a threshold value of 2.5 times of the bulk solvent density.
> 
> My understanding is that the iso value corresponding to the bulk solvent density is marked by the peak in the plot of the volume viewer. I am then multiplying the iso value of the peak by 2.5
> Is this the right way of identifying regions in protein that have a solvent density of 2.5 times of the bulk solvent density?
> 
> Kindly suggest.
> 
> Thanks,
> Mohan
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From nattressclare at hotmail.co.uk  Tue Sep  8 06:59:50 2015
From: nattressclare at hotmail.co.uk (Clare Nattress)
Date: Tue, 8 Sep 2015 13:59:50 +0000
Subject: [Chimera-users] Help needed urgently
Message-ID: <AM2PR09MB017774387F28EA5C3C0A25DCF3530@AM2PR09MB0177.eurprd09.prod.outlook.com>


Hello there,


I have just sent this file to a 3D printers and sadly it has disintegrated when post printed and the model has been bathed and washed.


Attached is the link to the STL. file https://www.dropbox.com/sh/2nytyw6989h0v2l/AADiXrhb8mUfi53J95co-Bvja?dl=0


I was wondering how I could perhaps make the structure 3D print safe. Would you be able to help me join the bonds and also make them a lot thicker?


Any help would be most appreciated as this is meant to be in an exhibition come Friday.


Best Wishes,



Clare Nattress
Artist/Writer
www.clare-nattress.com
LinkedIn - Clare Nattress
@ClareNattress

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From meng at cgl.ucsf.edu  Tue Sep  8 14:24:18 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 8 Sep 2015 14:24:18 -0700
Subject: [Chimera-users] Help needed urgently
In-Reply-To: <AM2PR09MB017774387F28EA5C3C0A25DCF3530@AM2PR09MB0177.eurprd09.prod.outlook.com>
References: <AM2PR09MB017774387F28EA5C3C0A25DCF3530@AM2PR09MB0177.eurprd09.prod.outlook.com>
Message-ID: <3089AB40-4CC7-4621-80B4-7B39FEC1123F@cgl.ucsf.edu>

Dear Clare,
It is recommended to use the ?struts? command on your structure in Chimera to strengthen it before exporting as STL.  As you have seen, the usual display ribbons alone are generally too flimsy for 3D printing.  This command has a few options.  By default, it fattens up the ribbons and adds strengthening rods.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/struts.html>

Example commands in Chimera:
open 1yvx
~display
struts @ca

(?then export as STL)

We don?t have tools in Chimera for editing the STL after it has been created, sorry.
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 Sep 8, 2015, at 6:59 AM, Clare Nattress <nattressclare at hotmail.co.uk> wrote:
> 
> Hello there,
> I have just sent this file to a 3D printers and sadly it has disintegrated when post printed and the model has been bathed and washed. 
> 
> Attached is the link to the STL. file https://www.dropbox.com/sh/2nytyw6989h0v2l/AADiXrhb8mUfi53J95co-Bvja?dl=0
> 
> I was wondering how I could perhaps make the structure 3D print safe. Would you be able to help me join the bonds and also make them a lot thicker?
> 
> Any help would be most appreciated as this is meant to be in an exhibition come Friday. 
> 
> Best Wishes,
> 
> Clare Nattress
> Artist/Writer
> www.clare-nattress.com
> LinkedIn - Clare Nattress
> @ClareNattress




From goddard at sonic.net  Tue Sep  8 15:49:29 2015
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 8 Sep 2015 15:49:29 -0700
Subject: [Chimera-users] Help needed urgently
In-Reply-To: <3089AB40-4CC7-4621-80B4-7B39FEC1123F@cgl.ucsf.edu>
References: <AM2PR09MB017774387F28EA5C3C0A25DCF3530@AM2PR09MB0177.eurprd09.prod.outlook.com>
	<3089AB40-4CC7-4621-80B4-7B39FEC1123F@cgl.ucsf.edu>
Message-ID: <CF28C502-6B8F-48C7-ADBC-C919B1C4FB4D@sonic.net>

Hi Clare,

  I don't think struts alone are going to fix your problem.  The ribbon is too thin unless you have some phenomenal printer or you are printing it large (e.g. 10 inch diameter).  The turns look to be about 1/200th diameter of the model.  At least with the uPrint printers we have the dot size is only 1/100 inch and you probably need at least 5x that to hold together.  If you are using a powder color printer those models are much more fragile than the ABS plastic printers.  At any rate I think you will have to thicken your ribbon a lot and the Chimera Ribbon Style Editor (under menu Tools / Depiction) will let you do that.  Even much thicker it will still need cross-bracing struts or it will be very fragile.

	Tom



> On Sep 8, 2015, at 2:24 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Dear Clare,
> It is recommended to use the ?struts? command on your structure in Chimera to strengthen it before exporting as STL.  As you have seen, the usual display ribbons alone are generally too flimsy for 3D printing.  This command has a few options.  By default, it fattens up the ribbons and adds strengthening rods.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/struts.html>
> 
> Example commands in Chimera:
> open 1yvx
> ~display
> struts @ca
> 
> (?then export as STL)
> 
> We don?t have tools in Chimera for editing the STL after it has been created, sorry.
> 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 Sep 8, 2015, at 6:59 AM, Clare Nattress <nattressclare at hotmail.co.uk> wrote:
>> 
>> Hello there,
>> I have just sent this file to a 3D printers and sadly it has disintegrated when post printed and the model has been bathed and washed. 
>> 
>> Attached is the link to the STL. file https://www.dropbox.com/sh/2nytyw6989h0v2l/AADiXrhb8mUfi53J95co-Bvja?dl=0
>> 
>> I was wondering how I could perhaps make the structure 3D print safe. Would you be able to help me join the bonds and also make them a lot thicker?
>> 
>> Any help would be most appreciated as this is meant to be in an exhibition come Friday. 
>> 
>> Best Wishes,
>> 
>> Clare Nattress
>> Artist/Writer
>> www.clare-nattress.com
>> LinkedIn - Clare Nattress
>> @ClareNattress
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 

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From agszabo at bell.net  Tue Sep  8 14:03:20 2015
From: agszabo at bell.net (A G Szabo)
Date: Tue, 8 Sep 2015 17:03:20 -0400
Subject: [Chimera-users] question
Message-ID: <BLU437-SMTP530A7BA771C59DFB35C6F5CF530@phx.gbl>

I go to tools and open the sequence of the protein that I am interested in.

The minimum number of amino acids in a row that I can select is 2.

I am interested in visualizing a selected number of amino acids that are not
in linked to one  another.

Eg. A specific Lys residue in a helical sequence.

I have found a work  around. I highlight two adjacent residues, and
visualize the two of  them as sticks. I  then select the amino acid I do not
wish to highlight together with the amino acid on the other side of the one
that  I am interested in. I can that way eventually deselect and not
highlight the amino acid I am not interested  in.  

There has to be a simpler way.

Thanks for  your assistance.

Arthur G. Szabo
Professor Emeritus Chemistry
Wilfrid Laurier University.
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From nattressclare at hotmail.co.uk  Tue Sep  8 15:17:57 2015
From: nattressclare at hotmail.co.uk (Clare Nattress)
Date: Tue, 8 Sep 2015 22:17:57 +0000
Subject: [Chimera-users] Help needed urgently
In-Reply-To: <3089AB40-4CC7-4621-80B4-7B39FEC1123F@cgl.ucsf.edu>
References: <AM2PR09MB017774387F28EA5C3C0A25DCF3530@AM2PR09MB0177.eurprd09.prod.outlook.com>,
	<3089AB40-4CC7-4621-80B4-7B39FEC1123F@cgl.ucsf.edu>
Message-ID: <AM2PR09MB0177C5E1AEEA7371D8EAB695F3530@AM2PR09MB0177.eurprd09.prod.outlook.com>

Dear Elaine,

Thank you so much for getting back to me so quickly. I have applied the command and will send again to my 3D printers. 

Best Regards,
Clare Nattress

________________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: 08 September 2015 21:24
To: Clare Nattress
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Help needed urgently

Dear Clare,
It is recommended to use the ?struts? command on your structure in Chimera to strengthen it before exporting as STL.  As you have seen, the usual display ribbons alone are generally too flimsy for 3D printing.  This command has a few options.  By default, it fattens up the ribbons and adds strengthening rods.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/struts.html>

Example commands in Chimera:
open 1yvx
~display
struts @ca

(?then export as STL)

We don?t have tools in Chimera for editing the STL after it has been created, sorry.
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 Sep 8, 2015, at 6:59 AM, Clare Nattress <nattressclare at hotmail.co.uk> wrote:
>
> Hello there,
> I have just sent this file to a 3D printers and sadly it has disintegrated when post printed and the model has been bathed and washed.
>
> Attached is the link to the STL. file https://www.dropbox.com/sh/2nytyw6989h0v2l/AADiXrhb8mUfi53J95co-Bvja?dl=0
>
> I was wondering how I could perhaps make the structure 3D print safe. Would you be able to help me join the bonds and also make them a lot thicker?
>
> Any help would be most appreciated as this is meant to be in an exhibition come Friday.
>
> Best Wishes,
>
> Clare Nattress
> Artist/Writer
> www.clare-nattress.com
> LinkedIn - Clare Nattress
> @ClareNattress




From meng at cgl.ucsf.edu  Tue Sep  8 16:00:47 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 8 Sep 2015 16:00:47 -0700
Subject: [Chimera-users] question
In-Reply-To: <BLU437-SMTP530A7BA771C59DFB35C6F5CF530@phx.gbl>
References: <BLU437-SMTP530A7BA771C59DFB35C6F5CF530@phx.gbl>
Message-ID: <A8BEF0E9-8079-468B-AF4D-D5702C3CE062@cgl.ucsf.edu>

Hi Arthur,
One can definitely select only one residue in the sequence ? just drag a very short distance.  Maybe it will be easier if you increase the font size in the Sequence dialog (in Sequence window menu, choose Preferences? Appearance, then in the "Single sequences" section on the right increase the point size, press return).
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 Sep 8, 2015, at 2:03 PM, A G Szabo <agszabo at bell.net> wrote:
> 
> I go to tools and open the sequence of the protein that I am interested in.
> 
> The minimum number of amino acids in a row that I can select is 2.
> I am interested in visualizing a selected number of amino acids that are not in linked to one  another.
> Eg. A specific Lys residue in a helical sequence.
> I have found a work  around. I highlight two adjacent residues, and visualize the two of  them as sticks. I  then select the amino acid I do not wish to highlight together with the amino acid on the other side of the one that  I am interested in. I can that way eventually deselect and not highlight the amino acid I am not interested  in. 
> 
> There has to be a simpler way.
> Thanks for  your assistance.
> Arthur G. Szabo
> Professor Emeritus Chemistry
> Wilfrid Laurier University.




From smith_liu123 at 163.com  Tue Sep  8 18:54:03 2015
From: smith_liu123 at 163.com (Smith Liu)
Date: Wed, 9 Sep 2015 09:54:03 +0800 (CST)
Subject: [Chimera-users] on mrc map
Message-ID: <4e74eb54.4a31.14fafcf4fa3.Coremail.smith_liu123@163.com>

Dear All,


Suppose I have a mcr map for a protein of 4 subunits. Will you please introduce to me how to split the whole map to 4 different maps, with each map corresponding to the part of each subunit in the whole map, without loosing any data in the spitted map  in comparison to that specific subunit part of the whole map?


Best regards.


Smith
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From meng at cgl.ucsf.edu  Wed Sep  9 09:30:40 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 9 Sep 2015 09:30:40 -0700
Subject: [Chimera-users] on mrc map
In-Reply-To: <4e74eb54.4a31.14fafcf4fa3.Coremail.smith_liu123@163.com>
References: <4e74eb54.4a31.14fafcf4fa3.Coremail.smith_liu123@163.com>
Message-ID: <6040BF4E-8F3E-4727-9ABE-779DC0DE96DC@cgl.ucsf.edu>

Dear Smith,
This is a broad question, with different approaches possible depending on the data and how much is known about it.  General possibilities are:
 
(A) segment the map, use segmentation surfaces to mask map to create new maps (see choices in the File menu of Segment Map)
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/segment.html>

(B) fit atomic structures, or if no atomic structures, place markers into the four areas, color each structure or marker differently, use Color Zone to color nearby map to match them and then split map by color
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html>

Each takes several steps and requires interaction and judgment, i.e. I can?t just give a recipe that exactly produces the desired result. 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 Sep 8, 2015, at 6:54 PM, Smith Liu <smith_liu123 at 163.com> wrote:

> Dear All,
> 
> Suppose I have a mcr map for a protein of 4 subunits. Will you please introduce to me how to split the whole map to 4 different maps, with each map corresponding to the part of each subunit in the whole map, without loosing any data in the spitted map  in comparison to that specific subunit part of the whole map?
> 
> Best regards.
> 
> Smith




From agszabo at bell.net  Tue Sep  8 16:29:53 2015
From: agszabo at bell.net (A G Szabo)
Date: Tue, 8 Sep 2015 19:29:53 -0400
Subject: [Chimera-users] question
In-Reply-To: <A8BEF0E9-8079-468B-AF4D-D5702C3CE062@cgl.ucsf.edu>
References: <BLU437-SMTP530A7BA771C59DFB35C6F5CF530@phx.gbl>
	<A8BEF0E9-8079-468B-AF4D-D5702C3CE062@cgl.ucsf.edu>
Message-ID: <BLU436-SMTP141DBE32775FAE09E9ADD6DCF530@phx.gbl>

Elaine

Our are wonderful!!

However I  figured it out by slowly moving the cursor from the left to the right. If I  move it  from the right to the left it seems to  want  to select two residues.

However, another matter which  perhaps I just haven't tried hard enough.

Is there a way in which I can alter the font size of the residue labels i.e. a bolder lettering.

Thank you for your continued assistance

Arthur

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: September-08-15 7:01 PM
To: A G Szabo
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] question

Hi Arthur,
One can definitely select only one residue in the sequence ? just drag a very short distance.  Maybe it will be easier if you increase the font size in the Sequence dialog (in Sequence window menu, choose Preferences? Appearance, then in the "Single sequences" section on the right increase the point size, press return).
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 Sep 8, 2015, at 2:03 PM, A G Szabo <agszabo at bell.net> wrote:
> 
> I go to tools and open the sequence of the protein that I am interested in.
> 
> The minimum number of amino acids in a row that I can select is 2.
> I am interested in visualizing a selected number of amino acids that are not in linked to one  another.
> Eg. A specific Lys residue in a helical sequence.
> I have found a work  around. I highlight two adjacent residues, and visualize the two of  them as sticks. I  then select the amino acid I do not wish to highlight together with the amino acid on the other side of the one that  I am interested in. I can that way eventually deselect and not highlight the amino acid I am not interested  in. 
> 
> There has to be a simpler way.
> Thanks for  your assistance.
> Arthur G. Szabo
> Professor Emeritus Chemistry
> Wilfrid Laurier University.





From CAG116 at pitt.edu  Wed Sep  9 08:28:53 2015
From: CAG116 at pitt.edu (Guirguis, Christopher Amin)
Date: Wed, 9 Sep 2015 15:28:53 +0000
Subject: [Chimera-users] Question regarding 3D surface coordinates
Message-ID: <8E4AE5C6-EC70-4E2F-863A-34718BC34A55@pitt.edu>

Hello,

A quick question: is there any output file type where coordinates of the surfaces are typed rather than just the center of the individual atoms? I want to insert my molecules into a modeling software like Maya to create an .obj file for viewing on mobile devices. Thank you for your time.

Best,

Chris Guirguis


From meng at cgl.ucsf.edu  Wed Sep  9 15:07:40 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 9 Sep 2015 15:07:40 -0700
Subject: [Chimera-users] label font and fontsize
In-Reply-To: <BLU436-SMTP141DBE32775FAE09E9ADD6DCF530@phx.gbl>
References: <BLU437-SMTP530A7BA771C59DFB35C6F5CF530@phx.gbl>
	<A8BEF0E9-8079-468B-AF4D-D5702C3CE062@cgl.ucsf.edu>
	<BLU436-SMTP141DBE32775FAE09E9ADD6DCF530@phx.gbl>
Message-ID: <4EC23251-F616-4433-A0BF-7AEBA5B0945D@cgl.ucsf.edu>

Hi Arthur,

You can change  the font (e.g. bold) and size of the main-window labels in the Preferences.  From the Chimera menu choose Favorites? Preferences, in the Preferences dialog choose Category: Labels.  After you change the settings to your liking, remember to click Save if you want them to apply to later uses of Chimera.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Labels>

Cheers,
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 Sep 8, 2015, at 4:29 PM, A G Szabo <agszabo at bell.net> wrote:

> Elaine
> 
> Our are wonderful!!
> 
> However I  figured it out by slowly moving the cursor from the left to the right. If I  move it  from the right to the left it seems to  want  to select two residues.
> 
> However, another matter which  perhaps I just haven't tried hard enough.
> 
> Is there a way in which I can alter the font size of the residue labels i.e. a bolder lettering.
> 
> Thank you for your continued assistance
> 
> Arthur





From meng at cgl.ucsf.edu  Wed Sep  9 15:11:25 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 9 Sep 2015 15:11:25 -0700
Subject: [Chimera-users] Question regarding 3D surface coordinates
In-Reply-To: <8E4AE5C6-EC70-4E2F-863A-34718BC34A55@pitt.edu>
References: <8E4AE5C6-EC70-4E2F-863A-34718BC34A55@pitt.edu>
Message-ID: <C0526E66-1444-4E48-8B5D-177B5AFA2765@cgl.ucsf.edu>

Hi Chris,
Take a look at the format choices in File? Export a Scene, details and caveats here:
 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html>

It includes OBJ (surfaces only), STL, and some others you might be interested in.
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 Sep 9, 2015, at 8:28 AM, Guirguis, Christopher Amin <CAG116 at pitt.edu> wrote:

> Hello,
> 
> A quick question: is there any output file type where coordinates of the surfaces are typed rather than just the center of the individual atoms? I want to insert my molecules into a modeling software like Maya to create an .obj file for viewing on mobile devices. Thank you for your time.
> 
> Best,
> 
> Chris Guirguis




From mohan.pradhan at ymail.com  Thu Sep 10 09:20:17 2015
From: mohan.pradhan at ymail.com (Mohan Pradhan)
Date: Thu, 10 Sep 2015 16:20:17 +0000 (UTC)
Subject: [Chimera-users] setting solvent density threshold at 2.5 times
 of the bulk solvent density
In-Reply-To: <08D59423-56CE-46CB-A99B-DC082DF98AA6@sonic.net>
References: <08D59423-56CE-46CB-A99B-DC082DF98AA6@sonic.net>
Message-ID: <1931929574.527688.1441902018233.JavaMail.yahoo@mail.yahoo.com>

Dear Tom and Elaine,
? ? ? ? ? ? ? ? ? Thank you both for your response. I think I was not very clear with my question. Let me rephrase my query here again in more detail.

I have done Molcular Dynamics simulation of my protein in explicit solvent. Following which I calculated the water density from the trajectory using grid-based approach with grid cells of size 0.5 X 0.5 X 0.5 ?. A sample of the grid-based density output file is attached here for your reference.

We then used Chimera to visualize the map using the volume viewer menu. We are attaching two image files here at two different isocountor threshold cutoff. One which was set to the isovalue at which we observe the maximum value of the historgram at an isovalue of 37. (image-1)

Second we set it to 2.5 times that isovalue 2.5 X 37 ~ 93) (Image-2).

The issue we wanted to clarify was what do these histogram actually depict with regard to the input grid file?

What is the histogram depicting at an iso-value of zero?

Why is there a sinusodial curve for the histogram towards the lower isovlaue?
Thanks,Mohan 


     On Wednesday, September 9, 2015 4:07 AM, Tom Goddard <goddard at sonic.net> wrote:
   

 Hi Mohan,
? What you suggest is not correct. ?I don't know if your map is from x-ray crystallography or electron microscopy but in both cases the map values are not literally "density" (ie mass per unit volume). ?The processing of the maps often introduces negative values, and often puts the most common map value (peak histogram) at zero or even a negative value. ?As Elaine, suggested you would need to ask someone expert in the processing of maps. ?Chimera only uses the numeric values in the map file, it knows nothing about how those values relate to physical properties. ?I have never seen an attempt to quantify mass density with x-ray or EM of biological samples. ?X-ray researchers instead usually look at a iso-contour 1 or 1.5 or 2 standard deviations above the mean map value.
 Tom

On Sep 8, 2015, at 1:52 AM, Mohan Pradhan wrote:
Dear Chimera users,
I am using the Volume Viewer application in Chimera to visualize the solvent density around protein at a threshold value of 2.5 times of the bulk solvent density.
My understanding is that the iso value corresponding to the bulk solvent density is marked by the peak in the plot of the volume viewer. I am then multiplying the iso value of the peak by 2.5Is this the right way of identifying regions in protein that have a solvent density of 2.5 times of the bulk solvent density?
Kindly suggest.
Thanks,Mohan_______________________________________________
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 Sep 10 09:50:10 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 10 Sep 2015 09:50:10 -0700
Subject: [Chimera-users] setting solvent density threshold at 2.5 times
	of the bulk solvent density
In-Reply-To: <1931929574.527688.1441902018233.JavaMail.yahoo@mail.yahoo.com>
References: <08D59423-56CE-46CB-A99B-DC082DF98AA6@sonic.net>
	<1931929574.527688.1441902018233.JavaMail.yahoo@mail.yahoo.com>
Message-ID: <011E5E93-79EC-498C-A269-DB22ED3CBD01@cgl.ucsf.edu>

Dear Mohan,
Yes, that is a very different question now that we know you calculated the map from MD.

Everything depends on how you calculated the ?density" to produce the input map. Rather than an actual density, it may just be counts of how many times there was a water inside each grid cell (such as if you used the occupancy analysis in the MD Movie tool).  If so, you could divide those values by the number of MD frames that the counts came from, to make them more meaningful; for example, a count of 40 for a sample of 100 MD frames means that a grid cell had a water in it 40% of the time. MD Movie occupancy analysis:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#occupancy>

Volume Viewer is just displaying this raw data, it isn?t doing anything to transform or normalize it. The data is just a grid of points with associated values.  The histogram shows the range of values horizontally, and the bar heights show how many grid points have those values.  It is not useful to show the contour surface for values near zero, and I would not read too much into the shape of the histogram.  The high value near zero just means many grid points have values of zero, and the other maximum just means many grid points have values of 37.  If you use a different size grid cell and/or sampled a different number of MD frames (if the values are simply counts), the maximum would be a different value.

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 Sep 10, 2015, at 9:20 AM, Mohan Pradhan <mohan.pradhan at ymail.com> wrote:
> 
> Dear Tom and Elaine,
>                   Thank you both for your response. I think I was not very clear with my question. Let me rephrase my query here again in more detail.
> 
> I have done Molcular Dynamics simulation of my protein in explicit solvent. Following which I calculated the water density from the trajectory using grid-based approach with grid cells of size 0.5 X 0.5 X 0.5 ?. A sample of the grid-based density output file is attached here for your reference.
> 
> We then used Chimera to visualize the map using the volume viewer menu. We are attaching two image files here at two different isocountor threshold cutoff. One which was set to the isovalue at which we observe the maximum value of the historgram at an isovalue of 37. (image-1)
> 
> Second we set it to 2.5 times that isovalue 2.5 X 37 ~ 93) (Image-2).
> 
> The issue we wanted to clarify was what do these histogram actually depict with regard to the input grid file?
> 
> What is the histogram depicting at an iso-value of zero?
> 
> Why is there a sinusodial curve for the histogram towards the lower isovlaue?
> 
> Thanks,
> Mohan
> 
> 



From CAG116 at pitt.edu  Wed Sep  9 15:16:26 2015
From: CAG116 at pitt.edu (Guirguis, Christopher Amin)
Date: Wed, 9 Sep 2015 22:16:26 +0000
Subject: [Chimera-users] Question regarding 3D surface coordinates
In-Reply-To: <C0526E66-1444-4E48-8B5D-177B5AFA2765@cgl.ucsf.edu>
References: <8E4AE5C6-EC70-4E2F-863A-34718BC34A55@pitt.edu>,
	<C0526E66-1444-4E48-8B5D-177B5AFA2765@cgl.ucsf.edu>
Message-ID: <5625DD91-0F4E-457F-93B4-05462FAE01E3@pitt.edu>

Dr. Meant,

That is wonderful. Thank you for your help. May I ask what the scope of usage is for this software? In regards to copyright and such, am I allowed to use the models I make in a mobile app for iPhone?

