From pett at cgl.ucsf.edu  Wed Dec  1 11:16:09 2010
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 1 Dec 2010 11:16:09 -0800
Subject: [Chimera-users] pythonw.exe error
In-Reply-To: <web-8058287@mail.chem.tamu.edu>
References: <web-8058287@mail.chem.tamu.edu>
Message-ID: <67F9B05B-AF3A-4BE5-8907-A122C6D489E4@cgl.ucsf.edu>

Hi Mike,
	Probably the first thing you should do is make sure that the drivers  
for your graphics card are up to date.  If Chimera continues to fail  
with up-to-date drivers, then run Chimera in "debug" mode and let us  
know what the output is.  You might want to send that to chimera-bugs at cgl.ucsf.edu 
  rather than chimera-users.  That will open a ticket in our bug  
database for your problem and will avoid having everyone on this list  
receiving the details of your problem -- which probably wouldn't  
interest them very much.
	This previous mail on chimera-users details how to run Chimera in  
debug mode:

http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-September/003120.html

--Eric

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

On Nov 29, 2010, at 2:55 PM, Hunmin JUNG wrote:

> Hi,
>
> Whenever I open the chimera after the installation, it gives me an
> error 'pythonw.exe has stopped working'.
> It didn't matter the version of the chimera.
> Please what I need to do to resolve the problem.



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From gregc at cgl.ucsf.edu  Wed Dec  1 13:22:47 2010
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Wed, 01 Dec 2010 13:22:47 -0800
Subject: [Chimera-users] Exporting .stl
Message-ID: <4CF6BCA7.1050708@cgl.ucsf.edu>

Forgot to reply to list as well.

-------- Original Message --------
Subject: 	Re: [Chimera-users] Exporting .stl
Date: 	Tue, 30 Nov 2010 13:33:23 -0800
From: 	Greg Couch <gregc at cgl.ucsf.edu>
To: 	Dennis Kolva <dk429 at cornell.edu>



On 11/25/2010 06:29 PM, Dennis Kolva wrote:
 > I have been using Chimera to export .stl files of proteins and RNA 
for 3D printing. The surface models print OK, but sticks or ribbons 
choke the printer. I looked close at the output meshes, and they have 
many extra surfaces which should be removed to make "legal" .stl format.
 >
 > Is that portion of the code open source? I'd like to take a closer 
look and see if it's possible to fix. It would be much easier to rectify 
the bad surfaces upon creation, rather than trying to remove them by 
post-processing.
 >
 > Thanks,
 >
 > Dennis Kolva
 > Cornell U.

Presumably , you don't have a Z-Corp printer and their ZPrint software,
otherwise you would output VRML from chimera and have ZPrint do the
proper conversion to STL.

So yes, the source code is available at
http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/apps/x3d2/stl, and
we would welcome improvements. I believe that the problem is that
chimera does not output manifold geometry and that the X3D to STL
converter would need to perform CSG operations on all of the geometry,
especially the spheres and cylinders, to eliminate interpenetrating
surfaces. Another issue to consider is what to do about ribbons and
cylinders that are too thin for the printer you're using.

Feel free to contact me directly with questions about the code or use
the chimera developers mailing list, chimera-dev at cgl.ucsf.edu,

Greg
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From biocjh at gmail.com  Wed Dec  1 22:03:51 2010
From: biocjh at gmail.com (C.J.)
Date: Thu, 2 Dec 2010 14:03:51 +0800
Subject: [Chimera-users]  how to product a color scale bar
Message-ID: <AANLkTi=Fr7ucXJ94xhxxxc4ue6Ny8nH2yLOGgi1ZRLhU@mail.gmail.com>

Dear all,

I am writing to ask how to product a scale bar to indicating different
radius with different color
when I visualizing a spheric structure with Chimera.
Thanks.

Regards!
C.J.


From gesa.volkers at uni-greifswald.de  Thu Dec  2 06:36:30 2010
From: gesa.volkers at uni-greifswald.de (Gesa Volkers)
Date: Thu, 02 Dec 2010 15:36:30 +0100
Subject: [Chimera-users] display angle label
Message-ID: <4CF7AEEE.1050103@uni-greifswald.de>

Dear all,

I measured an angle (or better torsion) between four atoms. How can I 
display the angle with a label? I only found how to diplay measured 
distances with a label, but not angles/torsions.