Best,

Chris Guirguis

> On Sep 9, 2015, at 6:11 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Chris,
> Take a look at the format choices in File? Export a Scene, details and caveats here:
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html>
> 
> It includes OBJ (surfaces only), STL, and some others you might be interested in.
> 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 Sep 9, 2015, at 8:28 AM, Guirguis, Christopher Amin <CAG116 at pitt.edu> wrote:
>> 
>> Hello,
>> 
>> A quick question: is there any output file type where coordinates of the surfaces are typed rather than just the center of the individual atoms? I want to insert my molecules into a modeling software like Maya to create an .obj file for viewing on mobile devices. Thank you for your time.
>> 
>> Best,
>> 
>> Chris Guirguis
> 



From meng at cgl.ucsf.edu  Thu Sep 10 12:22:58 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 10 Sep 2015 12:22:58 -0700
Subject: [Chimera-users] Question regarding 3D surface coordinates
In-Reply-To: <5625DD91-0F4E-457F-93B4-05462FAE01E3@pitt.edu>
References: <8E4AE5C6-EC70-4E2F-863A-34718BC34A55@pitt.edu>
	<C0526E66-1444-4E48-8B5D-177B5AFA2765@cgl.ucsf.edu>
	<5625DD91-0F4E-457F-93B4-05462FAE01E3@pitt.edu>
Message-ID: <1A184B62-8DC9-41CA-A2F8-BF2D350AA06B@cgl.ucsf.edu>

Hi Chris,
We?ll have to get back to you later on that.  Probably next week.
Best,
Elaine

> On Sep 9, 2015, at 3:16 PM, Guirguis, Christopher Amin <CAG116 at pitt.edu> wrote:
> 
> Dr. Meant,
> 
> That is wonderful. Thank you for your help. May I ask what the scope of usage is for this software? In regards to copyright and such, am I allowed to use the models I make in a mobile app for iPhone?
> 
> Best,
> 
> Chris Guirguis
> 
>> On Sep 9, 2015, at 6:11 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Hi Chris,
>> Take a look at the format choices in File? Export a Scene, details and caveats here:
>> 
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html>
>> 
>> It includes OBJ (surfaces only), STL, and some others you might be interested in.
>> 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 Sep 9, 2015, at 8:28 AM, Guirguis, Christopher Amin <CAG116 at pitt.edu> wrote:
>>> 
>>> Hello,
>>> 
>>> A quick question: is there any output file type where coordinates of the surfaces are typed rather than just the center of the individual atoms? I want to insert my molecules into a modeling software like Maya to create an .obj file for viewing on mobile devices. Thank you for your time.
>>> 
>>> Best,
>>> 
>>> Chris Guirguis




From goddard at sonic.net  Thu Sep 10 12:48:36 2015
From: goddard at sonic.net (Tom Goddard)
Date: Thu, 10 Sep 2015 12:48:36 -0700
Subject: [Chimera-users] Question regarding 3D surface coordinates
In-Reply-To: <5625DD91-0F4E-457F-93B4-05462FAE01E3@pitt.edu>
References: <8E4AE5C6-EC70-4E2F-863A-34718BC34A55@pitt.edu>
	<C0526E66-1444-4E48-8B5D-177B5AFA2765@cgl.ucsf.edu>
	<5625DD91-0F4E-457F-93B4-05462FAE01E3@pitt.edu>
Message-ID: <52B70F1E-C259-4835-8DAB-74034FADFC3F@sonic.net>

Hi Chris,

  If you use Chimera for commercial purposes it requires a negotiated license.  If you use it for academic purposes then the academic license is online and you agree to it when you download the program.  So it depends on whether your iPhone app is ?commercial? ? probably that comes down to do you charge money for it.  If you think your use is a gray area then you should discuss it with the head of our lab, Tom Ferrin.

	Tom


> On Sep 9, 2015, at 3:16 PM, Guirguis, Christopher Amin <CAG116 at pitt.edu> wrote:
> 
> Dr. Meant,
> 
> That is wonderful. Thank you for your help. May I ask what the scope of usage is for this software? In regards to copyright and such, am I allowed to use the models I make in a mobile app for iPhone?
> 
> Best,
> 
> Chris Guirguis
> 
>> On Sep 9, 2015, at 6:11 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Hi Chris,
>> Take a look at the format choices in File? Export a Scene, details and caveats here:
>> 
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html>
>> 
>> It includes OBJ (surfaces only), STL, and some others you might be interested in.
>> 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 Sep 9, 2015, at 8:28 AM, Guirguis, Christopher Amin <CAG116 at pitt.edu> wrote:
>>> 
>>> Hello,
>>> 
>>> A quick question: is there any output file type where coordinates of the surfaces are typed rather than just the center of the individual atoms? I want to insert my molecules into a modeling software like Maya to create an .obj file for viewing on mobile devices. Thank you for your time.
>>> 
>>> Best,
>>> 
>>> Chris Guirguis
>> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From goddard at sonic.net  Thu Sep 10 13:01:50 2015
From: goddard at sonic.net (Tom Goddard)
Date: Thu, 10 Sep 2015 13:01:50 -0700
Subject: [Chimera-users] setting solvent density threshold at 2.5 times
	of the bulk solvent density
In-Reply-To: <011E5E93-79EC-498C-A269-DB22ED3CBD01@cgl.ucsf.edu>
References: <08D59423-56CE-46CB-A99B-DC082DF98AA6@sonic.net>
	<1931929574.527688.1441902018233.JavaMail.yahoo@mail.yahoo.com>
	<011E5E93-79EC-498C-A269-DB22ED3CBD01@cgl.ucsf.edu>
Message-ID: <646AB4DD-0837-4BD9-8502-09C36CFA3B07@sonic.net>

Hi Mohan,

  I think your occupancy map histogram has a peak at 0 and peak at 37 is explained as follows.  The peak near means there are many grid points in the volume that water never reaches.  This must be the volume occupied by the protein.  The peak at 37 are grid points outside the protein where usually 37 waters are found per grid point over the course of your MD frames.  So I think you are correctly interpreting the values.  Using a threshold 2.5 * 37 would show grid points where waters are found 2.5 times more often than average ? you might think of those locations as ?bound waters? ? I?d expect them to be all at points adjacent to the protein.

  One extra bit of info about the histogram, the horizontal axis is the occupancy value (0-354 for your data) and the vertical axis is the number of grid points having a specific occupancy value.  The horizontal axis is linear, but the vertical axis is logarithmically scaled.  So on the vertical axis a slightly higher peak represents many times more grid points.

	Tom


> On Sep 10, 2015, at 9:50 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Dear Mohan,
> Yes, that is a very different question now that we know you calculated the map from MD.
> 
> Everything depends on how you calculated the ?density" to produce the input map. Rather than an actual density, it may just be counts of how many times there was a water inside each grid cell (such as if you used the occupancy analysis in the MD Movie tool).  If so, you could divide those values by the number of MD frames that the counts came from, to make them more meaningful; for example, a count of 40 for a sample of 100 MD frames means that a grid cell had a water in it 40% of the time. MD Movie occupancy analysis:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#occupancy>
> 
> Volume Viewer is just displaying this raw data, it isn?t doing anything to transform or normalize it. The data is just a grid of points with associated values.  The histogram shows the range of values horizontally, and the bar heights show how many grid points have those values.  It is not useful to show the contour surface for values near zero, and I would not read too much into the shape of the histogram.  The high value near zero just means many grid points have values of zero, and the other maximum just means many grid points have values of 37.  If you use a different size grid cell and/or sampled a different number of MD frames (if the values are simply counts), the maximum would be a different value.
> 
> 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 Sep 10, 2015, at 9:20 AM, Mohan Pradhan <mohan.pradhan at ymail.com> wrote:
>> 
>> Dear Tom and Elaine,
>>                  Thank you both for your response. I think I was not very clear with my question. Let me rephrase my query here again in more detail.
>> 
>> I have done Molcular Dynamics simulation of my protein in explicit solvent. Following which I calculated the water density from the trajectory using grid-based approach with grid cells of size 0.5 X 0.5 X 0.5 ?. A sample of the grid-based density output file is attached here for your reference.
>> 
>> We then used Chimera to visualize the map using the volume viewer menu. We are attaching two image files here at two different isocountor threshold cutoff. One which was set to the isovalue at which we observe the maximum value of the historgram at an isovalue of 37. (image-1)
>> 
>> Second we set it to 2.5 times that isovalue 2.5 X 37 ~ 93) (Image-2).
>> 
>> The issue we wanted to clarify was what do these histogram actually depict with regard to the input grid file?
>> 
>> What is the histogram depicting at an iso-value of zero?
>> 
>> Why is there a sinusodial curve for the histogram towards the lower isovlaue?
>> 
>> Thanks,
>> Mohan
>> 
>> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From mohan.pradhan at ymail.com  Thu Sep 10 22:48:53 2015
From: mohan.pradhan at ymail.com (Mohan Pradhan)
Date: Fri, 11 Sep 2015 05:48:53 +0000 (UTC)
Subject: [Chimera-users] setting solvent density threshold at 2.5 times
 of the bulk solvent density
In-Reply-To: <646AB4DD-0837-4BD9-8502-09C36CFA3B07@sonic.net>
References: <646AB4DD-0837-4BD9-8502-09C36CFA3B07@sonic.net>
Message-ID: <190953744.887850.1441950533092.JavaMail.yahoo@mail.yahoo.com>

Dear Tom and Elaine,

Thank you for your response. It helped me a lot in clarifying my concepts about volume viewer and solvent density maps.
Best Regards,Mohan 


     On Friday, September 11, 2015 4:01 AM, Tom Goddard <goddard at sonic.net> wrote:
   

 Hi Mohan,

? I think your occupancy map histogram has a peak at 0 and peak at 37 is explained as follows.? The peak near means there are many grid points in the volume that water never reaches.? This must be the volume occupied by the protein.? The peak at 37 are grid points outside the protein where usually 37 waters are found per grid point over the course of your MD frames.? So I think you are correctly interpreting the values.? Using a threshold 2.5 * 37 would show grid points where waters are found 2.5 times more often than average ? you might think of those locations as ?bound waters? ? I?d expect them to be all at points adjacent to the protein.

? One extra bit of info about the histogram, the horizontal axis is the occupancy value (0-354 for your data) and the vertical axis is the number of grid points having a specific occupancy value.? The horizontal axis is linear, but the vertical axis is logarithmically scaled.? So on the vertical axis a slightly higher peak represents many times more grid points.

??? Tom


> On Sep 10, 2015, at 9:50 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Dear Mohan,
> Yes, that is a very different question now that we know you calculated the map from MD.
> 
> Everything depends on how you calculated the ?density" to produce the input map. Rather than an actual density, it may just be counts of how many times there was a water inside each grid cell (such as if you used the occupancy analysis in the MD Movie tool).? If so, you could divide those values by the number of MD frames that the counts came from, to make them more meaningful; for example, a count of 40 for a sample of 100 MD frames means that a grid cell had a water in it 40% of the time. MD Movie occupancy analysis:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#occupancy>
> 
> Volume Viewer is just displaying this raw data, it isn?t doing anything to transform or normalize it. The data is just a grid of points with associated values.? The histogram shows the range of values horizontally, and the bar heights show how many grid points have those values.? It is not useful to show the contour surface for values near zero, and I would not read too much into the shape of the histogram.? The high value near zero just means many grid points have values of zero, and the other maximum just means many grid points have values of 37.? If you use a different size grid cell and/or sampled a different number of MD frames (if the values are simply counts), the maximum would be a different value.
> 
> 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 Sep 10, 2015, at 9:20 AM, Mohan Pradhan <mohan.pradhan at ymail.com> wrote:
>> 
>> Dear Tom and Elaine,
>>? ? ? ? ? ? ? ? ? Thank you both for your response. I think I was not very clear with my question. Let me rephrase my query here again in more detail.
>> 
>> I have done Molcular Dynamics simulation of my protein in explicit solvent. Following which I calculated the water density from the trajectory using grid-based approach with grid cells of size 0.5 X 0.5 X 0.5 ?. A sample of the grid-based density output file is attached here for your reference.
>> 
>> We then used Chimera to visualize the map using the volume viewer menu. We are attaching two image files here at two different isocountor threshold cutoff. One which was set to the isovalue at which we observe the maximum value of the historgram at an isovalue of 37. (image-1)
>> 
>> Second we set it to 2.5 times that isovalue 2.5 X 37 ~ 93) (Image-2).
>> 
>> The issue we wanted to clarify was what do these histogram actually depict with regard to the input grid file?
>> 
>> What is the histogram depicting at an iso-value of zero?
>> 
>> Why is there a sinusodial curve for the histogram towards the lower isovlaue?
>> 
>> Thanks,
>> Mohan
>> 
>> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 


  
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From olibclarke at gmail.com  Fri Sep 11 02:05:54 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Fri, 11 Sep 2015 10:05:54 +0100
Subject: [Chimera-users] Saving sessions including maps?
References: <89D7CA45-5C8A-4DB1-922F-64F5830E296C@cumc.columbia.edu>
Message-ID: <D3624411-CF50-4717-A338-EE02EC19F704@gmail.com>

Hi all,

Is there any possibility of altering the chimera session format (or adding a separate option) such that all maps (including those created during the session) are also saved? 

This would greatly facilitate sharing data with collaborators, and would also allow one to provide chimera sessions with saved scenes as supplementary data when publishing.

It would also make saving sessions more practical when many different volumes are created during the session - for example, when using a molmap low resolution representation for each domain.

This would not necessarily require creating a new format - just creating a tarball or folder with all the maps and relative paths specified in the python file would work fine I think?

Cheers,
Oli.





From goddard at sonic.net  Fri Sep 11 10:54:47 2015
From: goddard at sonic.net (Tom Goddard)
Date: Fri, 11 Sep 2015 10:54:47 -0700
Subject: [Chimera-users] Saving sessions including maps?
In-Reply-To: <D3624411-CF50-4717-A338-EE02EC19F704@gmail.com>
References: <89D7CA45-5C8A-4DB1-922F-64F5830E296C@cumc.columbia.edu>
	<D3624411-CF50-4717-A338-EE02EC19F704@gmail.com>
Message-ID: <A0539726-2C2E-424B-9E10-6B46C9ED0ED1@sonic.net>

Hi Oliver,

  This has long been a requested feature.

	http://plato.cgl.ucsf.edu/trac/chimera/ticket/12426 <http://plato.cgl.ucsf.edu/trac/chimera/ticket/12426>

And I agree it would be useful.  If Chimera packages up all the needed maps and the session file in a zip archive this would be convenient.  You can of course do this right now by hand, only it isn?t so convenient.  Unfortunately this has never reached a high enough priority relative to other enhancements we are working on, so it has not been implemented.  It is more likely to get into Chimera 2 than Chimera 1.

	Tom


> On Sep 11, 2015, at 2:05 AM, Oliver Clarke wrote:
> 
> Hi all,
> 
> Is there any possibility of altering the chimera session format (or adding a separate option) such that all maps (including those created during the session) are also saved? 
> 
> This would greatly facilitate sharing data with collaborators, and would also allow one to provide chimera sessions with saved scenes as supplementary data when publishing.
> 
> It would also make saving sessions more practical when many different volumes are created during the session - for example, when using a molmap low resolution representation for each domain.
> 
> This would not necessarily require creating a new format - just creating a tarball or folder with all the maps and relative paths specified in the python file would work fine I think?
> 
> Cheers,
> Oli.
> 
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 

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From olibclarke at gmail.com  Fri Sep 11 13:04:51 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Fri, 11 Sep 2015 21:04:51 +0100
Subject: [Chimera-users] Saving sessions including maps?
In-Reply-To: <A0539726-2C2E-424B-9E10-6B46C9ED0ED1@sonic.net>
References: <89D7CA45-5C8A-4DB1-922F-64F5830E296C@cumc.columbia.edu>
	<D3624411-CF50-4717-A338-EE02EC19F704@gmail.com>
	<A0539726-2C2E-424B-9E10-6B46C9ED0ED1@sonic.net>
Message-ID: <291266D0-AF31-4F77-920F-3C5CE21E69E3@gmail.com>

Thanks for the quick reply Tom, got it. Looking forward to Chimera 2!

One temporary work around I have thought about is the following alias:

#Save session with maps. saves in home dir with directory name same as session.
# Usage: save_session_dir session-name
# Don't use spaces or under_scores in session names.
alias ^save_session_dir volume # save ~/$1/map%d.mrc; save ~/$1/$1

This will save all maps in a subdir of the home directory with the desired session name, and then save the session in the same dir - this folder is then portable and has all the info needed to restore the session. The only caveat to this is that this only works if the directory already exists - otherwise it gives an error. Maybe it would be possible to add an option to save/write to make the dir if it does not already exist? Otherwise I can do it in python I guess. Also, map names are not preserved, but I don?t see any easy way to get around that. Only other problem with this is that because of the way aliases work in chimera, any underscores in the alias arguments will be converted to spaces, but that is not an issue so long as one is aware of it.

Cheers,
Oliver.
> On Sep 11, 2015, at 6:54 PM, Tom Goddard <goddard at sonic.net> wrote:
> 
> Hi Oliver,
> 
>   This has long been a requested feature.
> 
> 	http://plato.cgl.ucsf.edu/trac/chimera/ticket/12426 <http://plato.cgl.ucsf.edu/trac/chimera/ticket/12426>
> 
> And I agree it would be useful.  If Chimera packages up all the needed maps and the session file in a zip archive this would be convenient.  You can of course do this right now by hand, only it isn?t so convenient.  Unfortunately this has never reached a high enough priority relative to other enhancements we are working on, so it has not been implemented.  It is more likely to get into Chimera 2 than Chimera 1.
> 
> 	Tom
> 
> 
>> On Sep 11, 2015, at 2:05 AM, Oliver Clarke wrote:
>> 
>> Hi all,
>> 
>> Is there any possibility of altering the chimera session format (or adding a separate option) such that all maps (including those created during the session) are also saved? 
>> 
>> This would greatly facilitate sharing data with collaborators, and would also allow one to provide chimera sessions with saved scenes as supplementary data when publishing.
>> 
>> It would also make saving sessions more practical when many different volumes are created during the session - for example, when using a molmap low resolution representation for each domain.
>> 
>> This would not necessarily require creating a new format - just creating a tarball or folder with all the maps and relative paths specified in the python file would work fine I think?
>> 
>> Cheers,
>> Oli.
>> 
>> 
>> 
>> _______________________________________________
>> 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 olibclarke at gmail.com  Fri Sep 11 14:11:18 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Fri, 11 Sep 2015 22:11:18 +0100
Subject: [Chimera-users] Saving sessions including maps?
In-Reply-To: <291266D0-AF31-4F77-920F-3C5CE21E69E3@gmail.com>
References: <89D7CA45-5C8A-4DB1-922F-64F5830E296C@cumc.columbia.edu>
	<D3624411-CF50-4717-A338-EE02EC19F704@gmail.com>
	<A0539726-2C2E-424B-9E10-6B46C9ED0ED1@sonic.net>
	<291266D0-AF31-4F77-920F-3C5CE21E69E3@gmail.com>
Message-ID: <2A7F261F-65FE-4ECB-BAB2-DCFE7EE358A5@gmail.com>

Ok, so if I run the following python script at chimera startup (to add a mkdir command):

def mkdir(mkdir,dir1):
  import os
  import time
  if not os.path.exists(dir1):
    os.mkdir(dir1)
from Midas.midas_text import addCommand
addCommand("mkdir", mkdir, help=False)

And then add the following alias:

#Save session with maps. saves in home dir with directory name same as session.
# Usage: save_session_dir session-name
# Don't use spaces or under_scores in session names.
alias ^save_session_dir  cd ~; mkdir $1; volume # save ~/$1/$1%d.mrc; save ~/$1/$1

This seems to work okay. It will create a sub dir in the user?s home directory with maps and a chimera session file.

Incidentally, is there any easy way to add python code snippets to a Chimera command file (with aliases etc)? I guess the only ways are to either have it in a separate file and use open or runscript, or to make it one big python file and wrap all of the aliases in runcommand() calls. But then how does one tell Chimera to run a given python file at start up? When I add python files to the ?Files to read at startup? section of preferences, Chimera seems to interpret them as Chimera command files, and hence gives an error.

Cheers,
Oliver.
> On Sep 11, 2015, at 9:04 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Thanks for the quick reply Tom, got it. Looking forward to Chimera 2!
> 
> One temporary work around I have thought about is the following alias:
> 
> #Save session with maps. saves in home dir with directory name same as session.
> # Usage: save_session_dir session-name
> # Don't use spaces or under_scores in session names.
> alias ^save_session_dir volume # save ~/$1/map%d.mrc; save ~/$1/$1
> 
> This will save all maps in a subdir of the home directory with the desired session name, and then save the session in the same dir - this folder is then portable and has all the info needed to restore the session. The only caveat to this is that this only works if the directory already exists - otherwise it gives an error. Maybe it would be possible to add an option to save/write to make the dir if it does not already exist? Otherwise I can do it in python I guess. Also, map names are not preserved, but I don?t see any easy way to get around that. Only other problem with this is that because of the way aliases work in chimera, any underscores in the alias arguments will be converted to spaces, but that is not an issue so long as one is aware of it.
> 
> Cheers,
> Oliver.
>> On Sep 11, 2015, at 6:54 PM, Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
>> 
>> Hi Oliver,
>> 
>>   This has long been a requested feature.
>> 
>> 	http://plato.cgl.ucsf.edu/trac/chimera/ticket/12426 <http://plato.cgl.ucsf.edu/trac/chimera/ticket/12426>
>> 
>> And I agree it would be useful.  If Chimera packages up all the needed maps and the session file in a zip archive this would be convenient.  You can of course do this right now by hand, only it isn?t so convenient.  Unfortunately this has never reached a high enough priority relative to other enhancements we are working on, so it has not been implemented.  It is more likely to get into Chimera 2 than Chimera 1.
>> 
>> 	Tom
>> 
>> 
>>> On Sep 11, 2015, at 2:05 AM, Oliver Clarke wrote:
>>> 
>>> Hi all,
>>> 
>>> Is there any possibility of altering the chimera session format (or adding a separate option) such that all maps (including those created during the session) are also saved? 
>>> 
>>> This would greatly facilitate sharing data with collaborators, and would also allow one to provide chimera sessions with saved scenes as supplementary data when publishing.
>>> 
>>> It would also make saving sessions more practical when many different volumes are created during the session - for example, when using a molmap low resolution representation for each domain.
>>> 
>>> This would not necessarily require creating a new format - just creating a tarball or folder with all the maps and relative paths specified in the python file would work fine I think?
>>> 
>>> Cheers,
>>> Oli.
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> 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 <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
>>> 
>> 
> 

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From meng at cgl.ucsf.edu  Fri Sep 11 14:31:21 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 11 Sep 2015 14:31:21 -0700
Subject: [Chimera-users] Saving sessions including maps?
In-Reply-To: <2A7F261F-65FE-4ECB-BAB2-DCFE7EE358A5@gmail.com>
References: <89D7CA45-5C8A-4DB1-922F-64F5830E296C@cumc.columbia.edu>
	<D3624411-CF50-4717-A338-EE02EC19F704@gmail.com>
	<A0539726-2C2E-424B-9E10-6B46C9ED0ED1@sonic.net>
	<291266D0-AF31-4F77-920F-3C5CE21E69E3@gmail.com>
	<2A7F261F-65FE-4ECB-BAB2-DCFE7EE358A5@gmail.com>
Message-ID: <FD50A1B2-5C50-4706-9AA1-1245D5BF6F90@cgl.ucsf.edu>

Hi Oliver,
Yeah, as you observed, only Chimera command files can be specified for reading at startup in the Command Line section of Preferences.

Here?s one idea using the Presets section of the Preferences instead.  I haven?t actually tried it but I think it should work. Custom preset definitions are read at startup and they can be defined in either Chimera command or Python files, see:  
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Presets>

You could just think of your Python-defined preset as an alias (or macro or function definition).  The name of the preset comes from the name of the file.  You can execute it with the preset command, which could occur in a Chimera command file.  I don?t know if it could be in a startup command file? I guess it depends on whether the custom presets are read before the startup command file or not.
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 Sep 11, 2015, at 2:11 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Incidentally, is there any easy way to add python code snippets to a Chimera command file (with aliases etc)? I guess the only ways are to either have it in a separate file and use open or runscript, or to make it one big python file and wrap all of the aliases in runcommand() calls. But then how does one tell Chimera to run a given python file at start up? When I add python files to the ?Files to read at startup? section of preferences, Chimera seems to interpret them as Chimera command files, and hence gives an error.
> 
> Cheers,
> Oliver.



From matthewd at bcm.edu  Fri Sep 11 14:29:24 2015
From: matthewd at bcm.edu (Dougherty, Matthew T)
Date: Fri, 11 Sep 2015 21:29:24 +0000
Subject: [Chimera-users] Saving sessions including maps?
In-Reply-To: <291266D0-AF31-4F77-920F-3C5CE21E69E3@gmail.com>
References: <89D7CA45-5C8A-4DB1-922F-64F5830E296C@cumc.columbia.edu>
	<D3624411-CF50-4717-A338-EE02EC19F704@gmail.com>
	<A0539726-2C2E-424B-9E10-6B46C9ED0ED1@sonic.net>,
	<291266D0-AF31-4F77-920F-3C5CE21E69E3@gmail.com>
Message-ID: <SN2PR0601MB0973E6143D0A9359F937F4E9DE500@SN2PR0601MB0973.namprd06.prod.outlook.com>

The viz package Amira has something similar called 'pack and go'.   And the video editing software Final Cut Pro has 'media manager', which provides more control.


It would be a useful option  to bundle the whole working directory, including pdfs, spreadsheets, manuscript drafts.


I also recommend in the design something that can include archival concepts, as opposed to only a comprehensive & reliable session transfer from person A to person B.


When managing multiple session files over a period of years, it would  be useful to get summaries of the blob of data; list of sizes, types, dates, etc., that can be examined without loading everything (which can take a long time if the files are big)  just to get a status.   Having an archival snapshot button that generates jpegs that could be included would help sorting through large numbers of sessions, particularly if the person sorting them is not the person who created them.


For example, Tom you helped me out on some python code that would do a backbone trace 6-15 years ago; if someone asked me to create another animation like that, it would be a fishing expedition in a terabyte sea.



Matthew Dougherty
National Center for Macromolecular Imaging
Baylor College of Medicine
=================================================
=================================================


________________________________
From: chimera-users-bounces at cgl.ucsf.edu <chimera-users-bounces at cgl.ucsf.edu> on behalf of Oliver Clarke <olibclarke at gmail.com>
Sent: Friday, September 11, 2015 3:04 PM
To: Tom Goddard
Cc: chimera-users at cgl.ucsf.edu BB
Subject: Re: [Chimera-users] Saving sessions including maps?

Thanks for the quick reply Tom, got it. Looking forward to Chimera 2!

One temporary work around I have thought about is the following alias:

#Save session with maps. saves in home dir with directory name same as session.
# Usage: save_session_dir session-name
# Don't use spaces or under_scores in session names.
alias ^save_session_dir volume # save ~/$1/map%d.mrc; save ~/$1/$1

This will save all maps in a subdir of the home directory with the desired session name, and then save the session in the same dir - this folder is then portable and has all the info needed to restore the session. The only caveat to this is that this only works if the directory already exists - otherwise it gives an error. Maybe it would be possible to add an option to save/write to make the dir if it does not already exist? Otherwise I can do it in python I guess. Also, map names are not preserved, but I don?t see any easy way to get around that. Only other problem with this is that because of the way aliases work in chimera, any underscores in the alias arguments will be converted to spaces, but that is not an issue so long as one is aware of it.

Cheers,
Oliver.
On Sep 11, 2015, at 6:54 PM, Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>> wrote:

Hi Oliver,

  This has long been a requested feature.

http://plato.cgl.ucsf.edu/trac/chimera/ticket/12426

And I agree it would be useful.  If Chimera packages up all the needed maps and the session file in a zip archive this would be convenient.  You can of course do this right now by hand, only it isn?t so convenient.  Unfortunately this has never reached a high enough priority relative to other enhancements we are working on, so it has not been implemented.  It is more likely to get into Chimera 2 than Chimera 1.

Tom


On Sep 11, 2015, at 2:05 AM, Oliver Clarke wrote:

Hi all,

Is there any possibility of altering the chimera session format (or adding a separate option) such that all maps (including those created during the session) are also saved?

This would greatly facilitate sharing data with collaborators, and would also allow one to provide chimera sessions with saved scenes as supplementary data when publishing.

It would also make saving sessions more practical when many different volumes are created during the session - for example, when using a molmap low resolution representation for each domain.

This would not necessarily require creating a new format - just creating a tarball or folder with all the maps and relative paths specified in the python file would work fine I think?

Cheers,
Oli.



_______________________________________________
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 YZHANG56 at mgh.harvard.edu  Mon Sep 14 11:37:50 2015
From: YZHANG56 at mgh.harvard.edu (Zhang, Yinghui)
Date: Mon, 14 Sep 2015 18:37:50 +0000
Subject: [Chimera-users] how to move subunits of a pentamer receptor in a
	controlled way
Message-ID: <607150D615F12C478D98B3A53CACE54C874B764D@PHSX10MB24.partners.org>

Dear Sir,

This is Yinghui Zhang from Massachusetts General Hospital. I am a frequent user of Chimera to understand the structure of a neuronal pentamer receptor which is ion channel. Now we want to do some modification of the receptor by manipulating the coordinates of the atoms of the receptor pdb files. The aim is to move each subunit radially away from the receptor?s central symmetry axis(which should be the central channel axis ) or tilt each subunit outward. The symmetry of the receptor cannot be disrupted and we want to do it in a quantitative manner(move by a specific ?? or tilt by a specific degree value). Could you please give us some clues if we can realize these aims in Chimera?

Many thanks and regards!

Yinghui Zhang


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
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From goddard at sonic.net  Mon Sep 14 16:40:53 2015
From: goddard at sonic.net (Tom Goddard)
Date: Mon, 14 Sep 2015 16:40:53 -0700
Subject: [Chimera-users] how to move subunits of a pentamer receptor in
	a controlled way
In-Reply-To: <607150D615F12C478D98B3A53CACE54C874B764D@PHSX10MB24.partners.org>
References: <607150D615F12C478D98B3A53CACE54C874B764D@PHSX10MB24.partners.org>
Message-ID: <0A81AEE6-DB42-4E0D-90AF-926C9D537FD1@sonic.net>

Hi Yingui,

  Here are some ideas.  I?ll use nictotinic aceytlcholine receptor 2bg9 determined by electron microscopy as an example

	open 2bg9
	rainbow chain
	split #0
	turn z 30
	move x 1.5 model #0.3
	turn z 72
	move x 1.5 model #0.4
	turn z 72
	move x 1.5 model #0.5
	turn z 72
	move x 1.5 model #0.1
	turn z 72
	move x 1.5 model #0.2
	combine #0

Here I colored the chains, then split the model #0 into a model for each chain #0.1, #0.2, ?, #0.5 so I could easily move each chain, then I moved each chain radially.  I started with a z rotation by 30 degrees that put the green chain C along the x axis then to move radially I moved it along the z axis.  I moved each chain outward by 1.5 Angstroms.  I rotate 72 degrees (360 / 5) before moving the next chain in the sequence along x.  I could also have rotated each chain, for example using ?turn y 0.7 center #0.3:266.C at CA model #0.3? to rotate by 0.7 degrees using a specific atom in the chain as the pivot.

  All this seems simple enough except for a subtle problem.  This structure may not have its symmetry axis exactly aligned along the z axis.  So to do it right I?d first need to align the symmetry axis along z.  It is hard to say where the symmetry axis is because 4 of the 5 chains are different sequences and the structure isn?t really symmetric.  To get an idea of how asymmetric it is I open two copies and align one to a rotated copy of the other.

	open 2bg9
	open 2bg9
	match #1:.E:.A:.B:.C:.D #0:.A:.B:.C:.D:.E
	measure rotation #0 #1

The last command will show the rotation axis and in the reply log (Favorites menu) it will give the coordinates of the rotation axis 

  Axis   0.00785796  -0.00543703  -0.99995434
  Axis point  63.57681519  63.30528336   0.00000000
  Rotation angle (degrees)  72.08465763

To visually see the difference you can compare spinning the molecule about the z axis for 100 steps of 72 degrees

	turn z 72 100 center #2

versus spinning about the axis determined by this alignment (rotation axis is model #2)

	turn #2 72 100

If you don?t think the z axis is the correct symmetry axis and instead alignment axis is better you could align that axis perpendicular to the screen (align #2) then save the coordinates (with the "relative to" button in the File / Save PDB? dialog not checked so it uses screen coordinates).  Things are even trickier than they look.  The above ?match? command is wrong.  It is aligning the atoms of #1 with those of #0 in the order specified.  But the chains don?t have the same number of atoms.  So it doesn?t really align chain E to chain A, chain A to chain B, chain B to chain C, etc?.  It would be more sensible to use sequence alignment based matches for example with command

	mmaker #1:.E:.A:.B:.C:.D #0:.A:.B:.C:.D:.E pair ss

but this gave a worse alignment of the atoms near the center of the channel.  In any case it is up to you to figure out the best definition of the symmetry axis given that the structure has only approximate symmetry.

	Tom




> On Sep 14, 2015, at 11:37 AM, Zhang, Yinghui wrote:
> 
> Dear Sir,
>  
> This is Yinghui Zhang from Massachusetts General Hospital. I am a frequent user of Chimera to understand the structure of a neuronal pentamer receptor which is ion channel. Now we want to do some modification of the receptor by manipulating the coordinates of the atoms of the receptor pdb files. The aim is to move each subunit radially away from the receptor?s central symmetry axis(which should be the central channel axis ) or tilt each subunit outward. The symmetry of the receptor cannot be disrupted and we want to do it in a quantitative manner(move by a specific ?? or tilt by a specific degree value). Could you please give us some clues if we can realize these aims in Chimera?
>  
> Many thanks and regards!
>  
> Yinghui Zhang
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and properly
> dispose of the e-mail.
> 
> _______________________________________________
> 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 <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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From thapamb at mail.uc.edu  Tue Sep 15 09:04:16 2015
From: thapamb at mail.uc.edu (Mahendra B Thapa)
Date: Tue, 15 Sep 2015 12:04:16 -0400
Subject: [Chimera-users] eps image in publication quality
Message-ID: <CAM_0UTgj9bdb8s3Tj+qhsh5v22RVj2TjJkuJo27WDCOmqVTHUw@mail.gmail.com>

Dear Chimera Users,

Using the following procedures in chimera window, I saved a sequence
allignment image in eps format ( which looked like the first image of
"file:///opt/UCSF/Chimera64-1.6.1/share/chimera/helpdir/ContributedSoftware/multalignviewer/framemav.html").
The image in the pop of window is nice but the saved image in the eps
format is not so clear. Let me suggest how to save the image in the
publication quality.
(i) structure ---> matchmaker
(ii) Tools --->  sequence  ---> match  ---> align
(iii) file  ---> save as ---> eps

Thank you,
Mahendra Thapa
University of Cincinnati, OH
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From william.eliason at yale.edu  Tue Sep 15 11:52:20 2015
From: william.eliason at yale.edu (Eliason, William)
Date: Tue, 15 Sep 2015 18:52:20 +0000
Subject: [Chimera-users] large file size exporting scene with spheres
Message-ID: <CBB320FC066A0544A3A4AD61E2C526B3113EA39B@x10-mbx3.yu.yale.edu>

Chimera-users,

I am very new to chimera.  I would like to export a scene with spheres for 3d printing but the ( .stl) file size is enormous.  They contain way to many triangles.  I tested a smallish molecule in MeshLab and I could decrease the number of faces from 699732 (34MB) to 34986 faces (1.7MB) with minor flattening of the sphere.  Is there a way to have chimera generate spheres with fewer faces?

Thank you,

Bill Eliason
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From meng at cgl.ucsf.edu  Tue Sep 15 12:42:55 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 15 Sep 2015 12:42:55 -0700
Subject: [Chimera-users] large file size exporting scene with spheres
In-Reply-To: <CBB320FC066A0544A3A4AD61E2C526B3113EA39B@x10-mbx3.yu.yale.edu>
References: <CBB320FC066A0544A3A4AD61E2C526B3113EA39B@x10-mbx3.yu.yale.edu>
Message-ID: <38F3333E-EC64-46BD-959F-F4D7CA982F06@cgl.ucsf.edu>

Hi Bill,
You can decrease the ?subdivision? setting in the Effects dialog (menu Tools? Viewing Controls? Effects) and also zoom out the view before exporting.

These are discussed in more detail in this previous post:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-April/009753.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 Sep 15, 2015, at 11:52 AM, Eliason, William <william.eliason at yale.edu> wrote:
> 
> Chimera-users,
> 
> I am very new to chimera.  I would like to export a scene with spheres for 3d printing but the ( .stl) file size is enormous.  They contain way to many triangles.  I tested a smallish molecule in MeshLab and I could decrease the number of faces from 699732 (34MB) to 34986 faces (1.7MB) with minor flattening of the sphere.  Is there a way to have chimera generate spheres with fewer faces?
> 
> Thank you,
> 
> Bill Eliason




From pett at cgl.ucsf.edu  Tue Sep 15 17:16:58 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 15 Sep 2015 17:16:58 -0700
Subject: [Chimera-users] eps image in publication quality
In-Reply-To: <CAM_0UTgj9bdb8s3Tj+qhsh5v22RVj2TjJkuJo27WDCOmqVTHUw@mail.gmail.com>
References: <CAM_0UTgj9bdb8s3Tj+qhsh5v22RVj2TjJkuJo27WDCOmqVTHUw@mail.gmail.com>
Message-ID: <8AB7E09A-9DF6-4B23-8EC8-97401199C709@cgl.ucsf.edu>

EPS (Encapsulated PostScript) is resolution independent ? it essentially has infinite resolution.  If it doesn?t look good in a viewer it?s because the viewer is doing a poor job of rendering it.  What are you using to look at the EPS file?

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Sep 15, 2015, at 9:04 AM, Mahendra B Thapa <thapamb at mail.uc.edu> wrote:
> 
> Dear Chimera Users,
> 
> Using the following procedures in chimera window, I saved a sequence allignment image in eps format ( which looked like the first image of "file:///opt/UCSF/Chimera64-1.6.1/share/chimera/helpdir/ContributedSoftware/multalignviewer/framemav.html"). The image in the pop of window is nice but the saved image in the eps format is not so clear. Let me suggest how to save the image in the publication quality.
> (i) structure ---> matchmaker
> (ii) Tools --->  sequence  ---> match  ---> align
> (iii) file  ---> save as ---> eps
> 
> 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 gregc at cgl.ucsf.edu  Tue Sep 15 17:42:06 2015
From: gregc at cgl.ucsf.edu (gregc at cgl.ucsf.edu)
Date: Wed, 16 Sep 2015 00:42:06 +0000
Subject: [Chimera-users] eps image in publication quality
In-Reply-To: <8AB7E09A-9DF6-4B23-8EC8-97401199C709@cgl.ucsf.edu>
References: <8AB7E09A-9DF6-4B23-8EC8-97401199C709@cgl.ucsf.edu>
	<CAM_0UTgj9bdb8s3Tj+qhsh5v22RVj2TjJkuJo27WDCOmqVTHUw@mail.gmail.com>
Message-ID: <61be45aa99abc848723508064b69811b@mail.cgl.ucsf.edu>

Actually, chimera's EPS files are at a fixed resolution.? To get a higher resolution, save the image with a higher resolution.? An easy way to get a reasonable resolution is to switch to print units in the Save Image dialog, and choose a size in inches or cm.? The default "Print resolution" of 100dpi is generally more than adequate since printers need many dots to represent a single pixel and most computer monitors are roughly 100dpi.

Also, note that EPS files are huge compared to PNG or TIFF files.? Most, if not all, journals now accept TIFF or PNG images, so there is no need to generate an EPS file.

??? -- Greg

September 15 2015 5:18 PM, "Eric Pettersen"  wrote:
EPS (Encapsulated PostScript) is resolution independent ? it essentially has infinite resolution. ?If it doesn?t look good in a viewer it?s because the viewer is doing a poor job of rendering it. ?What are you using to look at the EPS file?

?Eric
?
Eric Pettersen
UCSF Computer Graphics Lab
?
?
On Sep 15, 2015, at 9:04 AM, Mahendra B Thapa  wrote:?
Dear Chimera Users,
Using the following procedures in chimera window, I saved a sequence allignment image in eps format ( which looked like the first image of "file:///opt/UCSF/Chimera64-1.6.1/share/chimera/helpdir/ContributedSoftware/multalignviewer/framemav.html (javascript:false)"). The image in the pop of window is nice but the saved image in the eps format is not so clear. Let me suggest how to save the image in the publication quality.(i) structure ---> matchmaker(ii) Tools ---> ?sequence ?---> match ?---> align(iii) file ?---> save as ---> eps
Thank you,
Mahendra Thapa
University of Cincinnati, OH_______________________________________________
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 (http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users)
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From thapamb at mail.uc.edu  Wed Sep 16 06:36:31 2015
From: thapamb at mail.uc.edu (Mahendra B Thapa)
Date: Wed, 16 Sep 2015 09:36:31 -0400
Subject: [Chimera-users] FW:  eps image in publication quality
In-Reply-To: <f932f53d57384c39bef1dc8c2f7b512b@CY1PR0101MB1084.prod.exchangelabs.com>
References: <8AB7E09A-9DF6-4B23-8EC8-97401199C709@cgl.ucsf.edu>
	<CAM_0UTgj9bdb8s3Tj+qhsh5v22RVj2TjJkuJo27WDCOmqVTHUw@mail.gmail.com>
	<61be45aa99abc848723508064b69811b@mail.cgl.ucsf.edu>
	<f932f53d57384c39bef1dc8c2f7b512b@CY1PR0101MB1084.prod.exchangelabs.com>
Message-ID: <CAM_0UThw-vCjkDBCHgOT0SpMyX79977FiQUJxJpSsCOb_8uQTQ@mail.gmail.com>

Dear Eric & Greg

Thank you for the suggestions. The only available option to save the *sequence
alignment image* is EPS format, actually I am looking  a way to save the
image in tif or png format.

In the pop-up window of sequence alignment image , there are following
options available under 'File' heading: Save as, save EPS, save Association
info, Hide & quit.

As Greg pointed out, I didn't find "Save Image dialog".

Eric, when I copied the so generated EPS  image in MS-Powerpoint for
further editing, the quality of the image was not good. I have attached one
of the EPS image ( in which I have aligned two structures: pdb id 4ICB &
3BCI.)

Thank you for help,
Mahendra Thapa
University of Cincinnati,OH


On Tue, Sep 15, 2015 at 8:42 PM, Thapa, Mahendra (thapamb) <
thapamb at mail.uc.edu> wrote:

>
> ------------------------------
> *From:* gregc at cgl.ucsf.edu
> *Sent:* Tuesday, September 15, 2015 6:42:06 PM (UTC-06:00) Central America
> *To:* Eric Pettersen; Thapa, Mahendra (thapamb)
> *Cc:* chimera-users at cgl.ucsf.edu
> *Subject:* Re: [Chimera-users] eps image in publication quality
>
> Actually, chimera's EPS files are at a fixed resolution.  To get a higher
> resolution, save the image with a higher resolution.  An easy way to get a
> reasonable resolution is to switch to print units in the Save Image dialog,
> and choose a size in inches or cm.  The default "Print resolution" of
> 100dpi is generally more than adequate since printers need many dots to
> represent a single pixel and most computer monitors are roughly 100dpi.
>
> Also, note that EPS files are huge compared to PNG or TIFF files.  Most,
> if not all, journals now accept TIFF or PNG images, so there is no need to
> generate an EPS file.
>
>     -- Greg
>
> September 15 2015 5:18 PM, "Eric Pettersen" <pett at cgl.ucsf.edu
> <%22Eric%20Pettersen%22%20%3Cpett at cgl.ucsf.edu%3E>> wrote:
>
> EPS (Encapsulated PostScript) is resolution independent ? it essentially
> has infinite resolution.  If it doesn?t look good in a viewer it?s because
> the viewer is doing a poor job of rendering it.  What are you using to look
> at the EPS file?
> ?Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
>
> On Sep 15, 2015, at 9:04 AM, Mahendra B Thapa <thapamb at mail.uc.edu> wrote:
>
> Dear Chimera Users,
> Using the following procedures in chimera window, I saved a sequence
> allignment image in eps format ( which looked like the first image of "
> file:///opt/UCSF/Chimera64-1.6.1/share/chimera/helpdir/ContributedSoftware/multalignviewer/framemav.html").
> The image in the pop of window is nice but the saved image in the eps
> format is not so clear. Let me suggest how to save the image in the
> publication quality.
> (i) structure ---> matchmaker
> (ii) Tools --->  sequence  ---> match  ---> align
> (iii) file  ---> save as ---> eps
> 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 Sep 16 11:12:10 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 16 Sep 2015 11:12:10 -0700
Subject: [Chimera-users] FW:  eps image in publication quality
In-Reply-To: <CAM_0UThw-vCjkDBCHgOT0SpMyX79977FiQUJxJpSsCOb_8uQTQ@mail.gmail.com>
References: <8AB7E09A-9DF6-4B23-8EC8-97401199C709@cgl.ucsf.edu>
	<CAM_0UTgj9bdb8s3Tj+qhsh5v22RVj2TjJkuJo27WDCOmqVTHUw@mail.gmail.com>
	<61be45aa99abc848723508064b69811b@mail.cgl.ucsf.edu>
	<f932f53d57384c39bef1dc8c2f7b512b@CY1PR0101MB1084.prod.exchangelabs.com>
	<CAM_0UThw-vCjkDBCHgOT0SpMyX79977FiQUJxJpSsCOb_8uQTQ@mail.gmail.com>
Message-ID: <816320AE-3F15-40CE-9A7D-32D5E001F818@cgl.ucsf.edu>

Hi Mahendra,
	Yeah, Greg?s response was appropriate for the main ?Save Image? dialog, not the ?Save EPS? from the sequence window.  The latter is, as I said earlier, ?infinite? resolution.  Nonetheless, Microsoft products may not do a good job of rendering PostScript files, particularly on Windows machines (PostScript is better supported on Mac).  Therefore you might want to use something like Photoshop if you have that available.  Nonetheless, if you *print* from PowerPoint I think you will see that you get a good looking result.  Also, zooming in in PowerPoint will give you a somewhat better looking image to look at / work with, but not as good as what gets printed.
	When I open your file on my Mac using Preview, it looks fine.  I?ve attached a screenshot.  I?ve also attached the PDF equivalent of your EPS files, in case PowerPoint can handle that better for whatever reason.
	One thing you might also possibly want to do is to change both your model?s colors to white, so you don?t get that garish magenta background on the second sequence name.  Just go to the model panel, click on the small color well on that model?s line which will bring up a color editor and change the model color to white.

?Eric




> On Sep 16, 2015, at 6:36 AM, Mahendra B Thapa <thapamb at mail.uc.edu> wrote:
> 
> Dear Eric & Greg
> 
> Thank you for the suggestions. The only available option to save the sequence alignment image is EPS format, actually I am looking  a way to save the image in tif or png format.
> 
> In the pop-up window of sequence alignment image , there are following options available under 'File' heading: Save as, save EPS, save Association info, Hide & quit.
> 
> As Greg pointed out, I didn't find "Save Image dialog". 
> 
> Eric, when I copied the so generated EPS  image in MS-Powerpoint for further editing, the quality of the image was not good. I have attached one of the EPS image ( in which I have aligned two structures: pdb id 4ICB & 3BCI.)
> 
> Thank you for help,
> Mahendra Thapa
> University of Cincinnati,OH
>  
> 
> On Tue, Sep 15, 2015 at 8:42 PM, Thapa, Mahendra (thapamb) <thapamb at mail.uc.edu <mailto:thapamb at mail.uc.edu>> wrote:
>  
>  From: gregc at cgl.ucsf.edu <mailto:gregc at cgl.ucsf.edu>
> Sent: Tuesday, September 15, 2015 6:42:06 PM (UTC-06:00) Central America
> To: Eric Pettersen; Thapa, Mahendra (thapamb)
> Cc: chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] eps image in publication quality
> 
> Actually, chimera's EPS files are at a fixed resolution.  To get a higher resolution, save the image with a higher resolution.  An easy way to get a reasonable resolution is to switch to print units in the Save Image dialog, and choose a size in inches or cm.  The default "Print resolution" of 100dpi is generally more than adequate since printers need many dots to represent a single pixel and most computer monitors are roughly 100dpi.
> 
> Also, note that EPS files are huge compared to PNG or TIFF files.  Most, if not all, journals now accept TIFF or PNG images, so there is no need to generate an EPS file.
> 
>     -- Greg
> 
> September 15 2015 5:18 PM, "Eric Pettersen" <pett at cgl.ucsf.edu <mailto:%22Eric%20Pettersen%22%20%3Cpett at cgl.ucsf.edu%3E>> wrote:
> EPS (Encapsulated PostScript) is resolution independent ? it essentially has infinite resolution.  If it doesn?t look good in a viewer it?s because the viewer is doing a poor job of rendering it.  What are you using to look at the EPS file?
> ?Eric
>  
> Eric Pettersen
> UCSF Computer Graphics Lab
>  
>  
>> 
>> On Sep 15, 2015, at 9:04 AM, Mahendra B Thapa <thapamb at mail.uc.edu <mailto:thapamb at mail.uc.edu>> wrote:
>>  
>> Dear Chimera Users,
>> Using the following procedures in chimera window, I saved a sequence allignment image in eps format ( which looked like the first image of "file:///opt/UCSF/Chimera64-1.6.1/share/chimera/helpdir/ContributedSoftware/multalignviewer/framemav.html <>"). The image in the pop of window is nice but the saved image in the eps format is not so clear. Let me suggest how to save the image in the publication quality.
>> (i) structure ---> matchmaker
>> (ii) Tools --->  sequence  ---> match  ---> align
>> (iii) file  ---> save as ---> eps
>> Thank you,
>> Mahendra Thapa
>> University of Cincinnati, OH
>> _______________________________________________
>> 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 <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
> <Match_3BCI_4ICB.eps>_______________________________________________
> 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 Sep 16 12:51:45 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 16 Sep 2015 12:51:45 -0700
Subject: [Chimera-users] Saving sessions including maps?
In-Reply-To: <2A7F261F-65FE-4ECB-BAB2-DCFE7EE358A5@gmail.com>
References: <89D7CA45-5C8A-4DB1-922F-64F5830E296C@cumc.columbia.edu>
	<D3624411-CF50-4717-A338-EE02EC19F704@gmail.com>
	<A0539726-2C2E-424B-9E10-6B46C9ED0ED1@sonic.net>
	<291266D0-AF31-4F77-920F-3C5CE21E69E3@gmail.com>
	<2A7F261F-65FE-4ECB-BAB2-DCFE7EE358A5@gmail.com>
Message-ID: <0D8B41F3-48B7-4BBC-8DAA-CFA2BEF00AF8@cgl.ucsf.edu>

Sorry this reply is kind of tardy.  Anyway, your little script has done 98% of the work needed to add that command at startup.  Look at the ?Adding Command-line Commands? example in the Chimera Programmer?s Guide:  http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html>

Basically, you need call the script file ?ChimeraExtension.py?, put it inside a folder (maybe named ?Mkdir?) and then tell Chimera to look for it by going to Tools section of Preferences and adding the parent folder of Mkdir (i.e. the folder that contains Mkdir) to the ?Locations? list that Chimera will look for tools in (and click the Save button!)