Thanks in advance,
Gesa

-- 
Gesa Volkers
Institut f?r Biochemie, Molekulare Strukturbiologie
Felix-Hausdorff-Stra?e 4
17489 Greifswald
Germany
+49 (3834)-864392




From gregc at cgl.ucsf.edu  Thu Dec  2 09:32:57 2010
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Thu, 02 Dec 2010 09:32:57 -0800
Subject: [Chimera-users] need examples of Chimera crash on Mac OS X 10.6.5
Message-ID: <4CF7D849.7000405@cgl.ucsf.edu>

There have been occasional reports of Chimera crashing in the graphics 
driver on Mac OS X 10.6.5.  However, the reports have not included 
enough information to allow us to reproduce the problem and debug it.  
If you observe this crash, please report it to Apple (a dialog to do 
this will appear when the crash happens).  The next time you start 
Chimera after the crash, another dialog will appear with the option to 
send us a bug report too.  Please go ahead and do that, including a 
description of what you were doing before the crash, and your email 
address in case we need to request further details.

     Thank you,

     Greg


From meng at cgl.ucsf.edu  Thu Dec  2 11:19:20 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 2 Dec 2010 11:19:20 -0800
Subject: [Chimera-users] display angle label
In-Reply-To: <4CF7AEEE.1050103@uni-greifswald.de>
References: <4CF7AEEE.1050103@uni-greifswald.de>
Message-ID: <6268B778-2591-44FB-97EB-49FFB6A12F62@cgl.ucsf.edu>

Hi Gesa,
There is no analogous way to simply display the angle values as labels.  If you wanted 3D labels (those that move around with the structure), you would first need to make the measurement and then manually label some atom or bond with that value.  For a torsion, you would probably label the bond in the middle.  The only way I can think of to manually label a bond is to Ctrl-click it in the main window to select it, then use the Selection Inspector dialog and enter a label for that bond.  You can show the Selection Inspector by clicking the magnifying glass in the lower right corner of the Chimera window or choosing "Actions... Inspect" from the menu.

To manually label an atom, you could select it, then use Selection Inspector or menu (Actions... Label... other...) to add an arbitrary label.  Yet another way is to use the command setattr, e.g.

setattr a label "45" :16.a at cb

If this is for a publication or presentation image, you could use 2D labels.  These don't move when you move the structure.  You would have to first position everything how it should be in the final figure, and then add 2D labels (this tool is under Tools... Utilities in the menu).  In that case you can include symbols such as the degree symbol, easily make each label whatever size and color you want, and drag it around anywhere within the Chimera window.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.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 Dec 2, 2010, at 6:36 AM, Gesa Volkers wrote:

> Dear all,
> I measured an angle (or better torsion) between four atoms. How can I 
> display the angle with a label? I only found how to diplay measured 
> distances with a label, but not angles/torsions.
> Thanks in advance,
> Gesa




From meng at cgl.ucsf.edu  Thu Dec  2 11:04:50 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 2 Dec 2010 11:04:50 -0800
Subject: [Chimera-users] how to product a color scale bar
In-Reply-To: <AANLkTi=Fr7ucXJ94xhxxxc4ue6Ny8nH2yLOGgi1ZRLhU@mail.gmail.com>
References: <AANLkTi=Fr7ucXJ94xhxxxc4ue6Ny8nH2yLOGgi1ZRLhU@mail.gmail.com>
Message-ID: <77DF67D0-02D3-40C7-8FAD-9B7D57044727@cgl.ucsf.edu>

Hi C.J.,
Sounds like you want to make a Color Key (under Tools... Utilities in the Chimera menu):
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html#colorkey>

Actually, if you are already using Surface Color to do the radial coloring, you don't need to start Color Key separately.  Instead just click the "Options" button near the bottom of the Surface Color dialog, and after you have done the coloring as you like, click "Create color key".  That will start up the Color Key tool with the same values already filled in, and you can click-drag with the mouse in the graphics window to draw the key.

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 Dec 1, 2010, at 10:03 PM, C.J. wrote:

> Dear all,
> 
> I am writing to ask how to product a scale bar to indicating different
> radius with different color
> when I visualizing a spheric structure with Chimera.
> Thanks.
> 
> Regards!
> C.J.