The above is good to know for adding tools in general.  However in the specific case of your mkdir command, you can do it directly in Chimera without making an extension.  The ?system? command will execute its arguments as a shell command, so ?system mkdir xyz? will create an xyz directory.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Sep 11, 2015, at 2:11 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Ok, so if I run the following python script at chimera startup (to add a mkdir command):
> 
> def mkdir(mkdir,dir1):
>   import os
>   import time
>   if not os.path.exists(dir1):
>     os.mkdir(dir1)
> from Midas.midas_text import addCommand
> addCommand("mkdir", mkdir, help=False)
> 
> And then add the following alias:
> 
> #Save session with maps. saves in home dir with directory name same as session.
> # Usage: save_session_dir session-name
> # Don't use spaces or under_scores in session names.
> alias ^save_session_dir  cd ~; mkdir $1; volume # save ~/$1/$1%d.mrc; save ~/$1/$1
> 
> This seems to work okay. It will create a sub dir in the user?s home directory with maps and a chimera session file.
> 
> Incidentally, is there any easy way to add python code snippets to a Chimera command file (with aliases etc)? I guess the only ways are to either have it in a separate file and use open or runscript, or to make it one big python file and wrap all of the aliases in runcommand() calls. But then how does one tell Chimera to run a given python file at start up? When I add python files to the ?Files to read at startup? section of preferences, Chimera seems to interpret them as Chimera command files, and hence gives an error.
> 
> Cheers,
> Oliver.
>> On Sep 11, 2015, at 9:04 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>> 
>> Thanks for the quick reply Tom, got it. Looking forward to Chimera 2!
>> 
>> One temporary work around I have thought about is the following alias:
>> 
>> #Save session with maps. saves in home dir with directory name same as session.
>> # Usage: save_session_dir session-name
>> # Don't use spaces or under_scores in session names.
>> alias ^save_session_dir volume # save ~/$1/map%d.mrc; save ~/$1/$1
>> 
>> This will save all maps in a subdir of the home directory with the desired session name, and then save the session in the same dir - this folder is then portable and has all the info needed to restore the session. The only caveat to this is that this only works if the directory already exists - otherwise it gives an error. Maybe it would be possible to add an option to save/write to make the dir if it does not already exist? Otherwise I can do it in python I guess. Also, map names are not preserved, but I don?t see any easy way to get around that. Only other problem with this is that because of the way aliases work in chimera, any underscores in the alias arguments will be converted to spaces, but that is not an issue so long as one is aware of it.
>> 
>> Cheers,
>> Oliver.
>>> On Sep 11, 2015, at 6:54 PM, Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
>>> 
>>> Hi Oliver,
>>> 
>>>   This has long been a requested feature.
>>> 
>>> 	http://plato.cgl.ucsf.edu/trac/chimera/ticket/12426 <http://plato.cgl.ucsf.edu/trac/chimera/ticket/12426>
>>> 
>>> And I agree it would be useful.  If Chimera packages up all the needed maps and the session file in a zip archive this would be convenient.  You can of course do this right now by hand, only it isn?t so convenient.  Unfortunately this has never reached a high enough priority relative to other enhancements we are working on, so it has not been implemented.  It is more likely to get into Chimera 2 than Chimera 1.
>>> 
>>> 	Tom
>>> 
>>> 
>>>> On Sep 11, 2015, at 2:05 AM, Oliver Clarke wrote:
>>>> 
>>>> Hi all,
>>>> 
>>>> Is there any possibility of altering the chimera session format (or adding a separate option) such that all maps (including those created during the session) are also saved? 
>>>> 
>>>> This would greatly facilitate sharing data with collaborators, and would also allow one to provide chimera sessions with saved scenes as supplementary data when publishing.
>>>> 
>>>> It would also make saving sessions more practical when many different volumes are created during the session - for example, when using a molmap low resolution representation for each domain.
>>>> 
>>>> This would not necessarily require creating a new format - just creating a tarball or folder with all the maps and relative paths specified in the python file would work fine I think?
>>>> 
>>>> Cheers,
>>>> Oli.
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> 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 <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

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From olibclarke at gmail.com  Wed Sep 16 12:59:20 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Wed, 16 Sep 2015 15:59:20 -0400
Subject: [Chimera-users] Saving sessions including maps?
In-Reply-To: <0D8B41F3-48B7-4BBC-8DAA-CFA2BEF00AF8@cgl.ucsf.edu>
References: <89D7CA45-5C8A-4DB1-922F-64F5830E296C@cumc.columbia.edu>
	<D3624411-CF50-4717-A338-EE02EC19F704@gmail.com>
	<A0539726-2C2E-424B-9E10-6B46C9ED0ED1@sonic.net>
	<291266D0-AF31-4F77-920F-3C5CE21E69E3@gmail.com>
	<2A7F261F-65FE-4ECB-BAB2-DCFE7EE358A5@gmail.com>
	<0D8B41F3-48B7-4BBC-8DAA-CFA2BEF00AF8@cgl.ucsf.edu>
Message-ID: <273C4226-1451-4602-AAFB-3357A91BCA4B@gmail.com>

Awesome, thanks Eric! I was looking for a chimera command to execute shell commands but somehow didn?t find it (even though it is certainly documented in the command index).

In that case the following alias works well to create a packaged session with all maps saved:

#Save session with maps. saves in home dir with directory name same as session.
# Usage: save_session_dir session-name
# Don't use spaces or under_scores in session names.
alias ^save_session_dir  cd ~; system mkdir chimera_session_dirs; cd chimera_session_dirs; system mkdir $1; volume # save ~/chimera_session_dirs/$1/$1%d.mrc; save ~/chimera_session_dirs/$1/$1

The only remaining issue is that Chimera treats underscores in alias arguments as special characters, and converts them to spaces. I don?t suppose there is some way to avoid that behaviour? E.g. like using a \ to escape a special character in a shell script?

Cheers,
Oli.

> On Sep 16, 2015, at 3:51 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> Sorry this reply is kind of tardy.  Anyway, your little script has done 98% of the work needed to add that command at startup.  Look at the ?Adding Command-line Commands? example in the Chimera Programmer?s Guide:  http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html>
> 
> Basically, you need call the script file ?ChimeraExtension.py?, put it inside a folder (maybe named ?Mkdir?) and then tell Chimera to look for it by going to Tools section of Preferences and adding the parent folder of Mkdir (i.e. the folder that contains Mkdir) to the ?Locations? list that Chimera will look for tools in (and click the Save button!)
> 
> The above is good to know for adding tools in general.  However in the specific case of your mkdir command, you can do it directly in Chimera without making an extension.  The ?system? command will execute its arguments as a shell command, so ?system mkdir xyz? will create an xyz directory.
> 
> ?Eric
> 
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> 
> 
>> On Sep 11, 2015, at 2:11 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>> 
>> Ok, so if I run the following python script at chimera startup (to add a mkdir command):
>> 
>> def mkdir(mkdir,dir1):
>>   import os
>>   import time
>>   if not os.path.exists(dir1):
>>     os.mkdir(dir1)
>> from Midas.midas_text import addCommand
>> addCommand("mkdir", mkdir, help=False)
>> 
>> And then add the following alias:
>> 
>> #Save session with maps. saves in home dir with directory name same as session.
>> # Usage: save_session_dir session-name
>> # Don't use spaces or under_scores in session names.
>> alias ^save_session_dir  cd ~; mkdir $1; volume # save ~/$1/$1%d.mrc; save ~/$1/$1
>> 
>> This seems to work okay. It will create a sub dir in the user?s home directory with maps and a chimera session file.
>> 
>> Incidentally, is there any easy way to add python code snippets to a Chimera command file (with aliases etc)? I guess the only ways are to either have it in a separate file and use open or runscript, or to make it one big python file and wrap all of the aliases in runcommand() calls. But then how does one tell Chimera to run a given python file at start up? When I add python files to the ?Files to read at startup? section of preferences, Chimera seems to interpret them as Chimera command files, and hence gives an error.
>> 
>> Cheers,
>> Oliver.
>>> On Sep 11, 2015, at 9:04 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>>> 
>>> Thanks for the quick reply Tom, got it. Looking forward to Chimera 2!
>>> 
>>> One temporary work around I have thought about is the following alias:
>>> 
>>> #Save session with maps. saves in home dir with directory name same as session.
>>> # Usage: save_session_dir session-name
>>> # Don't use spaces or under_scores in session names.
>>> alias ^save_session_dir volume # save ~/$1/map%d.mrc; save ~/$1/$1
>>> 
>>> This will save all maps in a subdir of the home directory with the desired session name, and then save the session in the same dir - this folder is then portable and has all the info needed to restore the session. The only caveat to this is that this only works if the directory already exists - otherwise it gives an error. Maybe it would be possible to add an option to save/write to make the dir if it does not already exist? Otherwise I can do it in python I guess. Also, map names are not preserved, but I don?t see any easy way to get around that. Only other problem with this is that because of the way aliases work in chimera, any underscores in the alias arguments will be converted to spaces, but that is not an issue so long as one is aware of it.
>>> 
>>> Cheers,
>>> Oliver.
>>>> On Sep 11, 2015, at 6:54 PM, Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
>>>> 
>>>> Hi Oliver,
>>>> 
>>>>   This has long been a requested feature.
>>>> 
>>>> 	http://plato.cgl.ucsf.edu/trac/chimera/ticket/12426 <http://plato.cgl.ucsf.edu/trac/chimera/ticket/12426>
>>>> 
>>>> And I agree it would be useful.  If Chimera packages up all the needed maps and the session file in a zip archive this would be convenient.  You can of course do this right now by hand, only it isn?t so convenient.  Unfortunately this has never reached a high enough priority relative to other enhancements we are working on, so it has not been implemented.  It is more likely to get into Chimera 2 than Chimera 1.
>>>> 
>>>> 	Tom
>>>> 
>>>> 
>>>>> On Sep 11, 2015, at 2:05 AM, Oliver Clarke wrote:
>>>>> 
>>>>> Hi all,
>>>>> 
>>>>> Is there any possibility of altering the chimera session format (or adding a separate option) such that all maps (including those created during the session) are also saved? 
>>>>> 
>>>>> This would greatly facilitate sharing data with collaborators, and would also allow one to provide chimera sessions with saved scenes as supplementary data when publishing.
>>>>> 
>>>>> It would also make saving sessions more practical when many different volumes are created during the session - for example, when using a molmap low resolution representation for each domain.
>>>>> 
>>>>> This would not necessarily require creating a new format - just creating a tarball or folder with all the maps and relative paths specified in the python file would work fine I think?
>>>>> 
>>>>> Cheers,
>>>>> Oli.
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> 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 <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
>>>>> 
>>>> 
>>> 
>> 
>> _______________________________________________
>> 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 pett at cgl.ucsf.edu  Wed Sep 16 13:14:46 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 16 Sep 2015 13:14:46 -0700
Subject: [Chimera-users] Saving sessions including maps?
In-Reply-To: <273C4226-1451-4602-AAFB-3357A91BCA4B@gmail.com>
References: <89D7CA45-5C8A-4DB1-922F-64F5830E296C@cumc.columbia.edu>
	<D3624411-CF50-4717-A338-EE02EC19F704@gmail.com>
	<A0539726-2C2E-424B-9E10-6B46C9ED0ED1@sonic.net>
	<291266D0-AF31-4F77-920F-3C5CE21E69E3@gmail.com>
	<2A7F261F-65FE-4ECB-BAB2-DCFE7EE358A5@gmail.com>
	<0D8B41F3-48B7-4BBC-8DAA-CFA2BEF00AF8@cgl.ucsf.edu>
	<273C4226-1451-4602-AAFB-3357A91BCA4B@gmail.com>
Message-ID: <FDFCF112-C16A-4182-BE82-BD15D3D4AF64@cgl.ucsf.edu>

Okay, the next daily build will allow the underscore-to-space conversion to be escaped by preceding the underscore with a backslash.

?Eric

> On Sep 16, 2015, at 12:59 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Awesome, thanks Eric! I was looking for a chimera command to execute shell commands but somehow didn?t find it (even though it is certainly documented in the command index).
> 
> In that case the following alias works well to create a packaged session with all maps saved:
> 
> #Save session with maps. saves in home dir with directory name same as session.
> # Usage: save_session_dir session-name
> # Don't use spaces or under_scores in session names.
> alias ^save_session_dir  cd ~; system mkdir chimera_session_dirs; cd chimera_session_dirs; system mkdir $1; volume # save ~/chimera_session_dirs/$1/$1%d.mrc; save ~/chimera_session_dirs/$1/$1
> 
> The only remaining issue is that Chimera treats underscores in alias arguments as special characters, and converts them to spaces. I don?t suppose there is some way to avoid that behaviour? E.g. like using a \ to escape a special character in a shell script?
> 
> Cheers,
> Oli.
> 
>> On Sep 16, 2015, at 3:51 PM, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
>> 
>> Sorry this reply is kind of tardy.  Anyway, your little script has done 98% of the work needed to add that command at startup.  Look at the ?Adding Command-line Commands? example in the Chimera Programmer?s Guide:  http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html>
>> 
>> Basically, you need call the script file ?ChimeraExtension.py?, put it inside a folder (maybe named ?Mkdir?) and then tell Chimera to look for it by going to Tools section of Preferences and adding the parent folder of Mkdir (i.e. the folder that contains Mkdir) to the ?Locations? list that Chimera will look for tools in (and click the Save button!)
>> 
>> The above is good to know for adding tools in general.  However in the specific case of your mkdir command, you can do it directly in Chimera without making an extension.  The ?system? command will execute its arguments as a shell command, so ?system mkdir xyz? will create an xyz directory.
>> 
>> ?Eric
>> 
>> 	Eric Pettersen
>> 	UCSF Computer Graphics Lab
>> 
>> 
>>> On Sep 11, 2015, at 2:11 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>>> 
>>> Ok, so if I run the following python script at chimera startup (to add a mkdir command):
>>> 
>>> def mkdir(mkdir,dir1):
>>>   import os
>>>   import time
>>>   if not os.path.exists(dir1):
>>>     os.mkdir(dir1)
>>> from Midas.midas_text import addCommand
>>> addCommand("mkdir", mkdir, help=False)
>>> 
>>> And then add the following alias:
>>> 
>>> #Save session with maps. saves in home dir with directory name same as session.
>>> # Usage: save_session_dir session-name
>>> # Don't use spaces or under_scores in session names.
>>> alias ^save_session_dir  cd ~; mkdir $1; volume # save ~/$1/$1%d.mrc; save ~/$1/$1
>>> 
>>> This seems to work okay. It will create a sub dir in the user?s home directory with maps and a chimera session file.
>>> 
>>> Incidentally, is there any easy way to add python code snippets to a Chimera command file (with aliases etc)? I guess the only ways are to either have it in a separate file and use open or runscript, or to make it one big python file and wrap all of the aliases in runcommand() calls. But then how does one tell Chimera to run a given python file at start up? When I add python files to the ?Files to read at startup? section of preferences, Chimera seems to interpret them as Chimera command files, and hence gives an error.
>>> 
>>> Cheers,
>>> Oliver.
>>>> On Sep 11, 2015, at 9:04 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>>>> 
>>>> Thanks for the quick reply Tom, got it. Looking forward to Chimera 2!
>>>> 
>>>> One temporary work around I have thought about is the following alias:
>>>> 
>>>> #Save session with maps. saves in home dir with directory name same as session.
>>>> # Usage: save_session_dir session-name
>>>> # Don't use spaces or under_scores in session names.
>>>> alias ^save_session_dir volume # save ~/$1/map%d.mrc; save ~/$1/$1
>>>> 
>>>> This will save all maps in a subdir of the home directory with the desired session name, and then save the session in the same dir - this folder is then portable and has all the info needed to restore the session. The only caveat to this is that this only works if the directory already exists - otherwise it gives an error. Maybe it would be possible to add an option to save/write to make the dir if it does not already exist? Otherwise I can do it in python I guess. Also, map names are not preserved, but I don?t see any easy way to get around that. Only other problem with this is that because of the way aliases work in chimera, any underscores in the alias arguments will be converted to spaces, but that is not an issue so long as one is aware of it.
>>>> 
>>>> Cheers,
>>>> Oliver.
>>>>> On Sep 11, 2015, at 6:54 PM, Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
>>>>> 
>>>>> Hi Oliver,
>>>>> 
>>>>>   This has long been a requested feature.
>>>>> 
>>>>> 	http://plato.cgl.ucsf.edu/trac/chimera/ticket/12426 <http://plato.cgl.ucsf.edu/trac/chimera/ticket/12426>
>>>>> 
>>>>> And I agree it would be useful.  If Chimera packages up all the needed maps and the session file in a zip archive this would be convenient.  You can of course do this right now by hand, only it isn?t so convenient.  Unfortunately this has never reached a high enough priority relative to other enhancements we are working on, so it has not been implemented.  It is more likely to get into Chimera 2 than Chimera 1.
>>>>> 
>>>>> 	Tom
>>>>> 
>>>>> 
>>>>>> On Sep 11, 2015, at 2:05 AM, Oliver Clarke wrote:
>>>>>> 
>>>>>> Hi all,
>>>>>> 
>>>>>> Is there any possibility of altering the chimera session format (or adding a separate option) such that all maps (including those created during the session) are also saved? 
>>>>>> 
>>>>>> This would greatly facilitate sharing data with collaborators, and would also allow one to provide chimera sessions with saved scenes as supplementary data when publishing.
>>>>>> 
>>>>>> It would also make saving sessions more practical when many different volumes are created during the session - for example, when using a molmap low resolution representation for each domain.
>>>>>> 
>>>>>> This would not necessarily require creating a new format - just creating a tarball or folder with all the maps and relative paths specified in the python file would work fine I think?
>>>>>> 
>>>>>> Cheers,
>>>>>> Oli.
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> _______________________________________________
>>>>>> 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 <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
>>>>>> 
>>>>> 
>>>> 
>>> 
>>> _______________________________________________
>>> 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 <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
>> 
> 

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From olibclarke at gmail.com  Wed Sep 16 13:26:57 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Wed, 16 Sep 2015 16:26:57 -0400
Subject: [Chimera-users] Saving sessions including maps?
In-Reply-To: <FDFCF112-C16A-4182-BE82-BD15D3D4AF64@cgl.ucsf.edu>
References: <89D7CA45-5C8A-4DB1-922F-64F5830E296C@cumc.columbia.edu>
	<D3624411-CF50-4717-A338-EE02EC19F704@gmail.com>
	<A0539726-2C2E-424B-9E10-6B46C9ED0ED1@sonic.net>
	<291266D0-AF31-4F77-920F-3C5CE21E69E3@gmail.com>
	<2A7F261F-65FE-4ECB-BAB2-DCFE7EE358A5@gmail.com>
	<0D8B41F3-48B7-4BBC-8DAA-CFA2BEF00AF8@cgl.ucsf.edu>
	<273C4226-1451-4602-AAFB-3357A91BCA4B@gmail.com>
	<FDFCF112-C16A-4182-BE82-BD15D3D4AF64@cgl.ucsf.edu>
Message-ID: <CAPghYOrX_kgqCPcSoeqohAOD4Z54GrY7sBp2Lks=H=DSgwm4Kw@mail.gmail.com>

Great, thanks Eric!

Oliver.

On Wed, Sep 16, 2015 at 4:14 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Okay, the next daily build will allow the underscore-to-space conversion
> to be escaped by preceding the underscore with a backslash.
>
> ?Eric
>
> On Sep 16, 2015, at 12:59 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
>
> Awesome, thanks Eric! I was looking for a chimera command to execute shell
> commands but somehow didn?t find it (even though it is certainly documented
> in the command index).
>
> In that case the following alias works well to create a packaged session
> with all maps saved:
>
> #Save session with maps. saves in home dir with directory name same as
> session.
> # Usage: save_session_dir session-name
> # Don't use spaces or under_scores in session names.
> alias ^save_session_dir  cd ~; system mkdir chimera_session_dirs; cd
> chimera_session_dirs; system mkdir $1; volume # save
> ~/chimera_session_dirs/$1/$1%d.mrc; save ~/chimera_session_dirs/$1/$1
>
> The only remaining issue is that Chimera treats underscores in alias
> arguments as special characters, and converts them to spaces. I don?t
> suppose there is some way to avoid that behaviour? E.g. like using a \ to
> escape a special character in a shell script?
>
> Cheers,
> Oli.
>
> On Sep 16, 2015, at 3:51 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>
> Sorry this reply is kind of tardy.  Anyway, your little script has done
> 98% of the work needed to add that command at startup.  Look at the ?Adding
> Command-line Commands? example in the Chimera Programmer?s Guide:
> http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html
>
> Basically, you need call the script file ?ChimeraExtension.py?, put it
> inside a folder (maybe named ?Mkdir?) and then tell Chimera to look for it
> by going to Tools section of Preferences and adding the *parent* folder
> of Mkdir (i.e. the folder that contains Mkdir) to the ?Locations? list that
> Chimera will look for tools in (and click the Save button!)
>
> The above is good to know for adding tools in general.  However in the
> specific case of your mkdir command, you can do it directly in Chimera
> without making an extension.  The ?system? command will execute its
> arguments as a shell command, so ?system mkdir xyz? will create an xyz
> directory.
>
> ?Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
> On Sep 11, 2015, at 2:11 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
>
> Ok, so if I run the following python script at chimera startup (to add a
> mkdir command):
>
> def mkdir(mkdir,dir1):
>   import os
>   import time
>   if not os.path.exists(dir1):
>     os.mkdir(dir1)
> from Midas.midas_text import addCommand
> addCommand("mkdir", mkdir, help=False)
>
> And then add the following alias:
>
> #Save session with maps. saves in home dir with directory name same as
> session.
> # Usage: save_session_dir session-name
> # Don't use spaces or under_scores in session names.
> alias ^save_session_dir  cd ~; mkdir $1; volume # save ~/$1/$1%d.mrc; save
> ~/$1/$1
>
> This seems to work okay. It will create a sub dir in the user?s home
> directory with maps and a chimera session file.
>
> Incidentally, is there any easy way to add python code snippets to a
> Chimera command file (with aliases etc)? I guess the only ways are to
> either have it in a separate file and use open or runscript, or to make it
> one big python file and wrap all of the aliases in runcommand() calls. But
> then how does one tell Chimera to run a given python file at start up? When
> I add python files to the ?Files to read at startup? section of
> preferences, Chimera seems to interpret them as Chimera command files, and
> hence gives an error.
>
> Cheers,
> Oliver.
>
> On Sep 11, 2015, at 9:04 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
>
> Thanks for the quick reply Tom, got it. Looking forward to Chimera 2!
>
> One temporary work around I have thought about is the following alias:
>
> #Save session with maps. saves in home dir with directory name same as
> session.
> # Usage: save_session_dir session-name
> # Don't use spaces or under_scores in session names.
> alias ^save_session_dir volume # save ~/$1/map%d.mrc; save ~/$1/$1
>
> This will save all maps in a subdir of the home directory with the desired
> session name, and then save the session in the same dir - this folder is
> then portable and has all the info needed to restore the session. The only
> caveat to this is that this only works if the directory already exists -
> otherwise it gives an error. Maybe it would be possible to add an option to
> save/write to make the dir if it does not already exist? Otherwise I can do
> it in python I guess. Also, map names are not preserved, but I don?t see
> any easy way to get around that. Only other problem with this is that
> because of the way aliases work in chimera, any underscores in the alias
> arguments will be converted to spaces, but that is not an issue so long as
> one is aware of it.
>
> Cheers,
> Oliver.
>
> On Sep 11, 2015, at 6:54 PM, Tom Goddard <goddard at sonic.net> wrote:
>
> Hi Oliver,
>
>   This has long been a requested feature.
>
> http://plato.cgl.ucsf.edu/trac/chimera/ticket/12426
>
> And I agree it would be useful.  If Chimera packages up all the needed
> maps and the session file in a zip archive this would be convenient.  You
> can of course do this right now by hand, only it isn?t so convenient.
> Unfortunately this has never reached a high enough priority relative to
> other enhancements we are working on, so it has not been implemented.  It
> is more likely to get into Chimera 2 than Chimera 1.
>
> Tom
>
>
> On Sep 11, 2015, at 2:05 AM, Oliver Clarke wrote:
>
> Hi all,
>
> Is there any possibility of altering the chimera session format (or adding
> a separate option) such that all maps (including those created during the
> session) are also saved?
>
> This would greatly facilitate sharing data with collaborators, and would
> also allow one to provide chimera sessions with saved scenes as
> supplementary data when publishing.
>
> It would also make saving sessions more practical when many different
> volumes are created during the session - for example, when using a molmap
> low resolution representation for each domain.
>
> This would not necessarily require creating a new format - just creating a
> tarball or folder with all the maps and relative paths specified in the
> python file would work fine I think?
>
> Cheers,
> Oli.
>
>
>
> _______________________________________________
> 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
>
>
>
>
>
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From william.eliason at yale.edu  Wed Sep 16 09:29:21 2015
From: william.eliason at yale.edu (Eliason, William)
Date: Wed, 16 Sep 2015 16:29:21 +0000
Subject: [Chimera-users] large file size exporting scene with spheres
In-Reply-To: <38F3333E-EC64-46BD-959F-F4D7CA982F06@cgl.ucsf.edu>
References: <CBB320FC066A0544A3A4AD61E2C526B3113EA39B@x10-mbx3.yu.yale.edu>,
	<38F3333E-EC64-46BD-959F-F4D7CA982F06@cgl.ucsf.edu>
Message-ID: <CBB320FC066A0544A3A4AD61E2C526B3113EA42A@x10-mbx3.yu.yale.edu>

Elaine,

Thank you for the information.  I will let you know how it goes.
Bill
________________________________________
From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Tuesday, September 15, 2015 3:42 PM
To: Eliason, William
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] large file size exporting scene with spheres

Hi Bill,
You can decrease the ?subdivision? setting in the Effects dialog (menu Tools? Viewing Controls? Effects) and also zoom out the view before exporting.

These are discussed in more detail in this previous post:
<https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_pipermail_chimera-2Dusers_2014-2DApril_009753.html&d=AwIF-g&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=GHLQ-YN3a3SZwmbxfQzG422WX8qFcxMwcqDhrmzYYig&m=82epIAtAXgjRN-pj6rQz0vxnLpXgRblFMlQ7tp8624A&s=ekvBZa1LD-g5eO8zKme9E80DrWt-4atfTpouu6hPG6E&e= >

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 Sep 15, 2015, at 11:52 AM, Eliason, William <william.eliason at yale.edu> wrote:
>
> Chimera-users,
>
> I am very new to chimera.  I would like to export a scene with spheres for 3d printing but the ( .stl) file size is enormous.  They contain way to many triangles.  I tested a smallish molecule in MeshLab and I could decrease the number of faces from 699732 (34MB) to 34986 faces (1.7MB) with minor flattening of the sphere.  Is there a way to have chimera generate spheres with fewer faces?
>
> Thank you,
>
> Bill Eliason




From olibclarke at gmail.com  Thu Sep 17 08:17:29 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Thu, 17 Sep 2015 11:17:29 -0400
Subject: [Chimera-users] Saving sessions including maps?
In-Reply-To: <FDFCF112-C16A-4182-BE82-BD15D3D4AF64@cgl.ucsf.edu>
References: <89D7CA45-5C8A-4DB1-922F-64F5830E296C@cumc.columbia.edu>
	<D3624411-CF50-4717-A338-EE02EC19F704@gmail.com>
	<A0539726-2C2E-424B-9E10-6B46C9ED0ED1@sonic.net>
	<291266D0-AF31-4F77-920F-3C5CE21E69E3@gmail.com>
	<2A7F261F-65FE-4ECB-BAB2-DCFE7EE358A5@gmail.com>
	<0D8B41F3-48B7-4BBC-8DAA-CFA2BEF00AF8@cgl.ucsf.edu>
	<273C4226-1451-4602-AAFB-3357A91BCA4B@gmail.com>
	<FDFCF112-C16A-4182-BE82-BD15D3D4AF64@cgl.ucsf.edu>
Message-ID: <68DA677F-E23E-44CD-B71A-6647166C6773@gmail.com>

Thanks Eric, this works great!

Also I tweaked the alias I was using to create packaged sessions so that it automatically creates a tar archive of the packaged session, for easy sharing with collaborators.

This alias and a bunch of others I find handy can be downloaded here:

https://www.dropbox.com/s/75e5c7f1vamtiiy/chimera_aliases_general.com?dl=0 <https://www.dropbox.com/s/75e5c7f1vamtiiy/chimera_aliases_general.com?dl=0>

Cheers,

Oliver.
> On Sep 16, 2015, at 4:14 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> Okay, the next daily build will allow the underscore-to-space conversion to be escaped by preceding the underscore with a backslash.
> 
> ?Eric
> 
>> On Sep 16, 2015, at 12:59 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>> 
>> Awesome, thanks Eric! I was looking for a chimera command to execute shell commands but somehow didn?t find it (even though it is certainly documented in the command index).
>> 
>> In that case the following alias works well to create a packaged session with all maps saved:
>> 
>> #Save session with maps. saves in home dir with directory name same as session.
>> # Usage: save_session_dir session-name
>> # Don't use spaces or under_scores in session names.
>> alias ^save_session_dir  cd ~; system mkdir chimera_session_dirs; cd chimera_session_dirs; system mkdir $1; volume # save ~/chimera_session_dirs/$1/$1%d.mrc; save ~/chimera_session_dirs/$1/$1
>> 
>> The only remaining issue is that Chimera treats underscores in alias arguments as special characters, and converts them to spaces. I don?t suppose there is some way to avoid that behaviour? E.g. like using a \ to escape a special character in a shell script?
>> 
>> Cheers,
>> Oli.
>> 
>>> On Sep 16, 2015, at 3:51 PM, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
>>> 
>>> Sorry this reply is kind of tardy.  Anyway, your little script has done 98% of the work needed to add that command at startup.  Look at the ?Adding Command-line Commands? example in the Chimera Programmer?s Guide:  http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html>
>>> 
>>> Basically, you need call the script file ?ChimeraExtension.py?, put it inside a folder (maybe named ?Mkdir?) and then tell Chimera to look for it by going to Tools section of Preferences and adding the parent folder of Mkdir (i.e. the folder that contains Mkdir) to the ?Locations? list that Chimera will look for tools in (and click the Save button!)
>>> 
>>> The above is good to know for adding tools in general.  However in the specific case of your mkdir command, you can do it directly in Chimera without making an extension.  The ?system? command will execute its arguments as a shell command, so ?system mkdir xyz? will create an xyz directory.
>>> 
>>> ?Eric
>>> 
>>> 	Eric Pettersen
>>> 	UCSF Computer Graphics Lab
>>> 
>>> 
>>>> On Sep 11, 2015, at 2:11 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>>>> 
>>>> Ok, so if I run the following python script at chimera startup (to add a mkdir command):
>>>> 
>>>> def mkdir(mkdir,dir1):
>>>>   import os
>>>>   import time
>>>>   if not os.path.exists(dir1):
>>>>     os.mkdir(dir1)
>>>> from Midas.midas_text import addCommand
>>>> addCommand("mkdir", mkdir, help=False)
>>>> 
>>>> And then add the following alias:
>>>> 
>>>> #Save session with maps. saves in home dir with directory name same as session.
>>>> # Usage: save_session_dir session-name
>>>> # Don't use spaces or under_scores in session names.
>>>> alias ^save_session_dir  cd ~; mkdir $1; volume # save ~/$1/$1%d.mrc; save ~/$1/$1
>>>> 
>>>> This seems to work okay. It will create a sub dir in the user?s home directory with maps and a chimera session file.
>>>> 
>>>> Incidentally, is there any easy way to add python code snippets to a Chimera command file (with aliases etc)? I guess the only ways are to either have it in a separate file and use open or runscript, or to make it one big python file and wrap all of the aliases in runcommand() calls. But then how does one tell Chimera to run a given python file at start up? When I add python files to the ?Files to read at startup? section of preferences, Chimera seems to interpret them as Chimera command files, and hence gives an error.
>>>> 
>>>> Cheers,
>>>> Oliver.
>>>>> On Sep 11, 2015, at 9:04 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>>>>> 
>>>>> Thanks for the quick reply Tom, got it. Looking forward to Chimera 2!
>>>>> 
>>>>> One temporary work around I have thought about is the following alias:
>>>>> 
>>>>> #Save session with maps. saves in home dir with directory name same as session.
>>>>> # Usage: save_session_dir session-name
>>>>> # Don't use spaces or under_scores in session names.
>>>>> alias ^save_session_dir volume # save ~/$1/map%d.mrc; save ~/$1/$1
>>>>> 
>>>>> This will save all maps in a subdir of the home directory with the desired session name, and then save the session in the same dir - this folder is then portable and has all the info needed to restore the session. The only caveat to this is that this only works if the directory already exists - otherwise it gives an error. Maybe it would be possible to add an option to save/write to make the dir if it does not already exist? Otherwise I can do it in python I guess. Also, map names are not preserved, but I don?t see any easy way to get around that. Only other problem with this is that because of the way aliases work in chimera, any underscores in the alias arguments will be converted to spaces, but that is not an issue so long as one is aware of it.
>>>>> 
>>>>> Cheers,
>>>>> Oliver.
>>>>>> On Sep 11, 2015, at 6:54 PM, Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
>>>>>> 
>>>>>> Hi Oliver,
>>>>>> 
>>>>>>   This has long been a requested feature.
>>>>>> 
>>>>>> 	http://plato.cgl.ucsf.edu/trac/chimera/ticket/12426 <http://plato.cgl.ucsf.edu/trac/chimera/ticket/12426>
>>>>>> 
>>>>>> And I agree it would be useful.  If Chimera packages up all the needed maps and the session file in a zip archive this would be convenient.  You can of course do this right now by hand, only it isn?t so convenient.  Unfortunately this has never reached a high enough priority relative to other enhancements we are working on, so it has not been implemented.  It is more likely to get into Chimera 2 than Chimera 1.
>>>>>> 
>>>>>> 	Tom
>>>>>> 
>>>>>> 
>>>>>>> On Sep 11, 2015, at 2:05 AM, Oliver Clarke wrote:
>>>>>>> 
>>>>>>> Hi all,
>>>>>>> 
>>>>>>> Is there any possibility of altering the chimera session format (or adding a separate option) such that all maps (including those created during the session) are also saved? 
>>>>>>> 
>>>>>>> This would greatly facilitate sharing data with collaborators, and would also allow one to provide chimera sessions with saved scenes as supplementary data when publishing.
>>>>>>> 
>>>>>>> It would also make saving sessions more practical when many different volumes are created during the session - for example, when using a molmap low resolution representation for each domain.
>>>>>>> 
>>>>>>> This would not necessarily require creating a new format - just creating a tarball or folder with all the maps and relative paths specified in the python file would work fine I think?
>>>>>>> 
>>>>>>> Cheers,
>>>>>>> Oli.
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> 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 <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
>>>>>>> 
>>>>>> 
>>>>> 
>>>> 
>>>> _______________________________________________
>>>> 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 <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
>>> 
>> 
> 

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From pett at cgl.ucsf.edu  Thu Sep 17 10:06:01 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 17 Sep 2015 10:06:01 -0700
Subject: [Chimera-users] Saving sessions including maps?
In-Reply-To: <68DA677F-E23E-44CD-B71A-6647166C6773@gmail.com>
References: <89D7CA45-5C8A-4DB1-922F-64F5830E296C@cumc.columbia.edu>
	<D3624411-CF50-4717-A338-EE02EC19F704@gmail.com>
	<A0539726-2C2E-424B-9E10-6B46C9ED0ED1@sonic.net>
	<291266D0-AF31-4F77-920F-3C5CE21E69E3@gmail.com>
	<2A7F261F-65FE-4ECB-BAB2-DCFE7EE358A5@gmail.com>
	<0D8B41F3-48B7-4BBC-8DAA-CFA2BEF00AF8@cgl.ucsf.edu>
	<273C4226-1451-4602-AAFB-3357A91BCA4B@gmail.com>
	<FDFCF112-C16A-4182-BE82-BD15D3D4AF64@cgl.ucsf.edu>
	<68DA677F-E23E-44CD-B71A-6647166C6773@gmail.com>
Message-ID: <C9E33FC0-E9B0-40F3-9028-DB5DB90614D3@cgl.ucsf.edu>

Hi Oliver, thanks for making those available.  I bet some people will find them very useful.

?Eric

> On Sep 17, 2015, at 8:17 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Thanks Eric, this works great!
> 
> Also I tweaked the alias I was using to create packaged sessions so that it automatically creates a tar archive of the packaged session, for easy sharing with collaborators.
> 
> This alias and a bunch of others I find handy can be downloaded here:
> 
> https://www.dropbox.com/s/75e5c7f1vamtiiy/chimera_aliases_general.com?dl=0 <https://www.dropbox.com/s/75e5c7f1vamtiiy/chimera_aliases_general.com?dl=0>
> 
> Cheers,
> 
> Oliver.
>> On Sep 16, 2015, at 4:14 PM, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
>> 
>> Okay, the next daily build will allow the underscore-to-space conversion to be escaped by preceding the underscore with a backslash.
>> 
>> ?Eric
>> 
>>> On Sep 16, 2015, at 12:59 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>>> 
>>> Awesome, thanks Eric! I was looking for a chimera command to execute shell commands but somehow didn?t find it (even though it is certainly documented in the command index).
>>> 
>>> In that case the following alias works well to create a packaged session with all maps saved:
>>> 
>>> #Save session with maps. saves in home dir with directory name same as session.
>>> # Usage: save_session_dir session-name
>>> # Don't use spaces or under_scores in session names.
>>> alias ^save_session_dir  cd ~; system mkdir chimera_session_dirs; cd chimera_session_dirs; system mkdir $1; volume # save ~/chimera_session_dirs/$1/$1%d.mrc; save ~/chimera_session_dirs/$1/$1
>>> 
>>> The only remaining issue is that Chimera treats underscores in alias arguments as special characters, and converts them to spaces. I don?t suppose there is some way to avoid that behaviour? E.g. like using a \ to escape a special character in a shell script?
>>> 
>>> Cheers,
>>> Oli.
>>> 
>>>> On Sep 16, 2015, at 3:51 PM, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
>>>> 
>>>> Sorry this reply is kind of tardy.  Anyway, your little script has done 98% of the work needed to add that command at startup.  Look at the ?Adding Command-line Commands? example in the Chimera Programmer?s Guide:  http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html>
>>>> 
>>>> Basically, you need call the script file ?ChimeraExtension.py?, put it inside a folder (maybe named ?Mkdir?) and then tell Chimera to look for it by going to Tools section of Preferences and adding the parent folder of Mkdir (i.e. the folder that contains Mkdir) to the ?Locations? list that Chimera will look for tools in (and click the Save button!)
>>>> 
>>>> The above is good to know for adding tools in general.  However in the specific case of your mkdir command, you can do it directly in Chimera without making an extension.  The ?system? command will execute its arguments as a shell command, so ?system mkdir xyz? will create an xyz directory.
>>>> 
>>>> ?Eric
>>>> 
>>>> 	Eric Pettersen
>>>> 	UCSF Computer Graphics Lab
>>>> 
>>>> 
>>>>> On Sep 11, 2015, at 2:11 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>>>>> 
>>>>> Ok, so if I run the following python script at chimera startup (to add a mkdir command):
>>>>> 
>>>>> def mkdir(mkdir,dir1):
>>>>>   import os
>>>>>   import time
>>>>>   if not os.path.exists(dir1):
>>>>>     os.mkdir(dir1)
>>>>> from Midas.midas_text import addCommand
>>>>> addCommand("mkdir", mkdir, help=False)
>>>>> 
>>>>> And then add the following alias:
>>>>> 
>>>>> #Save session with maps. saves in home dir with directory name same as session.
>>>>> # Usage: save_session_dir session-name
>>>>> # Don't use spaces or under_scores in session names.
>>>>> alias ^save_session_dir  cd ~; mkdir $1; volume # save ~/$1/$1%d.mrc; save ~/$1/$1
>>>>> 
>>>>> This seems to work okay. It will create a sub dir in the user?s home directory with maps and a chimera session file.
>>>>> 
>>>>> Incidentally, is there any easy way to add python code snippets to a Chimera command file (with aliases etc)? I guess the only ways are to either have it in a separate file and use open or runscript, or to make it one big python file and wrap all of the aliases in runcommand() calls. But then how does one tell Chimera to run a given python file at start up? When I add python files to the ?Files to read at startup? section of preferences, Chimera seems to interpret them as Chimera command files, and hence gives an error.
>>>>> 
>>>>> Cheers,
>>>>> Oliver.
>>>>>> On Sep 11, 2015, at 9:04 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>>>>>> 
>>>>>> Thanks for the quick reply Tom, got it. Looking forward to Chimera 2!
>>>>>> 
>>>>>> One temporary work around I have thought about is the following alias:
>>>>>> 
>>>>>> #Save session with maps. saves in home dir with directory name same as session.
>>>>>> # Usage: save_session_dir session-name
>>>>>> # Don't use spaces or under_scores in session names.
>>>>>> alias ^save_session_dir volume # save ~/$1/map%d.mrc; save ~/$1/$1
>>>>>> 
>>>>>> This will save all maps in a subdir of the home directory with the desired session name, and then save the session in the same dir - this folder is then portable and has all the info needed to restore the session. The only caveat to this is that this only works if the directory already exists - otherwise it gives an error. Maybe it would be possible to add an option to save/write to make the dir if it does not already exist? Otherwise I can do it in python I guess. Also, map names are not preserved, but I don?t see any easy way to get around that. Only other problem with this is that because of the way aliases work in chimera, any underscores in the alias arguments will be converted to spaces, but that is not an issue so long as one is aware of it.
>>>>>> 
>>>>>> Cheers,
>>>>>> Oliver.
>>>>>>> On Sep 11, 2015, at 6:54 PM, Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
>>>>>>> 
>>>>>>> Hi Oliver,
>>>>>>> 
>>>>>>>   This has long been a requested feature.
>>>>>>> 
>>>>>>> 	http://plato.cgl.ucsf.edu/trac/chimera/ticket/12426 <http://plato.cgl.ucsf.edu/trac/chimera/ticket/12426>
>>>>>>> 
>>>>>>> And I agree it would be useful.  If Chimera packages up all the needed maps and the session file in a zip archive this would be convenient.  You can of course do this right now by hand, only it isn?t so convenient.  Unfortunately this has never reached a high enough priority relative to other enhancements we are working on, so it has not been implemented.  It is more likely to get into Chimera 2 than Chimera 1.
>>>>>>> 
>>>>>>> 	Tom
>>>>>>> 
>>>>>>> 
>>>>>>>> On Sep 11, 2015, at 2:05 AM, Oliver Clarke wrote:
>>>>>>>> 
>>>>>>>> Hi all,
>>>>>>>> 
>>>>>>>> Is there any possibility of altering the chimera session format (or adding a separate option) such that all maps (including those created during the session) are also saved? 
>>>>>>>> 
>>>>>>>> This would greatly facilitate sharing data with collaborators, and would also allow one to provide chimera sessions with saved scenes as supplementary data when publishing.
>>>>>>>> 
>>>>>>>> It would also make saving sessions more practical when many different volumes are created during the session - for example, when using a molmap low resolution representation for each domain.
>>>>>>>> 
>>>>>>>> This would not necessarily require creating a new format - just creating a tarball or folder with all the maps and relative paths specified in the python file would work fine I think?
>>>>>>>> 
>>>>>>>> Cheers,
>>>>>>>> Oli.
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> 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 <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
>>>>>>>> 
>>>>>>> 
>>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> 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 <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
>>>> 
>>> 
>> 
> 

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From meng at cgl.ucsf.edu  Thu Sep 17 11:32:00 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 17 Sep 2015 11:32:00 -0700
Subject: [Chimera-users] large file size exporting scene with spheres
In-Reply-To: <CBB320FC066A0544A3A4AD61E2C526B3113EA4EB@x10-mbx3.yu.yale.edu>
References: <CBB320FC066A0544A3A4AD61E2C526B3113EA39B@x10-mbx3.yu.yale.edu>
	<38F3333E-EC64-46BD-959F-F4D7CA982F06@cgl.ucsf.edu>
	<CBB320FC066A0544A3A4AD61E2C526B3113EA4EB@x10-mbx3.yu.yale.edu>
Message-ID: <2E8C2D52-D612-492D-84C3-5D178ACCD0FB@cgl.ucsf.edu>

On Sep 17, 2015, at 10:48 AM, Tom Goddard <goddard at sonic.net> wrote:

Hi Elaine, Bill,

  Chimera export first writes x3d and then converts that to STL or VRML or whatever you requested.  For atom spheres it writes the center and radius of the sphere in x3d.  It does not write the number of triangles or the amount subdivision.  The Chimera program x3d2stl controls how many triangles a sphere is turned into.  It uses 100 triangles per square Angstrom.  There is no option to change that.  But it is possible to run x3d2stl by hand and specify the resolution option ?-r 1? to request 1 triangle per square Angstrom, resulting in a file that is 100 times smaller and the spheres still look fine (using about 40 triangles per atom).

	~/Desktop/Chimera\ 1.10.2.app/Contents/Resources/bin/.x3d2stl -o 1a0m_r1.stl -r 1 < 1a0m.x3d

Note that .x3d2stl has a period as the first character.  Eric Bell reported this problem about a year and a half ago but the ridiculous defaul STL sphere subdivision has unfortunately not been changed.

	http://plato.cgl.ucsf.edu/trac/chimera/ticket/13183

  Tom

> On Sep 17, 2015, at 9:51 AM, Eliason, William <william.eliason at yale.edu> wrote:
> 
> Elaine,
> 
> Thanks again for your suggestions.  I had already seen that previous post you listed and found that the stl file size for spheres was unchanged with changes to the zoom.  The subdivision box in the effects tool changes the spheres on on the chimera display but has no effect on the stl file size when exporting a scene.
> 
> I will keep looking for a solution.  If you have any other suggestions please email me.
> 
> Thanks Again,
> 
> Bill 
> ________________________________________
> From: Elaine Meng [meng at cgl.ucsf.edu]
> Sent: Tuesday, September 15, 2015 3:42 PM
> To: Eliason, William
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] large file size exporting scene with spheres
> 
> Hi Bill,
> You can decrease the ?subdivision? setting in the Effects dialog (menu Tools? Viewing Controls? Effects) and also zoom out the view before exporting.
> 
> These are discussed in more detail in this previous post:
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_pipermail_chimera-2Dusers_2014-2DApril_009753.html&d=AwIF-g&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=GHLQ-YN3a3SZwmbxfQzG422WX8qFcxMwcqDhrmzYYig&m=82epIAtAXgjRN-pj6rQz0vxnLpXgRblFMlQ7tp8624A&s=ekvBZa1LD-g5eO8zKme9E80DrWt-4atfTpouu6hPG6E&e= >
> 
> 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 Sep 15, 2015, at 11:52 AM, Eliason, William <william.eliason at yale.edu> wrote:
>> 
>> Chimera-users,
>> 
>> I am very new to chimera.  I would like to export a scene with spheres for 3d printing but the ( .stl) file size is enormous.  They contain way to many triangles.  I tested a smallish molecule in MeshLab and I could decrease the number of faces from 699732 (34MB) to 34986 faces (1.7MB) with minor flattening of the sphere.  Is there a way to have chimera generate spheres with fewer faces?
>> 
>> Thank you,
>> 
>> Bill Eliason
> 
> 




From ingvar at ebi.ac.uk  Fri Sep 18 05:10:56 2015
From: ingvar at ebi.ac.uk (Ingvar Lagerstedt)
Date: Fri, 18 Sep 2015 13:10:56 +0100
Subject: [Chimera-users] Fetch by ID EMDB + fit PDBs enhancement suggestion
Message-ID: <113110A5-6F6B-4D10-93CC-28B3FB7B1916@ebi.ac.uk>

Dear Chimera,

Attempting to Fetch by ID an EMDB entry with a fitted model, where the model does exist in PDB format, causes an error: No such ID.  The map is retrieved but not opened in Chimera.

The two main reasons that the model is not available:
A. The model is only available in mmCIF format.  Since a wwPDB remediation at the end of last year, entries that are larger than what the PDB format can handle are no longer distributed as split entries.  They are only distributed as mmCIF (and PDBx) files.  This is common for say ribosomes.  EMD-6315 with fitted model 3j9z is an example.  Changing the command so that it attempts to retrieve mmCIF files rather than PDB files would fix this issue.

B. The model has not been released, EMDB and PDB releases for maps and models are not always synchronised. An example would be EMD-6413, where the model 3jb9 is currently waiting for author approval.  In this case it would be nice if the map was loaded.

Many Thanks,
Ingvar


From goddard at sonic.net  Fri Sep 18 10:55:31 2015
From: goddard at sonic.net (Tom Goddard)
Date: Fri, 18 Sep 2015 10:55:31 -0700
Subject: [Chimera-users] Fetch by ID EMDB + fit PDBs enhancement
	suggestion
In-Reply-To: <113110A5-6F6B-4D10-93CC-28B3FB7B1916@ebi.ac.uk>
References: <113110A5-6F6B-4D10-93CC-28B3FB7B1916@ebi.ac.uk>
Message-ID: <DD87F89F-37D8-4F65-9A0E-85CF020DBDE8@sonic.net>

Hi Ingvar,

  I?ve made Chimera fetch the mmCIF file if the PDB format file is not available.  This will be in tonight?s daily build.  Unfortunately the Chimera mmCIF file reader is very slow since it is written all in Python ? opening 3j9z.cif, 150,000 atoms, took 40 seconds.  I also fixed fetch EMDB + fit PDBs to show the map even if one or more PDBs are not found.  Thanks for reporting these bugs.

	Tom


> On Sep 18, 2015, at 5:10 AM, Ingvar Lagerstedt  wrote:
> 
> Dear Chimera,
> 
> Attempting to Fetch by ID an EMDB entry with a fitted model, where the model does exist in PDB format, causes an error: No such ID.  The map is retrieved but not opened in Chimera.
> 
> The two main reasons that the model is not available:
> A. The model is only available in mmCIF format.  Since a wwPDB remediation at the end of last year, entries that are larger than what the PDB format can handle are no longer distributed as split entries.  They are only distributed as mmCIF (and PDBx) files.  This is common for say ribosomes.  EMD-6315 with fitted model 3j9z is an example.  Changing the command so that it attempts to retrieve mmCIF files rather than PDB files would fix this issue.
> 
> B. The model has not been released, EMDB and PDB releases for maps and models are not always synchronised. An example would be EMD-6413, where the model 3jb9 is currently waiting for author approval.  In this case it would be nice if the map was loaded.
> 
> Many Thanks,
> Ingvar




From ingvar at ebi.ac.uk  Mon Sep 21 02:50:19 2015
From: ingvar at ebi.ac.uk (Ingvar Lagerstedt)
Date: Mon, 21 Sep 2015 10:50:19 +0100
Subject: [Chimera-users] Fetch by ID EMDB + fit PDBs enhancement
	suggestion
In-Reply-To: <DD87F89F-37D8-4F65-9A0E-85CF020DBDE8@sonic.net>
References: <113110A5-6F6B-4D10-93CC-28B3FB7B1916@ebi.ac.uk>
	<DD87F89F-37D8-4F65-9A0E-85CF020DBDE8@sonic.net>
Message-ID: <29016E5E-43CE-416B-8BBD-9D0DC9EE8CFF@ebi.ac.uk>

Hi Tom,

Thank you for the usual quick fixes.  The daily build on the download page still says Sep/16, I will try out these changes when they become available.  

Ingvar

On 18 Sep 2015, at 18:55, Tom Goddard <goddard at sonic.net> wrote:

> Hi Ingvar,
> 
>  I?ve made Chimera fetch the mmCIF file if the PDB format file is not available.  This will be in tonight?s daily build.  Unfortunately the Chimera mmCIF file reader is very slow since it is written all in Python ? opening 3j9z.cif, 150,000 atoms, took 40 seconds.  I also fixed fetch EMDB + fit PDBs to show the map even if one or more PDBs are not found.  Thanks for reporting these bugs.
> 
> 	Tom
> 
> 
>> On Sep 18, 2015, at 5:10 AM, Ingvar Lagerstedt  wrote:
>> 
>> Dear Chimera,
>> 
>> Attempting to Fetch by ID an EMDB entry with a fitted model, where the model does exist in PDB format, causes an error: No such ID.  The map is retrieved but not opened in Chimera.
>> 
>> The two main reasons that the model is not available:
>> A. The model is only available in mmCIF format.  Since a wwPDB remediation at the end of last year, entries that are larger than what the PDB format can handle are no longer distributed as split entries.  They are only distributed as mmCIF (and PDBx) files.  This is common for say ribosomes.  EMD-6315 with fitted model 3j9z is an example.  Changing the command so that it attempts to retrieve mmCIF files rather than PDB files would fix this issue.
>> 
>> B. The model has not been released, EMDB and PDB releases for maps and models are not always synchronised. An example would be EMD-6413, where the model 3jb9 is currently waiting for author approval.  In this case it would be nice if the map was loaded.
>> 
>> Many Thanks,
>> Ingvar
> 




From goddard at sonic.net  Mon Sep 21 10:35:33 2015
From: goddard at sonic.net (Tom Goddard)
Date: Mon, 21 Sep 2015 10:35:33 -0700
Subject: [Chimera-users] Fetch by ID EMDB + fit PDBs enhancement
	suggestion
In-Reply-To: <29016E5E-43CE-416B-8BBD-9D0DC9EE8CFF@ebi.ac.uk>
References: <113110A5-6F6B-4D10-93CC-28B3FB7B1916@ebi.ac.uk>
	<DD87F89F-37D8-4F65-9A0E-85CF020DBDE8@sonic.net>
	<29016E5E-43CE-416B-8BBD-9D0DC9EE8CFF@ebi.ac.uk>
Message-ID: <4495754C-CC91-4396-90AC-C89CC385C6D7@sonic.net>

Hi Ingvar,

  The Chimera 1 nightly builds were hung.  We fixed it just now and tonight it should build the new code that fetches mmCIF files if the PDB format file does not exist.  We do almost all of our development of Chimera 2 now (not yet released), so we sometimes don?t notice immediately when something goes awry with Chimera 1.