From biocjh at gmail.com  Fri Dec  3 00:59:58 2010
From: biocjh at gmail.com (C.J.)
Date: Fri, 3 Dec 2010 16:59:58 +0800
Subject: [Chimera-users] how to product a color scale bar
In-Reply-To: <77DF67D0-02D3-40C7-8FAD-9B7D57044727@cgl.ucsf.edu>
References: <AANLkTi=Fr7ucXJ94xhxxxc4ue6Ny8nH2yLOGgi1ZRLhU@mail.gmail.com>
	<77DF67D0-02D3-40C7-8FAD-9B7D57044727@cgl.ucsf.edu>
Message-ID: <AANLkTikk_335ah01WWb9D4i9c7QfdDXY1hbnSYVX+ogS@mail.gmail.com>

Thanks, this is very helpful!

2010/12/3 Elaine Meng <meng at cgl.ucsf.edu>:
> Hi C.J.,
> Sounds like you want to make a Color Key (under Tools... Utilities in the Chimera menu):
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html#colorkey>
>
> Actually, if you are already using Surface Color to do the radial coloring, you don't need to start Color Key separately. ?Instead just click the "Options" button near the bottom of the Surface Color dialog, and after you have done the coloring as you like, click "Create color key". ?That will start up the Color Key tool with the same values already filled in, and you can click-drag with the mouse in the graphics window to draw the key.
>
> 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 Dec 1, 2010, at 10:03 PM, C.J. wrote:
>
>> Dear all,
>>
>> I am writing to ask how to product a scale bar to indicating different
>> radius with different color
>> when I visualizing a spheric structure with Chimera.
>> Thanks.
>>
>> Regards!
>> C.J.
>
>



-- 
Regards!
C.J.



From a.pandurangan at mail.cryst.bbk.ac.uk  Fri Dec  3 04:56:51 2010
From: a.pandurangan at mail.cryst.bbk.ac.uk (Arun Prasad Pandurangan)
Date: Fri, 03 Dec 2010 12:56:51 +0000
Subject: [Chimera-users] Query regarding Fit in Map
Message-ID: <4CF8E913.3000506@mail.cryst.bbk.ac.uk>

Hi all,

I would like to know whether its possible to automate the operations 
available with 'Fit in Map' tool and its options within a script. 
Actually I would like to calculate the correlation for certain segments 
of the atomic structure and it would be help if I could do it with a 
script rather that the GUI. Any suggestion is greatly appreciated.

Thank you,
Arun Prasad


From matthewd at bcm.edu  Fri Dec  3 05:42:30 2010
From: matthewd at bcm.edu (Dougherty, Matthew T)
Date: Fri, 3 Dec 2010 07:42:30 -0600
Subject: [Chimera-users] need examples of Chimera crash on Mac OS X
 10.6.5
In-Reply-To: <4CF7D849.7000405@cgl.ucsf.edu>
References: <4CF7D849.7000405@cgl.ucsf.edu>
Message-ID: <5A4EB281C1666D43919DEEA432B50533496F20F445@EXCMSMBX03.ad.bcm.edu>

I am still using 10.5.8.  Not seeing apple or chimera crash dialogs with this kind of problem.

I am seeing a lot of problems on my Mac Pro with the nvidia quadro card, sometimes 10 lockups/day.  See it on chimera, amira and Maya.  Had to switch to my mac laptop with a simple graphics device, and a linux box with the same model quadro card.  This seems to gotten worse since I installed a 2nd card (ATI/Radeon).

When the system hangs I can not access Force-Quit, which says a lot as to how deep this design problem is. So I end up doing a shutdown, cycling power.  Sometimes I let it run in lockup mode for 10-20 hours to see if it ever recovers, 1 time it did.  When it completes the reboot I login in, there is no message asking to send a report to Apple, I have seen these dialogs, but not with these graphic card hangs.  On top of that I am pretty disappointed on their graphics.  Same model quadro runs 10x faster on linux and does not choke.  Throw in their brick wall attitude about stereo X11 driver problem which wasted a lot of my time trying to get a straight answer from them, I do not count on them for mission critical big jobs.  My plan now is to use their default graphics card manufacturer and buy inexpensive cards from the same manufacturer on my next mac pro.  Wondering if I should setup a third boot partition on the mac to load linux, would be interesting to know if the problem is in the hardware or in the apple drivers.


________________________________________
From: chimera-users-bounces at cgl.ucsf.edu [chimera-users-bounces at cgl.ucsf.edu] On Behalf Of Greg Couch [gregc at cgl.ucsf.edu]
Sent: Thursday, December 02, 2010 11:32 AM
To: chimera-users at cgl.ucsf.edu BB
Subject: [Chimera-users] need examples of Chimera crash on Mac OS X 10.6.5

There have been occasional reports of Chimera crashing in the graphics
driver on Mac OS X 10.6.5.  However, the reports have not included
enough information to allow us to reproduce the problem and debug it.
If you observe this crash, please report it to Apple (a dialog to do
this will appear when the crash happens).  The next time you start
Chimera after the crash, another dialog will appear with the option to
send us a bug report too.  Please go ahead and do that, including a
description of what you were doing before the crash, and your email
address in case we need to request further details.

     Thank you,

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



From goddard at sonic.net  Fri Dec  3 08:17:30 2010
From: goddard at sonic.net (Tom Goddard)
Date: Fri, 03 Dec 2010 08:17:30 -0800
Subject: [Chimera-users] Query regarding Fit in Map
In-Reply-To: <4CF8E913.3000506@mail.cryst.bbk.ac.uk>
References: <4CF8E913.3000506@mail.cryst.bbk.ac.uk>
Message-ID: <4CF9181A.6080500@sonic.net>

  Hi Arun,

   Yes you can use Fit in Map in a script.  I've attached an example 
Python script.  This script comes from the Chimera Python scripts web 
page but that web site is down right now.  It is necessary to use Python 
rather than a simpler Chimera command script because there is no Chimera 
command to use Fit in Map.  There probably should be, but since Fit in 
Map only does a local optimization you need some way to initially 
position the molecule or map you are fitting.  That is the hard part and 
so there hasn't been much demand for the fitting command.

   The Python code for the Fit in Map dialog is included in all Chimera 
distributions in the directory

     chimera/share/FitMap

You could look at the __init__.py and gui.py to learn what the available 
functions are.  The gui.py (graphical user interface) file shows how 
those functions are called by the dialog.

     Tom

> Hi all,
>
> I would like to know whether its possible to automate the operations
> available with 'Fit in Map' tool and its options within a script.
> Actually I would like to calculate the correlation for certain segments
> of the atomic structure and it would be help if I could do it with a
> script rather that the GUI. Any suggestion is greatly appreciated.
>
> Thank you,
> Arun Prasad
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>


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From pardeepsagar at gmail.com  Thu Dec  2 18:43:18 2010
From: pardeepsagar at gmail.com (Pardeep kumar)
Date: Thu, 2 Dec 2010 20:43:18 -0600
Subject: [Chimera-users] problem in showing disulfide bonds
Message-ID: <AANLkTinkQqem-gUuxc0q6ukJzxK9PO7xuy1EUByPFw=8@mail.gmail.com>

Hi,
I am unable to show disulfide bonds in my final structure. It has at least
five disulfide bonds. Please tell me how can I do that???and how can I save
the image as a post script file....I tried it by save as .ps file but then
the save file was not there in the designated folder though other formats
(eg jpeg) were easily saved....
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From Mahlawat at uthscsa.edu  Thu Dec  2 18:51:24 2010
From: Mahlawat at uthscsa.edu (Mahlawat, Pardeep)
Date: Thu, 2 Dec 2010 20:51:24 -0600
Subject: [Chimera-users] unable to show disulfide bonds
Message-ID: <C7912E740A3B274CA2DA7C149A54478765093E9B53@HSC-M1.win.uthscsa.edu>

Hi,
I am unable to show disulfide bonds in my final structure. It has at least five disulfide bonds. Please tell me how can I do that???and how can I save the image as a post script file....I tried it by save as .ps file but then the save file was not there in the designated folder though other formats (eg jpeg) were easily saved....



From sharjanto at i2r.a-star.edu.sg  Mon Dec  6 01:35:29 2010
From: sharjanto at i2r.a-star.edu.sg (Sumitro Harjanto)
Date: Mon, 6 Dec 2010 17:35:29 +0800
Subject: [Chimera-users] "Surface calculation failed, mscalc returned code 5"
Message-ID: <162B8AFBFBBB2148A9A1B8F9C57534280BBDDD46@mailbe01.teak.local.net>

Hi Meng,

 

I've run into this problem a few times when I wanted to calculate and
show the surface of a pdb model. 