	Tom


> On Sep 21, 2015, at 2:50 AM, Ingvar Lagerstedt  wrote:
> 
> Hi Tom,
> 
> Thank you for the usual quick fixes.  The daily build on the download page still says Sep/16, I will try out these changes when they become available.  
> 
> Ingvar
> 
> On 18 Sep 2015, at 18:55, Tom Goddard <goddard at sonic.net> wrote:
> 
>> Hi Ingvar,
>> 
>> I?ve made Chimera fetch the mmCIF file if the PDB format file is not available.  This will be in tonight?s daily build.  Unfortunately the Chimera mmCIF file reader is very slow since it is written all in Python ? opening 3j9z.cif, 150,000 atoms, took 40 seconds.  I also fixed fetch EMDB + fit PDBs to show the map even if one or more PDBs are not found.  Thanks for reporting these bugs.
>> 
>> 	Tom
>> 
>> 
>>> On Sep 18, 2015, at 5:10 AM, Ingvar Lagerstedt  wrote:
>>> 
>>> Dear Chimera,
>>> 
>>> Attempting to Fetch by ID an EMDB entry with a fitted model, where the model does exist in PDB format, causes an error: No such ID.  The map is retrieved but not opened in Chimera.
>>> 
>>> The two main reasons that the model is not available:
>>> A. The model is only available in mmCIF format.  Since a wwPDB remediation at the end of last year, entries that are larger than what the PDB format can handle are no longer distributed as split entries.  They are only distributed as mmCIF (and PDBx) files.  This is common for say ribosomes.  EMD-6315 with fitted model 3j9z is an example.  Changing the command so that it attempts to retrieve mmCIF files rather than PDB files would fix this issue.
>>> 
>>> B. The model has not been released, EMDB and PDB releases for maps and models are not always synchronised. An example would be EMD-6413, where the model 3jb9 is currently waiting for author approval.  In this case it would be nice if the map was loaded.
>>> 
>>> Many Thanks,
>>> Ingvar
>> 
> 
> 




From afm at uky.edu  Mon Sep 21 13:35:40 2015
From: afm at uky.edu (Anne-Frances Miller)
Date: Mon, 21 Sep 2015 16:35:40 -0400
Subject: [Chimera-users] applying charges calculated by DFT to ligands in
	protein models
Message-ID: <0B4456D4-1A2A-4496-AD64-0E50D760A2BA@uky.edu>

Dear Sir or Madam,
Our protein has a bound FMN and the various tools accessible via Chimera are not able to apply charges to the atoms in FMN.  However I have NBO charges for all the atoms from DFT calculations. Is there a way I can provide these to the FMN in my pdb file or in my Chimera session in order to then display a Coulomb electrostatic potential for the protein + FMN?  My charges are not simply +1 or -1, but fractional charges for each atom.  Can Chimera accommodate this ?  If not, no problem, I will still benefit greatly even if all I can do is add -1 to the one atom at which most of the excess electron density is concentrated.

Many Thanks,
Anne-Frances

Anne-Frances Miller
Professor of Chemistry
Director, Magnetic Resonance Centre
University of Kentucky
Dept. Chemistry, 505 Rose Street
Lexington KY 40506-0055

?You never change things by fighting the existing reality. To change something, build a new model that makes the existing model obsolete.? Buckminster Fuller 




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From meng at cgl.ucsf.edu  Mon Sep 21 16:25:16 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 21 Sep 2015 16:25:16 -0700
Subject: [Chimera-users] applying charges calculated by DFT to ligands
	in protein models
In-Reply-To: <0B4456D4-1A2A-4496-AD64-0E50D760A2BA@uky.edu>
References: <0B4456D4-1A2A-4496-AD64-0E50D760A2BA@uky.edu>
Message-ID: <0BD88AEA-3327-4248-989A-1CA86DBD8113@cgl.ucsf.edu>

Dear Anne-Frances,
Yes, you can assign your own atomic partial charges.  If you?re doing it for the purposes of energy minimization, it is still necessary to run Add Charge because that tool assigns the atom types needed for minimization.  In Add Charge, just choose the quick Gasteiger method since you will be over-writing the charges with your own values anyway.  The (somewhat circuitous) process is outlined here:

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#user-specified>

As mentioned in that link, to assign your custom charges you would then need to either use a series of ?setattr? commands, each assigning the charge to a single atom in the FMN residue, or create an attribute assignment file listing all of the charges for the atoms of that residue and read it in with ?defattr? (or equivalently, the Define Attribute tool).  See that link for details.

If you aren?t doing energy minimization, for example if you?re just going to color the surface by electrostatic potential, you wouldn?t have to run Add Charge.  You?d just need to assign your charges with setattr or defattr as above, or read them in along with the coordinates of the FMN molecule if you had it in a separate Mol2 or PQR file, as described in the bottom section of this page.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.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 Sep 21, 2015, at 1:35 PM, Anne-Frances Miller <afm at uky.edu> wrote:
> 
> Dear Sir or Madam,
> Our protein has a bound FMN and the various tools accessible via Chimera are not able to apply charges to the atoms in FMN.  However I have NBO charges for all the atoms from DFT calculations. Is there a way I can provide these to the FMN in my pdb file or in my Chimera session in order to then display a Coulomb electrostatic potential for the protein + FMN?  My charges are not simply +1 or -1, but fractional charges for each atom.  Can Chimera accommodate this ?  If not, no problem, I will still benefit greatly even if all I can do is add -1 to the one atom at which most of the excess electron density is concentrated.
> 
> Many Thanks,
> Anne-Frances




From afm at uky.edu  Mon Sep 21 17:10:45 2015
From: afm at uky.edu (Anne-Frances Miller)
Date: Mon, 21 Sep 2015 20:10:45 -0400
Subject: [Chimera-users] applying charges calculated by DFT to ligands
	in protein models
In-Reply-To: <0BD88AEA-3327-4248-989A-1CA86DBD8113@cgl.ucsf.edu>
References: <0B4456D4-1A2A-4496-AD64-0E50D760A2BA@uky.edu>
	<0BD88AEA-3327-4248-989A-1CA86DBD8113@cgl.ucsf.edu>
Message-ID: <9388D83B-1623-4E1D-A9C4-AE463EA634AB@uky.edu>

This is very helpful,
Thank you Elaine.

Anne-Frances Miller
Professor of Chemistry
Director, Magnetic Resonance Centre
University of Kentucky
Dept. Chemistry, 505 Rose Street
Lexington KY 40506-0055

?You never change things by fighting the existing reality. To change something, build a new model that makes the existing model obsolete.? Buckminster Fuller 




> On Sep 21, 2015, at 7:25 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Dear Anne-Frances,
> Yes, you can assign your own atomic partial charges.  If you?re doing it for the purposes of energy minimization, it is still necessary to run Add Charge because that tool assigns the atom types needed for minimization.  In Add Charge, just choose the quick Gasteiger method since you will be over-writing the charges with your own values anyway.  The (somewhat circuitous) process is outlined here:
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#user-specified>
> 
> As mentioned in that link, to assign your custom charges you would then need to either use a series of ?setattr? commands, each assigning the charge to a single atom in the FMN residue, or create an attribute assignment file listing all of the charges for the atoms of that residue and read it in with ?defattr? (or equivalently, the Define Attribute tool).  See that link for details.
> 
> If you aren?t doing energy minimization, for example if you?re just going to color the surface by electrostatic potential, you wouldn?t have to run Add Charge.  You?d just need to assign your charges with setattr or defattr as above, or read them in along with the coordinates of the FMN molecule if you had it in a separate Mol2 or PQR file, as described in the bottom section of this page.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.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 Sep 21, 2015, at 1:35 PM, Anne-Frances Miller <afm at uky.edu> wrote:
>> 
>> Dear Sir or Madam,
>> Our protein has a bound FMN and the various tools accessible via Chimera are not able to apply charges to the atoms in FMN.  However I have NBO charges for all the atoms from DFT calculations. Is there a way I can provide these to the FMN in my pdb file or in my Chimera session in order to then display a Coulomb electrostatic potential for the protein + FMN?  My charges are not simply +1 or -1, but fractional charges for each atom.  Can Chimera accommodate this ?  If not, no problem, I will still benefit greatly even if all I can do is add -1 to the one atom at which most of the excess electron density is concentrated.
>> 
>> Many Thanks,
>> Anne-Frances
> 

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From hyeh at cse.tamu.edu  Wed Sep 23 11:09:52 2015
From: hyeh at cse.tamu.edu (Hsin-Yi Yeh)
Date: Wed, 23 Sep 2015 13:09:52 -0500
Subject: [Chimera-users] Rendering protein molecule to a geometry format by
	Chimera
Message-ID: <CAFyKXewYzRw8meGcsxhrp-fxHGT3e3DMtsXEPHOOYdbSjP8GDg@mail.gmail.com>

Hi,

I try to render a protein molecule to a geometry format (from .pdb format
to .obj format) by Chimera. I use 'Multiscale models' tool in 'Higher-Order
Structure' choice and then make the model by resurfacing at some
appropriate resolution. It turns out that the whole protein molecule can be
modeled pretty nicely.

However, I now have a similar problem; instead of rendering the whole
protein molecule, I would like to render the whole structure separately. I
want to render the exposed residues (those residues on the surface) and
non-exposed/buried residues separately, so I will have two obj files (one
for the exposed residues and the others for the non-exposed residues).

I haven't been able to figure this problem out yet. Thus, I am wondering
could you please give me some direction? Any advice will be greatly
appreciated!

Thank you,

Hsin-Yi (Cindy) Yeh


-- 
Hsin-Yi (Cindy) Yeh
PhD Student
Parasol Lab, Department of Computer Science and Engineering
Texas A&M University
Email: hyeh at cse.tamu.edu
https://parasol.tamu.edu/people/hyeh/
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From Joanne.Williams at ucsf.edu  Wed Sep 23 13:36:22 2015
From: Joanne.Williams at ucsf.edu (Williams, Joanne)
Date: Wed, 23 Sep 2015 20:36:22 +0000
Subject: [Chimera-users] FW: How can I find H-bond between ligand and
	protein residues within selected angstrom?
In-Reply-To: <1442651340829820.280547171@ums006.ecc.u-tokyo.ac.jp>
References: <1442651340829820.280547171@ums006.ecc.u-tokyo.ac.jp>
Message-ID: <D2285B49.C0B0C%Joanne.Williams@ucsf.edu>



On 9/19/15 1:29 AM, "?????" <kagaribi-firefly at bs.s.u-tokyo.ac.jp>
wrote:

> Dear Chimera creator,
> 
> I use Chimera to analyse protein-ligand interaction.
> Especially, I would like to find H-bond between these.
> I clicked HBonds and tried to search H-bond within selected distance.
> However,I could not.
> I guess the reason is that I was not able to understand "Relax
> constraints" in H-Bond parameter window.
> I ,of course, checked chimera's help.
> What is relax constraints?
> What does 0.4 angstroms indicate? Is this the Max distance between ligand
> and protein residue?
> I would like to find H-bond between them within selected angstrom.
> What should I do to know that?
> Please teach me how to do.
> Thank you for being patient with my English.
> 
> Best regards,
> 
> Yuriko Takagi
> Tokyo university student





From olibclarke at gmail.com  Wed Sep 23 14:42:40 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Wed, 23 Sep 2015 17:42:40 -0400
Subject: [Chimera-users] Suggestion - autofilter history by typed substring?
Message-ID: <312B2BD2-BFD6-42D1-8F29-6CB96BFE0878@gmail.com>

Hi all,

Just a suggestion (I guess for chimera 2) - would it be possible to autofilter the command history based on the typed substring? 

That is if I have typed ?sel? and hit the up arrow, to only cycle through those commands in the history that start with ?sel?.

This would be particularly handy for scrolling quickly through recent ?sel? and ?color? commands - a similar mechanism is implemented in several shells and it works well.

Cheers,
Oliver.


From goddard at sonic.net  Wed Sep 23 19:59:55 2015
From: goddard at sonic.net (Tom Goddard)
Date: Wed, 23 Sep 2015 19:59:55 -0700
Subject: [Chimera-users] Rendering protein molecule to a geometry format
	by Chimera
In-Reply-To: <CAFyKXewYzRw8meGcsxhrp-fxHGT3e3DMtsXEPHOOYdbSjP8GDg@mail.gmail.com>
References: <CAFyKXewYzRw8meGcsxhrp-fxHGT3e3DMtsXEPHOOYdbSjP8GDg@mail.gmail.com>
Message-ID: <96A8E2B5-F728-44E2-A5DB-D8DFE7DEC166@sonic.net>

Hi Hsin-Yi,

  There are lots of messages on the Chimera mailing list about how to identify surface exposed residues, for example,

	http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-May/006336.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-May/006336.html>

You can search the mailing list from the Chimera documentation web page:

	http://www.cgl.ucsf.edu/chimera/docindex.html <http://www.cgl.ucsf.edu/chimera/docindex.html>

The multiscale tool makes surfaces for each chain.  To make surfaces of any set of selected atoms use the molmap command, for example, ?molmap sel 5? to make a 5 Angstrom resolution surface.  Here are molmap docs:

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

Those surfaces can be exported as OBJ with menu File / Export Scene?.

  Tom


> On Sep 23, 2015, at 11:09 AM, Hsin-Yi Yeh <hyeh at cse.tamu.edu> wrote:
> 
> Hi,
> 
> I try to render a protein molecule to a geometry format (from .pdb format to .obj format) by Chimera. I use 'Multiscale models' tool in 'Higher-Order Structure' choice and then make the model by resurfacing at some appropriate resolution. It turns out that the whole protein molecule can be modeled pretty nicely. 
> 
> However, I now have a similar problem; instead of rendering the whole protein molecule, I would like to render the whole structure separately. I want to render the exposed residues (those residues on the surface) and non-exposed/buried residues separately, so I will have two obj files (one for the exposed residues and the others for the non-exposed residues).
> 
> I haven't been able to figure this problem out yet. Thus, I am wondering could you please give me some direction? Any advice will be greatly appreciated!
> 
> Thank you,
> 
> Hsin-Yi (Cindy) Yeh
> 
> 
> -- 
> Hsin-Yi (Cindy) Yeh
> PhD Student
> Parasol Lab, Department of Computer Science and Engineering
> Texas A&M University
> Email: hyeh at cse.tamu.edu <mailto:hyeh at cse.tamu.edu>
> https://parasol.tamu.edu/people/hyeh/ <https://parasol.tamu.edu/people/hyeh/>_______________________________________________
> 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 Sep 24 09:40:16 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 24 Sep 2015 09:40:16 -0700
Subject: [Chimera-users] FW: How can I find H-bond between ligand and
	protein residues within selected angstrom?
In-Reply-To: <D2285B49.C0B0C%Joanne.Williams@ucsf.edu>
References: <1442651340829820.280547171@ums006.ecc.u-tokyo.ac.jp>
	<D2285B49.C0B0C%Joanne.Williams@ucsf.edu>
Message-ID: <27158246-0DFF-48C4-B14F-004CFFB7BA5E@cgl.ucsf.edu>

Dear Yuriko Takagi,
The values in the FindHBond are not the distance and angle cutoffs, they are extra ?tolerance? values added to these cutoffs.  The cutoffs are not shown in the FindHBond dialog because there are many different distance and angle cutoffs depending on the types of the atoms.  For example, the distance and angle cutoff(s) would be different for N-H to O=C  than for O-H to O=C. 

This is mentioned in bottom section of the the FindHBond help page, 
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html#criteria>

...and the many different cutoff values are listed in tables 5-8 of the paper cited in that page:

Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. Mills JE, Dean PM. J Comput Aided Mol Des. 1996 Dec;10(6):607-22.
<http://www.ncbi.nlm.nih.gov/pubmed/9007693>

Then if you use a ?relax? distance value of 0.4 angstrom, 0.4 will be added to all of those different distance cutoff values.

With FindHBond you cannot just use a single same distance for everything, but you can show distance labels on the results and/or write output information (including distances) to the Reply Log or to a file.  Then if you want to, you can ignore the results with longer than a certain distance.

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 9/19/15 1:29 AM, "?????" <kagaribi-firefly at bs.s.u-tokyo.ac.jp>
wrote:

> Dear Chimera creator,
> 
> I use Chimera to analyse protein-ligand interaction.
> Especially, I would like to find H-bond between these.
> I clicked HBonds and tried to search H-bond within selected distance.
> However,I could not.
> I guess the reason is that I was not able to understand "Relax
> constraints" in H-Bond parameter window.
> I ,of course, checked chimera's help.
> What is relax constraints?
> What does 0.4 angstroms indicate? Is this the Max distance between ligand
> and protein residue?
> I would like to find H-bond between them within selected angstrom.
> What should I do to know that?
> Please teach me how to do.
> Thank you for being patient with my English.
> 
> Best regards,
> 
> Yuriko Takagi
> Tokyo university student




From olibclarke at gmail.com  Thu Sep 24 13:39:54 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Thu, 24 Sep 2015 16:39:54 -0400
Subject: [Chimera-users] Way to extract path to file from model ID
Message-ID: <E7058AE0-3DE7-4D49-82A2-D375DCFFBFF3@gmail.com>

Hi all, I?m wondering, is there any way (presumably via a python function) to get the path to the original file from the model ID?

I?ve written a little python jiffy (below) so I can lowpass filter maps to a specified resolution on the fly inside chimera using EMAN, but is quite slow because I need to first write a copy of the map out (so I know where it is) and then modify it. If anyone knows of an easier way to do such things I would be most grateful.

Cheers,
Oli.

Script:

def cmd_lowpass(lowpass,args):
  from Midas.midas_text import doExtensionFunc
  def lowpass(model,resol):
    import os
    from chimera import runCommand
    import subprocess
    import sys
    #You may need to change the below to .bash_profile if on mac.
    #You must have EMAN2 in your bash path for this to work correctly.
    #If running multiple times, you need to close the first instance of lowpass.mrc before creating a second.
    bashrc_path=os.path.expanduser("~/.bashrc")
    freq=1.0/resol
    command="cd ~; system mkdir chimera_tmp; cd chimera_tmp; volume "+model+" save ./tmp1.mrc"
    runCommand(command)
    pathvar=os.path.expanduser("~/chimera_tmp")
    os.chdir(pathvar)
    e2string="--process=filter.lowpass.gauss:cutoff_freq="+str(freq)
    print(e2string)
    mrc_in=pathvar+"/tmp1.mrc"
    mrc_out=pathvar+"/lowpass.mrc"
    e2command="source "+bashrc_path+"; bash -c \"e2proc3d.py"+" "+mrc_in+" "+mrc_out+" "+e2string+"\""
    print(e2command)
    proc=subprocess.Popen(e2command,stdout=subprocess.PIPE, stderr=subprocess.PIPE,shell=True)
    out, err = proc.communicate()
    print 'stdout:', out
    print 'stderr:', err
    runCommand("open lowpass.mrc")
  doExtensionFunc(lowpass,args)
from Midas.midas_text import addCommand
addCommand("lowpass", cmd_lowpass, help=False)


From pett at cgl.ucsf.edu  Thu Sep 24 13:58:45 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 24 Sep 2015 13:58:45 -0700
Subject: [Chimera-users] Way to extract path to file from model ID
In-Reply-To: <E7058AE0-3DE7-4D49-82A2-D375DCFFBFF3@gmail.com>
References: <E7058AE0-3DE7-4D49-82A2-D375DCFFBFF3@gmail.com>
Message-ID: <472835B4-5D55-477D-A870-FB6F6B8EFE01@cgl.ucsf.edu>

If a model has an ?openedAs? attribute (which I believe all models opened from files have), then openedAs[0] is the path of the input file.

?Eric

> On Sep 24, 2015, at 1:39 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Hi all, I?m wondering, is there any way (presumably via a python function) to get the path to the original file from the model ID?
> 
> I?ve written a little python jiffy (below) so I can lowpass filter maps to a specified resolution on the fly inside chimera using EMAN, but is quite slow because I need to first write a copy of the map out (so I know where it is) and then modify it. If anyone knows of an easier way to do such things I would be most grateful.
> 
> Cheers,
> Oli.
> 
> Script:
> 
> def cmd_lowpass(lowpass,args):
>  from Midas.midas_text import doExtensionFunc
>  def lowpass(model,resol):
>    import os
>    from chimera import runCommand
>    import subprocess
>    import sys
>    #You may need to change the below to .bash_profile if on mac.
>    #You must have EMAN2 in your bash path for this to work correctly.
>    #If running multiple times, you need to close the first instance of lowpass.mrc before creating a second.
>    bashrc_path=os.path.expanduser("~/.bashrc")
>    freq=1.0/resol
>    command="cd ~; system mkdir chimera_tmp; cd chimera_tmp; volume "+model+" save ./tmp1.mrc"
>    runCommand(command)
>    pathvar=os.path.expanduser("~/chimera_tmp")
>    os.chdir(pathvar)
>    e2string="--process=filter.lowpass.gauss:cutoff_freq="+str(freq)
>    print(e2string)
>    mrc_in=pathvar+"/tmp1.mrc"
>    mrc_out=pathvar+"/lowpass.mrc"
>    e2command="source "+bashrc_path+"; bash -c \"e2proc3d.py"+" "+mrc_in+" "+mrc_out+" "+e2string+"\""
>    print(e2command)
>    proc=subprocess.Popen(e2command,stdout=subprocess.PIPE, stderr=subprocess.PIPE,shell=True)
>    out, err = proc.communicate()
>    print 'stdout:', out
>    print 'stderr:', err
>    runCommand("open lowpass.mrc")
>  doExtensionFunc(lowpass,args)
> from Midas.midas_text import addCommand
> addCommand("lowpass", cmd_lowpass, help=False)
> _______________________________________________
> 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 Sep 24 14:00:27 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Thu, 24 Sep 2015 17:00:27 -0400
Subject: [Chimera-users] Way to extract path to file from model ID
In-Reply-To: <472835B4-5D55-477D-A870-FB6F6B8EFE01@cgl.ucsf.edu>
References: <E7058AE0-3DE7-4D49-82A2-D375DCFFBFF3@gmail.com>
	<472835B4-5D55-477D-A870-FB6F6B8EFE01@cgl.ucsf.edu>
Message-ID: <20A777BC-C8C8-4389-B545-C84D478CCC48@gmail.com>

Aha, great. Thanks Eric!?