I got the following on my reply log:

 

C:\Chimera\bin\mscalc.exe 1.400000 2.000000 1

Calculation of some surface components failed.

Falling back to single-component calculation.

C:\Chimera\bin\mscalc.exe 1.400000 2.000000 0

Surface calculation failed, mscalc returned code 5

 

Sometimes I managed to go around it by resaving the pdb file in Chimera,
or removing some irrelevant chains. but other times it just doesn't
work. Any suggestions?

 

One particular file that gives me the problem is 1IGT from PDB. I've
tried removing all the heteroatoms and water molec, for I only need the
chains A, B, C and D.  but still the problem persists.

 

Thanks!

 

Cheers,

Sumitro

Institute for Infocomm Research disclaimer:  "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."
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From meng at cgl.ucsf.edu  Mon Dec  6 14:00:51 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 6 Dec 2010 14:00:51 -0800
Subject: [Chimera-users] problem in showing disulfide bonds
In-Reply-To: <AANLkTinkQqem-gUuxc0q6ukJzxK9PO7xuy1EUByPFw=8@mail.gmail.com>
References: <AANLkTinkQqem-gUuxc0q6ukJzxK9PO7xuy1EUByPFw=8@mail.gmail.com>
Message-ID: <57786A68-1E3C-4A15-BE65-A8EE5F929975@cgl.ucsf.edu>

Hi Pardeep,
Chimera does not automatically create bonds -- it shows whatever bonds are in the input , such as described in CONECT or SSBOND lines in the PDB file.  

However, you can add bonds that are not in your input file already using the command "bond" or the "Adjust Bonds" tab in the Build Structure tool (under Tools... Structure Editing in the menu):

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>

I just tried saving an image as a PS file and did not have any problems.  Maybe the application you are using to show images does not show PS and does not list that format in its open dialog?  That is my only idea.  However, if you continue to have problems you could use "Help... Report a Bug" in the Chimera window and include all information needed to reproduce the problem, and your email if you wish a response.

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 Dec 2, 2010, at 6:43 PM, Pardeep kumar wrote:

> Hi,
> I am unable to show disulfide bonds in my final structure. It has at least five disulfide bonds. Please tell me how can I do that???and how can I save the image as a post script file....I tried it by save as .ps file but then the save file was not there in the designated folder though other formats (eg jpeg) were easily saved....

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From meng at cgl.ucsf.edu  Mon Dec  6 15:16:27 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 6 Dec 2010 15:16:27 -0800
Subject: [Chimera-users] "Surface calculation failed,
	mscalc returned code 5"
In-Reply-To: <162B8AFBFBBB2148A9A1B8F9C57534280BBDDD46@mailbe01.teak.local.net>
References: <162B8AFBFBBB2148A9A1B8F9C57534280BBDDD46@mailbe01.teak.local.net>
Message-ID: <20F24A45-0DF8-42D3-A0A2-69C85FBDE741@cgl.ucsf.edu>

Hi Sumitro,
This is a commonly reported problem and represents a numerical failure of the MSMS code included with Chimera for calculating molecular surfaces.

Sometimes when there is an error, it can still fall back to a "single component" calculation.  The problem may be in some inside bubble, whereas the "single component" is the main outer surface.  If you get that "falling back" message but it still shows the surface you want, you can ignore the message.

If you didn't get any surface, however, there are several things to try; unfortunately none is a magic bullet that works in all situations.   One easy thing to try if your structure has multiple chains is to simply split the model before showing the surface (just enter the command "split"), which makes each chain have its own separate surface.   If that doesn't work, or you didn't want separate surfaces, see this previous post for additional things to try:

<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/002954.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 Dec 6, 2010, at 1:35 AM, Sumitro Harjanto wrote:

> Hi Meng,
> I?ve run into this problem a few times when I wanted to calculate and show the surface of a pdb model.
> I got the following on my reply log:
>  
> C:\Chimera\bin\mscalc.exe 1.400000 2.000000 1
> Calculation of some surface components failed.
> Falling back to single-component calculation.
> C:\Chimera\bin\mscalc.exe 1.400000 2.000000 0
> Surface calculation failed, mscalc returned code 5
>  
> Sometimes I managed to go around it by resaving the pdb file in Chimera, or removing some irrelevant chains. but other times it just doesn?t work. Any suggestions?
>  
> One particular file that gives me the problem is 1IGT from PDB. I?ve tried removing all the heteroatoms and water molec, for I only need the chains A, B, C and D.  but still the problem persists.
> Thanks!
> Cheers,
> Sumitro