Oliver.
> On Sep 24, 2015, at 4:58 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> If a model has an ?openedAs? attribute (which I believe all models opened from files have), then openedAs[0] is the path of the input file.
> 
> ?Eric
> 
>> On Sep 24, 2015, at 1:39 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
>> 
>> Hi all, I?m wondering, is there any way (presumably via a python function) to get the path to the original file from the model ID?
>> 
>> I?ve written a little python jiffy (below) so I can lowpass filter maps to a specified resolution on the fly inside chimera using EMAN, but is quite slow because I need to first write a copy of the map out (so I know where it is) and then modify it. If anyone knows of an easier way to do such things I would be most grateful.
>> 
>> Cheers,
>> Oli.
>> 
>> Script:
>> 
>> def cmd_lowpass(lowpass,args):
>> from Midas.midas_text import doExtensionFunc
>> def lowpass(model,resol):
>>   import os
>>   from chimera import runCommand
>>   import subprocess
>>   import sys
>>   #You may need to change the below to .bash_profile if on mac.
>>   #You must have EMAN2 in your bash path for this to work correctly.
>>   #If running multiple times, you need to close the first instance of lowpass.mrc before creating a second.
>>   bashrc_path=os.path.expanduser("~/.bashrc")
>>   freq=1.0/resol
>>   command="cd ~; system mkdir chimera_tmp; cd chimera_tmp; volume "+model+" save ./tmp1.mrc"
>>   runCommand(command)
>>   pathvar=os.path.expanduser("~/chimera_tmp")
>>   os.chdir(pathvar)
>>   e2string="--process=filter.lowpass.gauss:cutoff_freq="+str(freq)
>>   print(e2string)
>>   mrc_in=pathvar+"/tmp1.mrc"
>>   mrc_out=pathvar+"/lowpass.mrc"
>>   e2command="source "+bashrc_path+"; bash -c \"e2proc3d.py"+" "+mrc_in+" "+mrc_out+" "+e2string+"\""
>>   print(e2command)
>>   proc=subprocess.Popen(e2command,stdout=subprocess.PIPE, stderr=subprocess.PIPE,shell=True)
>>   out, err = proc.communicate()
>>   print 'stdout:', out
>>   print 'stderr:', err
>>   runCommand("open lowpass.mrc")
>> doExtensionFunc(lowpass,args)
>> from Midas.midas_text import addCommand
>> addCommand("lowpass", cmd_lowpass, help=False)
>> _______________________________________________
>> 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 Sep 24 14:26:28 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Thu, 24 Sep 2015 17:26:28 -0400
Subject: [Chimera-users] Way to extract path to file from model ID
In-Reply-To: <20A777BC-C8C8-4389-B545-C84D478CCC48@gmail.com>
References: <E7058AE0-3DE7-4D49-82A2-D375DCFFBFF3@gmail.com>
	<472835B4-5D55-477D-A870-FB6F6B8EFE01@cgl.ucsf.edu>
	<20A777BC-C8C8-4389-B545-C84D478CCC48@gmail.com>
Message-ID: <8971C631-395A-4BD3-8B79-F0F4048A2BCD@gmail.com>

That worked - here is the amended python snippet in case it is useful to anyone else:

def cmd_lowpass(lowpass,args):
  from Midas.midas_text import doExtensionFunc
  def lowpass(model,resol):
    import os
    from chimera import runCommand
    from chimera import openModels
    import subprocess
    import sys
    #You may need to change the below to .bash_profile if on mac.
    #You must have EMAN2 in your bash path for this to work correctly.
    bashrc_path=os.path.expanduser("~/.bashrc")
    freq=1.0/resol
    command="cd ~; system mkdir chimera_tmp; cd chimera_tmp"
    runCommand(command)
    pathvar=os.path.expanduser("~/chimera_tmp")
    os.chdir(pathvar)
    e2string="--process=filter.lowpass.gauss:cutoff_freq="+str(freq)
    model_no=int(model[1])
    mrc_in=openModels.list()[model_no].openedAs[0]
    mrc_out=pathvar+"/lowpass.mrc"
    e2command="source "+bashrc_path+"; bash -c \"e2proc3d.py"+" "+mrc_in+" "+mrc_out+" "+e2string+"\""
    for mol in openModels.list():
      if mol.openedAs[0]=="lowpass.mrc":
        runCommand("close {}".format(mol))
    proc=subprocess.Popen(e2command,stdout=subprocess.PIPE, stderr=subprocess.PIPE,shell=True)
    out, err = proc.communicate()
    print 'stdout:', out
    print 'stderr:', err
    runCommand("open lowpass.mrc")
  doExtensionFunc(lowpass,args)
from Midas.midas_text import addCommand
addCommand("lowpass", cmd_lowpass, help=False)


> On Sep 24, 2015, at 5:00 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Aha, great. Thanks Eric!?
> 
> Oliver.
>> On Sep 24, 2015, at 4:58 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>> 
>> If a model has an ?openedAs? attribute (which I believe all models opened from files have), then openedAs[0] is the path of the input file.
>> 
>> ?Eric
>> 
>>> On Sep 24, 2015, at 1:39 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
>>> 
>>> Hi all, I?m wondering, is there any way (presumably via a python function) to get the path to the original file from the model ID?
>>> 
>>> I?ve written a little python jiffy (below) so I can lowpass filter maps to a specified resolution on the fly inside chimera using EMAN, but is quite slow because I need to first write a copy of the map out (so I know where it is) and then modify it. If anyone knows of an easier way to do such things I would be most grateful.
>>> 
>>> Cheers,
>>> Oli.
>>> 
>>> Script:
>>> 
>>> def cmd_lowpass(lowpass,args):
>>> from Midas.midas_text import doExtensionFunc
>>> def lowpass(model,resol):
>>>  import os
>>>  from chimera import runCommand
>>>  import subprocess
>>>  import sys
>>>  #You may need to change the below to .bash_profile if on mac.
>>>  #You must have EMAN2 in your bash path for this to work correctly.
>>>  #If running multiple times, you need to close the first instance of lowpass.mrc before creating a second.
>>>  bashrc_path=os.path.expanduser("~/.bashrc")
>>>  freq=1.0/resol
>>>  command="cd ~; system mkdir chimera_tmp; cd chimera_tmp; volume "+model+" save ./tmp1.mrc"
>>>  runCommand(command)
>>>  pathvar=os.path.expanduser("~/chimera_tmp")
>>>  os.chdir(pathvar)
>>>  e2string="--process=filter.lowpass.gauss:cutoff_freq="+str(freq)
>>>  print(e2string)
>>>  mrc_in=pathvar+"/tmp1.mrc"
>>>  mrc_out=pathvar+"/lowpass.mrc"
>>>  e2command="source "+bashrc_path+"; bash -c \"e2proc3d.py"+" "+mrc_in+" "+mrc_out+" "+e2string+"\""
>>>  print(e2command)
>>>  proc=subprocess.Popen(e2command,stdout=subprocess.PIPE, stderr=subprocess.PIPE,shell=True)
>>>  out, err = proc.communicate()
>>>  print 'stdout:', out
>>>  print 'stderr:', err
>>>  runCommand("open lowpass.mrc")
>>> doExtensionFunc(lowpass,args)
>>> from Midas.midas_text import addCommand
>>> addCommand("lowpass", cmd_lowpass, help=False)
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>> 
>> 
> 




From cmartin013 at drury.edu  Wed Sep 23 14:15:24 2015
From: cmartin013 at drury.edu (Cale Martin)
Date: Wed, 23 Sep 2015 21:15:24 +0000
Subject: [Chimera-users] Forcefields and Molecular Radii
Message-ID: <BLUPR02MB169702BC7B5073ED0B4FF58794440@BLUPR02MB1697.namprd02.prod.outlook.com>

Dear Chimera users,

Over the last few days I have been using Chimera 1.9 to model the Poisson-Boltzmann surface potential of a protein.  I have been using the APBS software and the two main forcefields I have been using are the TYL06 and AMBER.  When I model the chemokine using the AMBER forcefield the result seems to be normal and as expected, but when using the TYL06 forcefield, the final molecule surface seems to have larger molecule radii almost making it look a little more "bubbly" for lack of a better term.  Is this a function of the forcefield in any way?  Should this be expected from these two different forcefields?

Another issue that I have had along the same line involves the APBS program.  The settings allow for the selection of a "Smoothed Molecular Surface" and one that is just "Molecular Surface" but when I run the program with every thing the same except these settings, the results look exactly the same.  Should this setting affect the visualization of my molecule surface in any way?

Thank you,
Cale Martin
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From kagaribi-firefly at bs.s.u-tokyo.ac.jp  Fri Sep 25 01:53:19 2015
From: kagaribi-firefly at bs.s.u-tokyo.ac.jp (=?ISO-2022-JP?B?GyRCOWJMWk0nTX07UhsoQg==?=)
Date: Fri, 25 Sep 2015 17:53:19 +0900
Subject: [Chimera-users] FW: How can I find H-bond between ligand and
 protein residues within selected angstrom?
In-Reply-To: <27158246-0DFF-48C4-B14F-004CFFB7BA5E@cgl.ucsf.edu>
References: <1442651340829820.280547171@ums006.ecc.u-tokyo.ac.jp>
	<D2285B49.C0B0C%Joanne.Williams@ucsf.edu>
	<27158246-0DFF-48C4-B14F-004CFFB7BA5E@cgl.ucsf.edu>
Message-ID: <1443171199207826.1288815341@ums008.ecc.u-tokyo.ac.jp>

Dear Meng,

Thank you for your reply and kind description.
I will try the way to find protein-ligand interaction.
If I have some questions after this,I will ask your team.

Best regards,

Yuriko Takagi
Tokyo university student

 
----- Original Message -----
>> From: Elaine Meng <meng at cgl.ucsf.edu>
>> To: kagaribi-firefly at bs.s.u-tokyo.ac.jp
>> Cc: Chimera_mailing_list <chimera-users at cgl.ucsf.edu>
>> Date: 2015-09-25 01:40:16
>> Subject: Re: [Chimera-users] FW: How can I find H-bond between ligand and protein residues within selected angstrom?
>> 
>> Dear Yuriko Takagi,
>> The values in the FindHBond are not the distance and angle cutoffs, they are extra ?tolerance? values added to these cutoffs.  The cutoffs are not shown in the FindHBond dialog because there are many different distance and angle cutoffs depending on the types of the atoms.  For example, the distance and angle cutoff(s) would be different for N-H to O=C  than for O-H to O=C. 
>> 
>> This is mentioned in bottom section of the the FindHBond help page, 
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html#criteria>
>> 
>> ...and the many different cutoff values are listed in tables 5-8 of the paper cited in that page:
>> 
>> Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. Mills JE, Dean PM. J Comput Aided Mol Des. 1996 Dec;10(6):607-22.
>> <http://www.ncbi.nlm.nih.gov/pubmed/9007693>
>> 
>> Then if you use a ?relax? distance value of 0.4 angstrom, 0.4 will be added to all of those different distance cutoff values.
>> 
>> With FindHBond you cannot just use a single same distance for everything, but you can show distance labels on the results and/or write output information (including distances) to the Reply Log or to a file.  Then if you want to, you can ignore the results with longer than a certain distance.
>> 
>> 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 9/19/15 1:29 AM, "?????" <kagaribi-firefly at bs.s.u-tokyo.ac.jp>
>> wrote:
>> 
>> > Dear Chimera creator,
>> > 
>> > I use Chimera to analyse protein-ligand interaction.
>> > Especially, I would like to find H-bond between these.
>> > I clicked HBonds and tried to search H-bond within selected distance.
>> > However,I could not.
>> > I guess the reason is that I was not able to understand "Relax
>> > constraints" in H-Bond parameter window.
>> > I ,of course, checked chimera's help.
>> > What is relax constraints?
>> > What does 0.4 angstroms indicate? Is this the Max distance between ligand
>> > and protein residue?
>> > I would like to find H-bond between them within selected angstrom.
>> > What should I do to know that?
>> > Please teach me how to do.
>> > Thank you for being patient with my English.
>> > 
>> > Best regards,
>> > 
>> > Yuriko Takagi
>> > Tokyo university student
>> 
>> 


From meng at cgl.ucsf.edu  Fri Sep 25 10:08:52 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 25 Sep 2015 10:08:52 -0700
Subject: [Chimera-users] Forcefields and Molecular Radii
In-Reply-To: <BLUPR02MB169702BC7B5073ED0B4FF58794440@BLUPR02MB1697.namprd02.prod.outlook.com>
References: <BLUPR02MB169702BC7B5073ED0B4FF58794440@BLUPR02MB1697.namprd02.prod.outlook.com>
Message-ID: <C0817FBC-C79A-49B7-8C23-523401A0DB39@cgl.ucsf.edu>

Dear Cale,
Bear in mind that the PDB2PQR and APBS tools in Chimera are interfaces to web services running software developed by others (not the Chimera team), so we generally refer to the authors of the software for detailed documentation.

Nevertheless, in the Chimera manual we try to include brief explanations and links to external sites as appropriate. 

(A) I don?t know anything about the TYL06 forcefield specifically, but the Chimera-PDB2PQR manpage gives a literature reference for it that might discuss the radii:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html>
"TYL06 - a Poisson-Boltzmann-optimized force field (Tang, Yang, and Luo, J Phys Chem B 110:18680 (2006))"
<http://www.ncbi.nlm.nih.gov/pubmed/16970499>

You coulld also text-edit the output PQR file to see the radius values directly.

(2) As described in the Chimera-APBS manpage
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html>
? smoothed molecular surface is one of the APBS options for mapping dielectric values to 3D coordinates, and there are details at the APBS website: <http://www.poissonboltzmann.org/apbs/user-guide/running-apbs/input-files/elec-input-file-section/elec-keywords/srfm>  

In other words, it is simply one of the ways to partition the grid into low- and high-dielectric areas for the PB calculation.  Choosing a different method will change (perhaps only slightly) the calculated potential values in the output grid.  It doesn?t have anything to do with the shape of surface that Chimera draws later.  It could only affect the values that are mapped onto the Chimera surface with color, and the differences with different partitioning methods may be subtle.

If you actually want to make a smoother surface in Chimera, you could increase vertex density as described here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#smoothness>
? you may need to reapply the electrostatic coloring after that.

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 Sep 23, 2015, at 2:15 PM, Cale Martin <cmartin013 at drury.edu> wrote:

> Dear Chimera users,
> 
> Over the last few days I have been using Chimera 1.9 to model the Poisson-Boltzmann surface potential of a protein.  I have been using the APBS software and the two main forcefields I have been using are the TYL06 and AMBER.  When I model the chemokine using the AMBER forcefield the result seems to be normal and as expected, but when using the TYL06 forcefield, the final molecule surface seems to have larger molecule radii almost making it look a little more "bubbly" for lack of a better term.  Is this a function of the forcefield in any way?  Should this be expected from these two different forcefields?
> 
> Another issue that I have had along the same line involves the APBS program.  The settings allow for the selection of a "Smoothed Molecular Surface" and one that is just "Molecular Surface" but when I run the program with every thing the same except these settings, the results look exactly the same.  Should this setting affect the visualization of my molecule surface in any way?
> 
> Thank you,
> Cale Martin




From olibclarke at gmail.com  Sat Sep 26 12:36:26 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Sat, 26 Sep 2015 15:36:26 -0400
Subject: [Chimera-users] Proportional representation of missing segments?
Message-ID: <AF16E343-61A3-46EC-9751-B501F783242A@gmail.com>

Hi all,

I think it would be handy, in a future version of chimera, to have an option to represent missing segments in a manner that is proportional to the volume of protein missing - this would be very useful for getting a sense of which chain breaks correspond to very large missing regions (e.g. whole domains), and which correspond to short linkers or loops that are missing.

For example, in the structure of the ryanodine receptor, there are missing segments ranging in length from ~5-250 residues in length - it would be very handy to be able to get a quick sense, upon first opening a structure, about what fraction of the crystallized or reconstructed protein is actually present in the model.

I can think of a couple of ways of doing this. One way would be to associate an attribute with each missing segment, corresponding to the number of missing residues, and allow the user to scale the radius, color or opacity of the missing segments in proportion to this value (maybe this attribute already exists somewhere internally?).

Another way might be to create a completely different missing segment representation - perhaps an ellipsoid, with the ends of the ellipsoid at the N and C-terminal breakpoints, and the volume of the ellipsoid scaled to the volume of a random polymer of the known number of missing residues.

I would try to do this myself by creating an extension, but I don?t really know where to start to get the information that would be required - I don?t know how to iterate over all missing segments, calculate the number of residues in each, and create a new representation. I guess there is probably a list somewhere in Chimera corresponding to the missing segments and their properties, but I have no idea how to find it.

Cheers,
Oliver.





From olibclarke at gmail.com  Sun Sep 27 08:01:57 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Sun, 27 Sep 2015 11:01:57 -0400
Subject: [Chimera-users] Saving images of all scenes in session?
Message-ID: <FE625C86-2B23-427D-9DE0-CB41116A4C15@gmail.com>

Hi all,

Apologies for yet another post and thank you for your patience! :-)

Feature suggestion (or maybe this exists already?): I would like a way to iterate over all scenes in a session and save an image at each scene, with the same display settings (e.g keep background or make transparent, image format, wall-eye/cross-eye stereo, etc).

This would be really very helpful when making, remaking and updating figures. Most of the time, I will have a session, say ?Fig1.py?, within which I will have a bunch of scenes corresponding to each panel. It would be really advantageous to be able to take images of each scene all at once, saving each as (for example) Fig1_scene_name.jpg, Fig1_scene_name2.jpg etc. This could work in the same way as saving series of maps or models does now - just have a checkbox in the Save Image dialog for ?save images for all scenes in session?, or something similar.

It can take quite a while to save each image when on a slow computer, or when using graphics intensive settings such as silhouettes and shadows, so being able to save matched sets of images (e.g. low and hi-res versions, stereo versions, etc) with a couple of clicks would save a lot of time, particularly for example if you realize that the versions you saved the first time were all too low res and you want to go back and save a higher res version of every panel.

I realize you guys might not have time to implement this for Chimera 1, as development of Chimera 2 is top priority, so maybe I can write a script to do this in the meantime? Is there any way to return a list of scene names using one of the built in python functions? I guess something in Animate.Scenes ought to do this, but not being much of a python programmer I can?t quite figure it out - any tips much appreciated.

Cheers,
Oli.


From olibclarke at gmail.com  Mon Sep 28 07:30:14 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Mon, 28 Sep 2015 10:30:14 -0400
Subject: [Chimera-users] Saving images of all scenes in session?
In-Reply-To: <FE625C86-2B23-427D-9DE0-CB41116A4C15@gmail.com>
References: <FE625C86-2B23-427D-9DE0-CB41116A4C15@gmail.com>
Message-ID: <3AB8BDC8-57D3-4009-B8BF-9DAF20549FF5@gmail.com>

OK, sort of figured out the second part of this - here is a basic extension that will iterate over each scene and take an image at each with the defined parameters - I still think it would be very handy if something similar were to be incorporated into the image saving part of the GUI though:

from Midas.midas_text import addCommand
def cmd_scenesnap(scenesnap,args):
  from Midas.midas_text import doExtensionFunc
  def scenesnap(rootname):
    from chimera import runCommand
    from Animate import Scenes
    scene_list=Scenes.scenes.dispnames()
    mkdir_cmd="cd ~; system mkdir chimera_tmp; cd chimera_tmp; system mkdir {0}; cd {0}".format(rootname)
    runCommand(mkdir_cmd)
    for scene in scene_list:
      runCommand("scene {} reset".format(scene))
      img_name=str(rootname)+"_"+str(scene)
      runCommand("copy file {} png width 2000 supersample 4".format(img_name))
  doExtensionFunc(scenesnap,args)
addCommand("scenesnap", cmd_scenesnap, help=False)


> On Sep 27, 2015, at 11:01 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Hi all,
> 
> Apologies for yet another post and thank you for your patience! :-)
> 
> Feature suggestion (or maybe this exists already?): I would like a way to iterate over all scenes in a session and save an image at each scene, with the same display settings (e.g keep background or make transparent, image format, wall-eye/cross-eye stereo, etc).
> 
> This would be really very helpful when making, remaking and updating figures. Most of the time, I will have a session, say ?Fig1.py?, within which I will have a bunch of scenes corresponding to each panel. It would be really advantageous to be able to take images of each scene all at once, saving each as (for example) Fig1_scene_name.jpg, Fig1_scene_name2.jpg etc. This could work in the same way as saving series of maps or models does now - just have a checkbox in the Save Image dialog for ?save images for all scenes in session?, or something similar.
> 
> It can take quite a while to save each image when on a slow computer, or when using graphics intensive settings such as silhouettes and shadows, so being able to save matched sets of images (e.g. low and hi-res versions, stereo versions, etc) with a couple of clicks would save a lot of time, particularly for example if you realize that the versions you saved the first time were all too low res and you want to go back and save a higher res version of every panel.
> 
> I realize you guys might not have time to implement this for Chimera 1, as development of Chimera 2 is top priority, so maybe I can write a script to do this in the meantime? Is there any way to return a list of scene names using one of the built in python functions? I guess something in Animate.Scenes ought to do this, but not being much of a python programmer I can?t quite figure it out - any tips much appreciated.
> 
> Cheers,
> Oli.




From meng at cgl.ucsf.edu  Mon Sep 28 12:40:52 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 28 Sep 2015 12:40:52 -0700
Subject: [Chimera-users] Proportional representation of missing segments?
In-Reply-To: <AF16E343-61A3-46EC-9751-B501F783242A@gmail.com>
References: <AF16E343-61A3-46EC-9751-B501F783242A@gmail.com>
Message-ID: <6240FD41-0012-4425-ACD8-D9996CB64177@cgl.ucsf.edu>

Hi Oliver,
Thanks for the suggestion.  Currently there is something like this in a different context: given a query sequence, the MultiDomain Assembler (command ?mda?) finds known related structures and arranges them left->right according to N->C of the query.  Where the sequence is not covered by structural data, it draws spheres of different sizes representing the lengths of the gaps.  More info including example images (and another image is attached below):

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

Not sure if the associated code may be useful, because in that case one is not constrained to connect specific points in space.  Nevertheless, just thought I?d mention it?
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 Sep 26, 2015, at 12:36 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Hi all,
> 
> I think it would be handy, in a future version of chimera, to have an option to represent missing segments in a manner that is proportional to the volume of protein missing - this would be very useful for getting a sense of which chain breaks correspond to very large missing regions (e.g. whole domains), and which correspond to short linkers or loops that are missing.
> 
> For example, in the structure of the ryanodine receptor, there are missing segments ranging in length from ~5-250 residues in length - it would be very handy to be able to get a quick sense, upon first opening a structure, about what fraction of the crystallized or reconstructed protein is actually present in the model.
> 
> I can think of a couple of ways of doing this. One way would be to associate an attribute with each missing segment, corresponding to the number of missing residues, and allow the user to scale the radius, color or opacity of the missing segments in proportion to this value (maybe this attribute already exists somewhere internally?).
> 
> Another way might be to create a completely different missing segment representation - perhaps an ellipsoid, with the ends of the ellipsoid at the N and C-terminal breakpoints, and the volume of the ellipsoid scaled to the volume of a random polymer of the known number of missing residues.
> 
> I would try to do this myself by creating an extension, but I don?t really know where to start to get the information that would be required - I don?t know how to iterate over all missing segments, calculate the number of residues in each, and create a new representation. I guess there is probably a list somewhere in Chimera corresponding to the missing segments and their properties, but I have no idea how to find it.
> 
> Cheers,
> Oliver.

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From pett at cgl.ucsf.edu  Mon Sep 28 14:09:48 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 28 Sep 2015 14:09:48 -0700
Subject: [Chimera-users] Proportional representation of missing segments?
In-Reply-To: <AF16E343-61A3-46EC-9751-B501F783242A@gmail.com>
References: <AF16E343-61A3-46EC-9751-B501F783242A@gmail.com>
Message-ID: <435DD6BD-DF14-4FDE-96EB-7BD6D4E4C85E@cgl.ucsf.edu>

Hi Oliver,
	This is good idea, but like the mantra you?ve been hearing recently ? more likely to show up in Chimera 2.  Aside from Elaine?s suggestions, there are couple of things you can do in Chimera 1.  By far the easiest is to show the sequence for the chain.  The red boxes on the sequence will be as long as the number of missing residues.  You could select the residues that bookend the box to get an idea of which missing segment it is in the 3D model.
	The harder thing, but which you seem willing to try, is to write an extension to create an alternate depiction.  Your extension could register for the PseudoBond trigger (http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_AtomTrigger.html <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_AtomTrigger.html>) and in your callback function look through the PseudoBond ?created? list and if pb.category is chimera.LONGBOND_PBG_NAME then that pseudobond is a missing segment pseudobond and you can go to town.  One simple thing you could do is label the pseudobond with the number of missing residues, e.g.:

	pb.label = str(abs(pb.atoms[0].residue.if.position - pb.atoms[1].residue.id.position) - 1) + ? residues?

While the above is accurate in most situations, there are some where it would be slightly off, if say there were insertion codes in the missing segment.  A more accurate method would be to look in the chain?s Sequence and see how far apart the residues are in the Sequence?s ?residues? list.  Seems a little like overkill, but I?m just putting it out there.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Sep 26, 2015, at 12:36 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Hi all,
> 
> I think it would be handy, in a future version of chimera, to have an option to represent missing segments in a manner that is proportional to the volume of protein missing - this would be very useful for getting a sense of which chain breaks correspond to very large missing regions (e.g. whole domains), and which correspond to short linkers or loops that are missing.
> 
> For example, in the structure of the ryanodine receptor, there are missing segments ranging in length from ~5-250 residues in length - it would be very handy to be able to get a quick sense, upon first opening a structure, about what fraction of the crystallized or reconstructed protein is actually present in the model.
> 
> I can think of a couple of ways of doing this. One way would be to associate an attribute with each missing segment, corresponding to the number of missing residues, and allow the user to scale the radius, color or opacity of the missing segments in proportion to this value (maybe this attribute already exists somewhere internally?).
> 
> Another way might be to create a completely different missing segment representation - perhaps an ellipsoid, with the ends of the ellipsoid at the N and C-terminal breakpoints, and the volume of the ellipsoid scaled to the volume of a random polymer of the known number of missing residues.
> 
> I would try to do this myself by creating an extension, but I don?t really know where to start to get the information that would be required - I don?t know how to iterate over all missing segments, calculate the number of residues in each, and create a new representation. I guess there is probably a list somewhere in Chimera corresponding to the missing segments and their properties, but I have no idea how to find it.
> 
> 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 olibclarke at gmail.com  Mon Sep 28 14:24:06 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Mon, 28 Sep 2015 17:24:06 -0400
Subject: [Chimera-users] Proportional representation of missing segments?
In-Reply-To: <435DD6BD-DF14-4FDE-96EB-7BD6D4E4C85E@cgl.ucsf.edu>
References: <AF16E343-61A3-46EC-9751-B501F783242A@gmail.com>
	<435DD6BD-DF14-4FDE-96EB-7BD6D4E4C85E@cgl.ucsf.edu>
Message-ID: <CAPghYOofsutC7JqaxEnt_T_yncCf_0k7+D2b7=zNt_-yP+pc=w@mail.gmail.com>

Thanks Eric and Elaine as always! I will take a look at the documentation
you linked to Eric, this looks interesting and if I have a way to iterate
through all the long bonds I can probably figure something out - I will
post back to the bb if I get something working that I think might be useful
to anyone else out there.

Cheers,
Oliver.

On Mon, Sep 28, 2015 at 5:09 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Oliver,
> This is good idea, but like the mantra you?ve been hearing recently ? more
> likely to show up in Chimera 2.  Aside from Elaine?s suggestions, there are
> couple of things you can do in Chimera 1.  By far the easiest is to show
> the sequence for the chain.  The red boxes on the sequence will be as long
> as the number of missing residues.  You could select the residues that
> bookend the box to get an idea of which missing segment it is in the 3D
> model.
> The harder thing, but which you seem willing to try, is to write an
> extension to create an alternate depiction.  Your extension could register
> for the PseudoBond trigger (
> http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_AtomTrigger.html)
> and in your callback function look through the PseudoBond ?created? list
> and if pb.category is chimera.LONGBOND_PBG_NAME then that pseudobond is a
> missing segment pseudobond and you can go to town.  One simple thing you
> could do is label the pseudobond with the number of missing residues, e.g.:
>
> pb.label = str(abs(pb.atoms[0].residue.if.position -
> pb.atoms[1].residue.id.position) - 1) + ? residues?
>
> While the above is accurate in most situations, there are some where it
> would be slightly off, if say there were insertion codes in the missing
> segment.  A more accurate method would be to look in the chain?s Sequence
> and see how far apart the residues are in the Sequence?s ?residues? list.
> Seems a little like overkill, but I?m just putting it out there.
>
> ?Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
> On Sep 26, 2015, at 12:36 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
>
> Hi all,
>
> I think it would be handy, in a future version of chimera, to have an
> option to represent missing segments in a manner that is proportional to
> the volume of protein missing - this would be very useful for getting a
> sense of which chain breaks correspond to very large missing regions (e.g.
> whole domains), and which correspond to short linkers or loops that are
> missing.
>
> For example, in the structure of the ryanodine receptor, there are missing
> segments ranging in length from ~5-250 residues in length - it would be
> very handy to be able to get a quick sense, upon first opening a structure,
> about what fraction of the crystallized or reconstructed protein is
> actually present in the model.
>
> I can think of a couple of ways of doing this. One way would be to
> associate an attribute with each missing segment, corresponding to the
> number of missing residues, and allow the user to scale the radius, color
> or opacity of the missing segments in proportion to this value (maybe this
> attribute already exists somewhere internally?).
>
> Another way might be to create a completely different missing segment
> representation - perhaps an ellipsoid, with the ends of the ellipsoid at
> the N and C-terminal breakpoints, and the volume of the ellipsoid scaled to
> the volume of a random polymer of the known number of missing residues.
>
> I would try to do this myself by creating an extension, but I don?t really
> know where to start to get the information that would be required - I don?t
> know how to iterate over all missing segments, calculate the number of
> residues in each, and create a new representation. I guess there is
> probably a list somewhere in Chimera corresponding to the missing segments
> and their properties, but I have no idea how to find it.
>
> 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 pett at cgl.ucsf.edu  Tue Sep 29 11:29:27 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 29 Sep 2015 11:29:27 -0700
Subject: [Chimera-users] metal coordination to display off
Message-ID: <CA740417-FE12-4EF9-83C7-AE3C474F40CC@cgl.ucsf.edu>

On 9/28/15 6:13 PM, "Luigi Di Costanzo" <dicostanzo at rcsb.rutgers.edu <mailto:dicostanzo at rcsb.rutgers.edu>>
wrote:

> 
> We have fetched 2MHR with Chimera and noticed that the middle nitrogen
> of azide is bonded through a dashed line as following:
> 
> FE2  FEO A 119                 N2  AZI A 120
> 
> From the "structure analysis" tool and "metal geometry" window we are
> unable to display off that dashed lines that is incorrect.
> 
> The coordination table does not show that particular link and we can not
> deselect it.
> 
> Could you please look into it and provide some suggestions?
> 
> Thanks.

Hi Luigi,
	The spurious dashed line is due to a corresponding CONECT record in the PDB file.  So one option is to locate that CONECT record and delete it.  The other is to use the Metal Coordination tool to clean up the coordination of that iron.  First, it is highly unlikely that the histidine nitrogens coordinating the iron are protonated, so you should select those hydrogens and ?del sel? to get rid of them.  Then if you bring up the metal coordination tool for the iron it will properly show the nitrogens as coordinating.  If you already had the tool up when you deleted the hydrogens then you will have to force the tool to consider the newly deprotonated nitrogens by selecting them and clicking the ?Add atoms selected in the graphics window" button.  You can now remove the spurious coordination you noted above by first clicking the last atom in the coordination table (HIS 25.A NE2) and then clicking the ?Create/Update metal-complex pseudobonds? button.
	I hope this helps.  Let me know if you have any questions.

?Eric


	Eric Pettersen
	UCSF Computer Graphics Lab




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From dicostanzo at rcsb.rutgers.edu  Tue Sep 29 11:57:46 2015
From: dicostanzo at rcsb.rutgers.edu (Luigi Di Costanzo)
Date: Tue, 29 Sep 2015 14:57:46 -0400
Subject: [Chimera-users] metal coordination to display off
In-Reply-To: <CA740417-FE12-4EF9-83C7-AE3C474F40CC@cgl.ucsf.edu>
References: <CA740417-FE12-4EF9-83C7-AE3C474F40CC@cgl.ucsf.edu>
Message-ID: <560ADF2A.70409@rcsb.rutgers.edu>

Eric -- Thanks. yes i did those trials. For the Hs it works as you 
suggested. For the N2 link...  I removed also the link from the pdb file 
and reload but the dashed lines does not go away.

On 09/29/2015 02:29 PM, Eric Pettersen wrote:
> On 9/28/15 6:13 PM, "Luigi Di Costanzo" <dicostanzo at rcsb.rutgers.edu
> <mailto:dicostanzo at rcsb.rutgers.edu>>
> wrote:
>
>>
>> We have fetched 2MHR with Chimera and noticed that the middle nitrogen
>> of azide is bonded through a dashed line as following:
>>
>> FE2  FEO A 119                 N2  AZI A 120
>>
>> From the "structure analysis" tool and "metal geometry" window we are
>> unable to display off that dashed lines that is incorrect.
>>
>> The coordination table does not show that particular link and we can not
>> deselect it.
>>
>> Could you please look into it and provide some suggestions?
>>
>> Thanks.
>
> Hi Luigi,
> The spurious dashed line is due to a corresponding CONECT record in the
> PDB file.  So one option is to locate that CONECT record and delete it.
>   The other is to use the Metal Coordination tool to clean up the
> coordination of that iron.  First, it is highly unlikely that the
> histidine nitrogens coordinating the iron are protonated, so you should
> select those hydrogens and ?del sel? to get rid of them.  Then if you
> bring up the metal coordination tool for the iron it will properly show
> the nitrogens as coordinating.  If you already had the tool up when you
> deleted the hydrogens then you will have to force the tool to consider
> the newly deprotonated nitrogens by selecting them and clicking the ?Add
> atoms selected in the graphics window" button.  You can now remove the
> spurious coordination you noted above by first clicking the last atom in
> the coordination table (HIS 25.A NE2) and then clicking the
> ?Create/Update metal-complex pseudobonds? button.
> I hope this helps.  Let me know if you have any questions.
>
> ?Eric
>
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
>
>

-- 

Regards

Luigi


=================================
Luigi Franklin Di Costanzo, Ph.D.
Biocurator, RCSB Protein Data Bank
Center for Integrative Proteomics Research
Rutgers The State University of New Jersey
174 Frelinghuysen Rd.
Piscataway, NJ 08854-8076

Email:  dicostanzo at rcsb.rutgers.edu
Phone:  848-445-4955 Fax:    (732)-445-4320


As of July 19, 2015: ADIT closed for all X-ray depositions.

Please use the wwPDB Deposition Tool,http://deposit.wwpdb.org/deposition
to submit new crystal structure data.
========================================================================


From pett at cgl.ucsf.edu  Tue Sep 29 12:40:44 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 29 Sep 2015 12:40:44 -0700
Subject: [Chimera-users] metal coordination to display off
In-Reply-To: <560ADF2A.70409@rcsb.rutgers.edu>
References: <CA740417-FE12-4EF9-83C7-AE3C474F40CC@cgl.ucsf.edu>
	<560ADF2A.70409@rcsb.rutgers.edu>
Message-ID: <510E928C-047B-4D1A-94A2-A295F9A091D5@cgl.ucsf.edu>

Hmm, okay there?s more editing to the PDB file necessary than I mentioned by I failed to note the the file has LINK records.  So you need to delete the LINK record and edit the two CONECT records corresponding to the endpoint atoms.  I?ve attached a diff of the original file vs. the edited file, and I will send you the edited file directly (instead of to the whole list).

?Eric



> On Sep 29, 2015, at 11:57 AM, Luigi Di Costanzo <dicostanzo at rcsb.rutgers.edu> wrote:
> 
> Eric -- Thanks. yes i did those trials. For the Hs it works as you suggested. For the N2 link...  I removed also the link from the pdb file and reload but the dashed lines does not go away.
> 
> On 09/29/2015 02:29 PM, Eric Pettersen wrote:
>> On 9/28/15 6:13 PM, "Luigi Di Costanzo" <dicostanzo at rcsb.rutgers.edu <mailto:dicostanzo at rcsb.rutgers.edu>
>> <mailto:dicostanzo at rcsb.rutgers.edu <mailto:dicostanzo at rcsb.rutgers.edu>>>
>> wrote:
>> 
>>> 
>>> We have fetched 2MHR with Chimera and noticed that the middle nitrogen
>>> of azide is bonded through a dashed line as following:
>>> 
>>> FE2  FEO A 119                 N2  AZI A 120
>>> 
>>> From the "structure analysis" tool and "metal geometry" window we are
>>> unable to display off that dashed lines that is incorrect.
>>> 
>>> The coordination table does not show that particular link and we can not
>>> deselect it.
>>> 
>>> Could you please look into it and provide some suggestions?
>>> 
>>> Thanks.
>> 
>> Hi Luigi,
>> The spurious dashed line is due to a corresponding CONECT record in the
>> PDB file.  So one option is to locate that CONECT record and delete it.
>>  The other is to use the Metal Coordination tool to clean up the
>> coordination of that iron.  First, it is highly unlikely that the
>> histidine nitrogens coordinating the iron are protonated, so you should
>> select those hydrogens and ?del sel? to get rid of them.  Then if you
>> bring up the metal coordination tool for the iron it will properly show
>> the nitrogens as coordinating.  If you already had the tool up when you
>> deleted the hydrogens then you will have to force the tool to consider
>> the newly deprotonated nitrogens by selecting them and clicking the ?Add
>> atoms selected in the graphics window" button.  You can now remove the
>> spurious coordination you noted above by first clicking the last atom in
>> the coordination table (HIS 25.A NE2) and then clicking the
>> ?Create/Update metal-complex pseudobonds? button.
>> I hope this helps.  Let me know if you have any questions.
>> 
>> ?Eric
>> 
>> 
>> Eric Pettersen
>> UCSF Computer Graphics Lab
>> 
>> 
>> 
>> 
> 
> -- 
> 
> Regards
> 
> Luigi
> 
> 
> =================================
> Luigi Franklin Di Costanzo, Ph.D.
> Biocurator, RCSB Protein Data Bank
> Center for Integrative Proteomics Research
> Rutgers The State University of New Jersey
> 174 Frelinghuysen Rd.
> Piscataway, NJ 08854-8076
> 
> Email:  dicostanzo at rcsb.rutgers.edu <mailto:dicostanzo at rcsb.rutgers.edu>
> Phone:  848-445-4955 Fax:    (732)-445-4320
> 
> 
> As of July 19, 2015: ADIT closed for all X-ray depositions.
> 
> Please use the wwPDB Deposition Tool,http://deposit.wwpdb.org/deposition <http://deposit.wwpdb.org/deposition>
> to submit new crystal structure data.
> ========================================================================

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From skere at lf1.cuni.cz  Tue Sep 29 23:54:20 2015
From: skere at lf1.cuni.cz (Dr Kereiche)
Date: Wed, 30 Sep 2015 08:54:20 +0200
Subject: [Chimera-users] Morphs
Message-ID: <564BCC60-7853-45CC-9C35-37CF5B548C65@lf1.cuni.cz>

Dear Chimera team,

 lately I am facing some problems for creating a movie in which I would like to combine 2 morphs with each other. 
To make it clearer, I  hope, 
I have 2 Em maps representing 2 states of my structure (vol #1 & vol #2) I did a morph maps (volume/ Morph map) after having recenter and align the 2 maps. it works perfectly.
 I did similar procedure with 2 pdb files (1.pdb & 2.pdb), corresponding to the fitted molecular structures of the 2 states (vol#1 & vol #2) ,  using the tool/Structures comparison/ morph conformation. The pbds are aligned with the EM map using VOP command.
Now I would like to combine the 2 morphs together to have a final morph of the EM maps with the molecular structure, but I could not find a way to combine them. Thus I would like to know if it is possible to do it ? and if yes how to do it. 
Moreover is it possible to play the morph of the pdbs in way of the morph of the EM maps back and forth?

Thank you in advance, 

Sincerely 


Sami




From dicostanzo at rcsb.rutgers.edu  Wed Sep 30 06:59:40 2015
From: dicostanzo at rcsb.rutgers.edu (Luigi Di Costanzo)
Date: Wed, 30 Sep 2015 09:59:40 -0400
Subject: [Chimera-users] metal coordination to display off
In-Reply-To: <510E928C-047B-4D1A-94A2-A295F9A091D5@cgl.ucsf.edu>
References: <CA740417-FE12-4EF9-83C7-AE3C474F40CC@cgl.ucsf.edu>
	<560ADF2A.70409@rcsb.rutgers.edu>
	<510E928C-047B-4D1A-94A2-A295F9A091D5@cgl.ucsf.edu>
Message-ID: <560BEACC.4070809@rcsb.rutgers.edu>

Eric -- Yes it works.. I should have known better about editing the pdb 
file :-)

Btw if you selet the bond with Ctrl-click, then click on the green icon 
that shows up on the bottom corner right of the screen. from the pseudo 
bond click false and that bond disappears.

Luigi

On 09/29/2015 03:40 PM, Eric Pettersen wrote:
> Hmm, okay there?s more editing to the PDB file necessary than I
> mentioned by I failed to note the the file has LINK records.  So you
> need to delete the LINK record and edit the two CONECT records
> corresponding to the endpoint atoms.  I?ve attached a diff of the
> original file vs. the edited file, and I will send you the edited file
> directly (instead of to the whole list).
>
> ?Eric
>
>
>
>
>> On Sep 29, 2015, at 11:57 AM, Luigi Di Costanzo
>> <dicostanzo at rcsb.rutgers.edu <mailto:dicostanzo at rcsb.rutgers.edu>> wrote:
>>
>> Eric -- Thanks. yes i did those trials. For the Hs it works as you
>> suggested. For the N2 link...  I removed also the link from the pdb
>> file and reload but the dashed lines does not go away.
>>
>> On 09/29/2015 02:29 PM, Eric Pettersen wrote:
>>> On 9/28/15 6:13 PM, "Luigi Di Costanzo" <dicostanzo at rcsb.rutgers.edu
>>> <mailto:dicostanzo at rcsb.rutgers.edu>
>>> <mailto:dicostanzo at rcsb.rutgers.edu>>
>>> wrote:
>>>
>>>>
>>>> We have fetched 2MHR with Chimera and noticed that the middle nitrogen
>>>> of azide is bonded through a dashed line as following:
>>>>
>>>> FE2  FEO A 119                 N2  AZI A 120
>>>>
>>>> From the "structure analysis" tool and "metal geometry" window we are
>>>> unable to display off that dashed lines that is incorrect.
>>>>
>>>> The coordination table does not show that particular link and we can not
>>>> deselect it.
>>>>
>>>> Could you please look into it and provide some suggestions?
>>>>
>>>> Thanks.
>>>
>>> Hi Luigi,
>>> The spurious dashed line is due to a corresponding CONECT record in the
>>> PDB file.  So one option is to locate that CONECT record and delete it.
>>>  The other is to use the Metal Coordination tool to clean up the
>>> coordination of that iron.  First, it is highly unlikely that the
>>> histidine nitrogens coordinating the iron are protonated, so you should
>>> select those hydrogens and ?del sel? to get rid of them.  Then if you
>>> bring up the metal coordination tool for the iron it will properly show
>>> the nitrogens as coordinating.  If you already had the tool up when you
>>> deleted the hydrogens then you will have to force the tool to consider
>>> the newly deprotonated nitrogens by selecting them and clicking the ?Add
>>> atoms selected in the graphics window" button.  You can now remove the
>>> spurious coordination you noted above by first clicking the last atom in
>>> the coordination table (HIS 25.A NE2) and then clicking the
>>> ?Create/Update metal-complex pseudobonds? button.
>>> I hope this helps.  Let me know if you have any questions.
>>>
>>> ?Eric
>>>
>>>
>>> Eric Pettersen
>>> UCSF Computer Graphics Lab
>>>
>>>
>>>
>>>
>>
>> --
>>
>> Regards
>>
>> Luigi
>>
>>
>> =================================
>> Luigi Franklin Di Costanzo, Ph.D.
>> Biocurator, RCSB Protein Data Bank
>> Center for Integrative Proteomics Research
>> Rutgers The State University of New Jersey
>> 174 Frelinghuysen Rd.
>> Piscataway, NJ 08854-8076
>>
>> Email: dicostanzo at rcsb.rutgers.edu <mailto:dicostanzo at rcsb.rutgers.edu>
>> Phone:  848-445-4955 Fax:    (732)-445-4320
>>
>>
>> As of July 19, 2015: ADIT closed for all X-ray depositions.
>>
>> Please use the wwPDB Deposition Tool,http://deposit.wwpdb.org/deposition
>> to submit new crystal structure data.
>> ========================================================================
>

-- 

Regards

Luigi


=================================
Luigi Franklin Di Costanzo, Ph.D.
Biocurator, RCSB Protein Data Bank
Center for Integrative Proteomics Research
Rutgers The State University of New Jersey
174 Frelinghuysen Rd.
Piscataway, NJ 08854-8076

Email:  dicostanzo at rcsb.rutgers.edu
Phone:  848-445-4955 Fax:    (732)-445-4320


As of July 19, 2015: ADIT closed for all X-ray depositions.

Please use the wwPDB Deposition Tool,http://deposit.wwpdb.org/deposition
to submit new crystal structure data.
========================================================================


From giovanna.scapin at merck.com  Wed Sep 30 09:44:44 2015
From: giovanna.scapin at merck.com (Scapin, Giovanna)
Date: Wed, 30 Sep 2015 12:44:44 -0400
Subject: [Chimera-users] Chimera
Message-ID: <C80EB6EE0CA3DE498FDA3F4520BB08451192EDA335@USCTMXP51010.merck.com>

Good afternoon
I am interested in downloading and installing CHIMERA.  Could you let me know if there is any licensing cost involved and if so whom I should contact?

Thank you very much

Giovanna Scapin



Giovanna Scapin
Principal Scientist
Structural Chemistry
Merck & Co., Inc.
2000 Galloping Hill Rd
K15-1800
Room B133C
Kenilworth NJ 07033
Phone +1 908  740 3632

Notice:  This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth,
New Jersey, USA 07033), and/or its affiliates Direct contact information
for affiliates is available at 
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from 
your system.
-------------- next part --------------
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From meng at cgl.ucsf.edu  Wed Sep 30 10:06:50 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 30 Sep 2015 10:06:50 -0700
Subject: [Chimera-users] Morphs
In-Reply-To: <564BCC60-7853-45CC-9C35-37CF5B548C65@lf1.cuni.cz>
References: <564BCC60-7853-45CC-9C35-37CF5B548C65@lf1.cuni.cz>
Message-ID: <8FFC6CAE-784A-446D-833E-C8A982255366@cgl.ucsf.edu>

Dear Sami,
Yes, you can play a map morph and molecule morph at the same time, and you can play them both back and forth as you wish.  It requires using Chimera commands instead of the GUIs, however.  For more information please see this previous post and links therein:

<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-April/008752.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 Sep 29, 2015, at 11:54 PM, Dr Kereiche <skere at lf1.cuni.cz> wrote:

> Dear Chimera team,
> 
> lately I am facing some problems for creating a movie in which I would like to combine 2 morphs with each other. 
> To make it clearer, I  hope, 
> I have 2 Em maps representing 2 states of my structure (vol #1 & vol #2) I did a morph maps (volume/ Morph map) after having recenter and align the 2 maps. it works perfectly.
> I did similar procedure with 2 pdb files (1.pdb & 2.pdb), corresponding to the fitted molecular structures of the 2 states (vol#1 & vol #2) ,  using the tool/Structures comparison/ morph conformation. The pbds are aligned with the EM map using VOP command.
> Now I would like to combine the 2 morphs together to have a final morph of the EM maps with the molecular structure, but I could not find a way to combine them. Thus I would like to know if it is possible to do it ? and if yes how to do it. 
> Moreover is it possible to play the morph of the pdbs in way of the morph of the EM maps back and forth?
> 
> Thank you in advance, 
> Sincerely 
> Sami




From meng at cgl.ucsf.edu  Wed Sep 30 10:13:58 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 30 Sep 2015 10:13:58 -0700
Subject: [Chimera-users] Chimera
In-Reply-To: <C80EB6EE0CA3DE498FDA3F4520BB08451192EDA335@USCTMXP51010.merck.com>
References: <C80EB6EE0CA3DE498FDA3F4520BB08451192EDA335@USCTMXP51010.merck.com>
Message-ID: <36ED150A-2B3A-41D1-B621-B68920A8668C@cgl.ucsf.edu>

Dear Giovanna Scapin,
Thanks for your interest ? yes, for commercial licensing there is a cost, and inquiries should be sent to chimera at cgl.ucsf.edu (which I have CC?d here, so someone should be responding to you presently).  The cost depends on the situation.
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

<http://www.rbvi.ucsf.edu/chimera/docs/feedback.html>

On Sep 30, 2015, at 9:44 AM, Scapin, Giovanna <giovanna.scapin at merck.com> wrote:

> Good afternoon
> I am interested in downloading and installing CHIMERA.  Could you let me know if there is any licensing cost involved and if so whom I should contact?
>  
> Thank you very much
>  
> Giovanna Scapin
>  
>  
>  
> Giovanna Scapin
> Principal Scientist
> Structural Chemistry
> Merck & Co., Inc.
> 2000 Galloping Hill Rd
> K15-1800
> Room B133C
> Kenilworth NJ 07033
> Phone +1 908  740 3632
>  
> Notice:  This e-mail message, together with any attachments, contains
> information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, 
> New Jersey, USA 07033), and/or its affiliates Direct contact information
> for affiliates is available at 
> http://www.merck.com/contact/contacts.html) that may be confidential,
> proprietary copyrighted and/or legally privileged. It is intended solely
> for the use of the individual or entity named on this message. If you are
> not the intended recipient, and have received this message in error,
> please notify us immediately by reply e-mail and then delete it from 
> your system.
> 
> _______________________________________________
> 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 Sep 30 10:15:19 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 30 Sep 2015 10:15:19 -0700
Subject: [Chimera-users] metal coordination to display off
In-Reply-To: <560BEACC.4070809@rcsb.rutgers.edu>
References: <CA740417-FE12-4EF9-83C7-AE3C474F40CC@cgl.ucsf.edu>
	<560ADF2A.70409@rcsb.rutgers.edu>
	<510E928C-047B-4D1A-94A2-A295F9A091D5@cgl.ucsf.edu>
	<560BEACC.4070809@rcsb.rutgers.edu>
Message-ID: <ED6E7944-35C7-4AAC-B225-2D5AB5F74237@cgl.ucsf.edu>


> On Sep 30, 2015, at 6:59 AM, Luigi Di Costanzo <dicostanzo at rcsb.rutgers.edu> wrote:
> 
> Btw if you selet the bond with Ctrl-click, then click on the green icon that shows up on the bottom corner right of the screen. from the pseudo bond click false and that bond disappears.

Hmmm, I should have thought of that!

?Eric

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From pett at cgl.ucsf.edu  Wed Sep 30 11:19:38 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 30 Sep 2015 11:19:38 -0700
Subject: [Chimera-users] Suggestion - autofilter history by typed
	substring?
In-Reply-To: <312B2BD2-BFD6-42D1-8F29-6CB96BFE0878@gmail.com>
References: <312B2BD2-BFD6-42D1-8F29-6CB96BFE0878@gmail.com>
Message-ID: <F79C06E2-52BA-4CDC-A7A8-97AA03561FEB@cgl.ucsf.edu>

Hi Oliver,
	This seems like a useful suggestion.  I have implemented it in a slightly different form.  If you use the shift key while navigating the command history (i.e. shift up/down arrow or control-N/P), then it will jump to the next history entry that matches the current command name.  Available in the next daily build.

?Eric

> On Sep 23, 2015, at 2:42 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Hi all,
> 
> Just a suggestion (I guess for chimera 2) - would it be possible to autofilter the command history based on the typed substring? 
> 
> That is if I have typed ?sel? and hit the up arrow, to only cycle through those commands in the history that start with ?sel?.
> 
> This would be particularly handy for scrolling quickly through recent ?sel? and ?color? commands - a similar mechanism is implemented in several shells and it works well.
> 
> Cheers,
> 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  Wed Sep 30 11:46:43 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Wed, 30 Sep 2015 14:46:43 -0400
Subject: [Chimera-users] Suggestion - autofilter history by typed
	substring?
In-Reply-To: <F79C06E2-52BA-4CDC-A7A8-97AA03561FEB@cgl.ucsf.edu>
References: <312B2BD2-BFD6-42D1-8F29-6CB96BFE0878@gmail.com>
	<F79C06E2-52BA-4CDC-A7A8-97AA03561FEB@cgl.ucsf.edu>
Message-ID: <CAPghYOrU6twhkEHAseKRBA4CWOj4v=52LRdzu0apWwQ-=YfrSg@mail.gmail.com>

That sounds great, thanks Eric! I look forward to trying it out, think
it'll be a real timesaver!

Cheers,
Oli.

On Wed, Sep 30, 2015 at 2:19 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Oliver,
>         This seems like a useful suggestion.  I have implemented it in a
> slightly different form.  If you use the shift key while navigating the
> command history (i.e. shift up/down arrow or control-N/P), then it will
> jump to the next history entry that matches the current command name.
> Available in the next daily build.
>
> ?Eric
>
> > On Sep 23, 2015, at 2:42 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> >
> > Hi all,
> >
> > Just a suggestion (I guess for chimera 2) - would it be possible to
> autofilter the command history based on the typed substring?
> >
> > That is if I have typed ?sel? and hit the up arrow, to only cycle
> through those commands in the history that start with ?sel?.
> >
> > This would be particularly handy for scrolling quickly through recent
> ?sel? and ?color? commands - a similar mechanism is implemented in several
> shells and it works well.
> >
> > 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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