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From meng at cgl.ucsf.edu  Mon Dec  6 15:21:46 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 6 Dec 2010 15:21:46 -0800
Subject: [Chimera-users] "Surface calculation failed,
	mscalc returned code 5"
In-Reply-To: <20F24A45-0DF8-42D3-A0A2-69C85FBDE741@cgl.ucsf.edu>
References: <162B8AFBFBBB2148A9A1B8F9C57534280BBDDD46@mailbe01.teak.local.net>
	<20F24A45-0DF8-42D3-A0A2-69C85FBDE741@cgl.ucsf.edu>
Message-ID: <77DC6FCE-6D41-4D40-9255-BB52D8224032@cgl.ucsf.edu>

Whoops, sent the wrong "previous post" link.  Here is the one I meant to send.

<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-April/003816.html>

Elaine
On Dec 6, 2010, at 3:16 PM, Elaine Meng wrote:

> Hi Sumitro,
> This is a commonly reported problem and represents a numerical failure of the MSMS code included with Chimera for calculating molecular surfaces.
> 
> Sometimes when there is an error, it can still fall back to a "single component" calculation.  The problem may be in some inside bubble, whereas the "single component" is the main outer surface.  If you get that "falling back" message but it still shows the surface you want, you can ignore the message.
> 
> If you didn't get any surface, however, there are several things to try; unfortunately none is a magic bullet that works in all situations.   One easy thing to try if your structure has multiple chains is to simply split the model before showing the surface (just enter the command "split"), which makes each chain have its own separate surface.   If that doesn't work, or you didn't want separate surfaces, see this previous post for additional things to try:
> 
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/002954.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 Dec 6, 2010, at 1:35 AM, Sumitro Harjanto wrote:
> 
>> Hi Meng,
>> I?ve run into this problem a few times when I wanted to calculate and show the surface of a pdb model.
>> I got the following on my reply log:
>>  
>> C:\Chimera\bin\mscalc.exe 1.400000 2.000000 1
>> Calculation of some surface components failed.
>> Falling back to single-component calculation.
>> C:\Chimera\bin\mscalc.exe 1.400000 2.000000 0
>> Surface calculation failed, mscalc returned code 5
>>  
>> Sometimes I managed to go around it by resaving the pdb file in Chimera, or removing some irrelevant chains. but other times it just doesn?t work. Any suggestions?
>>  
>> One particular file that gives me the problem is 1IGT from PDB. I?ve tried removing all the heteroatoms and water molec, for I only need the chains A, B, C and D.  but still the problem persists.
>> Thanks!
>> Cheers,
>> Sumitro
> 

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From Mahlawat at uthscsa.edu  Mon Dec  6 17:59:08 2010
From: Mahlawat at uthscsa.edu (Mahlawat, Pardeep)
Date: Mon, 6 Dec 2010 19:59:08 -0600
Subject: [Chimera-users] problem in showing disulfide bonds
In-Reply-To: <57786A68-1E3C-4A15-BE65-A8EE5F929975@cgl.ucsf.edu>
References: <AANLkTinkQqem-gUuxc0q6ukJzxK9PO7xuy1EUByPFw=8@mail.gmail.com>,
	<57786A68-1E3C-4A15-BE65-A8EE5F929975@cgl.ucsf.edu>
Message-ID: <C7912E740A3B274CA2DA7C149A54478765093E9B5E@HSC-M1.win.uthscsa.edu>

Thanks a lot for the advice....it worked
________________________________________
From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Monday, December 06, 2010 4:00 PM
To: Pardeep kumar; Mahlawat, Pardeep
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] problem in showing disulfide bonds

Hi Pardeep,
Chimera does not automatically create bonds -- it shows whatever bonds are in the input , such as described in CONECT or SSBOND lines in the PDB file.

However, you can add bonds that are not in your input file already using the command "bond" or the "Adjust Bonds" tab in the Build Structure tool (under Tools... Structure Editing in the menu):

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>

I just tried saving an image as a PS file and did not have any problems.  Maybe the application you are using to show images does not show PS and does not list that format in its open dialog?  That is my only idea.  However, if you continue to have problems you could use "Help... Report a Bug" in the Chimera window and include all information needed to reproduce the problem, and your email if you wish a response.

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 Dec 2, 2010, at 6:43 PM, Pardeep kumar wrote:

Hi,
I am unable to show disulfide bonds in my final structure. It has at least five disulfide bonds. Please tell me how can I do that???and how can I save the image as a post script file....I tried it by save as .ps file but then the save file was not there in the designated folder though other formats (eg jpeg) were easily saved....




From goddard at sonic.net  Tue Dec  7 12:05:46 2010
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 07 Dec 2010 12:05:46 -0800
Subject: [Chimera-users] Query regarding Fit in Map
In-Reply-To: <4CFE3F2E.4090609@mail.cryst.bbk.ac.uk>
References: <4CF8E913.3000506@mail.cryst.bbk.ac.uk>
	<4CF9181A.6080500@sonic.net>
	<4CFE3F2E.4090609@mail.cryst.bbk.ac.uk>
Message-ID: <4CFE939A.6000209@sonic.net>

Hi Arun,

   So you just want to measure the correlation for a selected atoms in a 
map, no fit optimization.  This can be done without Python.  Make a 
simulated map with the Chimera "molmap" command, and report the 
correlation with "measure correlation".

     molmap sel 12.5 modelId #5
     measure correlation #5 #0

Here the map is #0, selected atoms are referred to using "sel" and a 
simulated map for those atoms is created as model #5. Results with be in 
Chimera reply log (menu Favorites / Reply Log).

I don't think you want to turn off the "use only data above contour 
level".  If you do it will measure the correlation of the entire box of 
simulated data including all the zeros far from the atom, which probably 
will not match the non-zeros in your map.  If you really want that use 
option "aboveThreshold false" with the measure correlation command.

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

     Tom

> Hi Tom,
>
> Thank you very much for your kind reply. It is quite helpful to know. 
> I am able to run the script and fit a map on to a map. But the problem 
> at had is slightly different. I have got the fits done already  with 
> Flex-EM and I am actually trying to measure (ideally automate it with 
> the Chimera script)  the correlation for the currently selected atoms 
> in the given map using the 'Update' option available in the Fit in Map 
> dialog. I would also like to specify the following option in the script.
>
> Real-time correlation / average update (turn off within the script)
> Use map simulated from atoms, resolution = value
> use only date above contour level from the first map (turn off within 
> the script)
> optimize correlation
> correlation calculates about mean data value (turn off within the script)
> rotation (turn off within the script)
> shitf (turn off within the script)
> Move whole molecule (turn off within the script)
>
> I am not sure how to put all this options in a script and calculate 
> the correlation for the currently selected atoms with the Update 
> option. I would greatly appreciate if you could provide me with some 
> more insight on how to change the code specifically. Thanking you.
>
> with kind regards,
> Arun Prasad
>
>
> Tom Goddard wrote:
>>  Hi Arun,
>>
>>   Yes you can use Fit in Map in a script.  I've attached an example 
>> Python script.  This script comes from the Chimera Python scripts web 
>> page but that web site is down right now.  It is necessary to use 
>> Python rather than a simpler Chimera command script because there is 
>> no Chimera command to use Fit in Map.  There probably should be, but 
>> since Fit in Map only does a local optimization you need some way to 
>> initially position the molecule or map you are fitting.  That is the 
>> hard part and so there hasn't been much demand for the fitting command.
>>
>>   The Python code for the Fit in Map dialog is included in all 
>> Chimera distributions in the directory
>>
>>     chimera/share/FitMap
>>
>> You could look at the __init__.py and gui.py to learn what the 
>> available functions are.  The gui.py (graphical user interface) file 
>> shows how those functions are called by the dialog.
>>
>>     Tom
>>
>>> Hi all,
>>>
>>> I would like to know whether its possible to automate the operations
>>> available with 'Fit in Map' tool and its options within a script.
>>> Actually I would like to calculate the correlation for certain segments
>>> of the atomic structure and it would be help if I could do it with a
>>> script rather that the GUI. Any suggestion is greatly appreciated.
>>>
>>> Thank you,
>>> Arun Prasad
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>
>>
>>
>




From goddard at sonic.net  Tue Dec  7 12:16:16 2010
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 07 Dec 2010 12:16:16 -0800
Subject: [Chimera-users] Query regarding Fit in Map
In-Reply-To: <4CFE939A.6000209@sonic.net>
References: <4CF8E913.3000506@mail.cryst.bbk.ac.uk>	<4CF9181A.6080500@sonic.net>	<4CFE3F2E.4090609@mail.cryst.bbk.ac.uk>
	<4CFE939A.6000209@sonic.net>
Message-ID: <4CFE9610.7090405@sonic.net>

Oops.  Just noticed "measure correlation" is giving an error in Chimera 
1.5 release candidates and daily builds.  I've fixed it and it will work 
in tonight's builds.

Also I noticed that measure correlation was not reporting both 
correlation about mean and correlation without subtracting mean.  
Today's changes will make it report both values.

     Tom

> Hi Arun,
>
>     So you just want to measure the correlation for a selected atoms in a
> map, no fit optimization.  This can be done without Python.  Make a
> simulated map with the Chimera "molmap" command, and report the
> correlation with "measure correlation".
>
>       molmap sel 12.5 modelId #5
>       measure correlation #5 #0
>
> Here the map is #0, selected atoms are referred to using "sel" and a
> simulated map for those atoms is created as model #5. Results with be in
> Chimera reply log (menu Favorites / Reply Log).
>
> I don't think you want to turn off the "use only data above contour
> level".  If you do it will measure the correlation of the entire box of
> simulated data including all the zeros far from the atom, which probably
> will not match the non-zeros in your map.  If you really want that use
> option "aboveThreshold false" with the measure correlation command.
>
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#correlation
>
>       Tom
>
>> Hi Tom,
>>
>> Thank you very much for your kind reply. It is quite helpful to know.
>> I am able to run the script and fit a map on to a map. But the problem
>> at had is slightly different. I have got the fits done already  with
>> Flex-EM and I am actually trying to measure (ideally automate it with
>> the Chimera script)  the correlation for the currently selected atoms
>> in the given map using the 'Update' option available in the Fit in Map
>> dialog. I would also like to specify the following option in the script.
>>
>> Real-time correlation / average update (turn off within the script)
>> Use map simulated from atoms, resolution = value
>> use only date above contour level from the first map (turn off within
>> the script)
>> optimize correlation
>> correlation calculates about mean data value (turn off within the script)
>> rotation (turn off within the script)
>> shitf (turn off within the script)
>> Move whole molecule (turn off within the script)
>>
>> I am not sure how to put all this options in a script and calculate
>> the correlation for the currently selected atoms with the Update
>> option. I would greatly appreciate if you could provide me with some
>> more insight on how to change the code specifically. Thanking you.
>>
>> with kind regards,
>> Arun Prasad
>>
>>
>> Tom Goddard wrote:
>>>   Hi Arun,
>>>
>>>    Yes you can use Fit in Map in a script.  I've attached an example
>>> Python script.  This script comes from the Chimera Python scripts web
>>> page but that web site is down right now.  It is necessary to use
>>> Python rather than a simpler Chimera command script because there is
>>> no Chimera command to use Fit in Map.  There probably should be, but
>>> since Fit in Map only does a local optimization you need some way to
>>> initially position the molecule or map you are fitting.  That is the
>>> hard part and so there hasn't been much demand for the fitting command.
>>>
>>>    The Python code for the Fit in Map dialog is included in all
>>> Chimera distributions in the directory
>>>
>>>      chimera/share/FitMap
>>>
>>> You could look at the __init__.py and gui.py to learn what the
>>> available functions are.  The gui.py (graphical user interface) file
>>> shows how those functions are called by the dialog.
>>>
>>>      Tom
>>>
>>>> Hi all,
>>>>
>>>> I would like to know whether its possible to automate the operations
>>>> available with 'Fit in Map' tool and its options within a script.
>>>> Actually I would like to calculate the correlation for certain segments
>>>> of the atomic structure and it would be help if I could do it with a
>>>> script rather that the GUI. Any suggestion is greatly appreciated.
>>>>
>>>> Thank you,
>>>> Arun Prasad
>>>> _______________________________________________
>>>> Chimera-users mailing list
>>>> Chimera-users at cgl.ucsf.edu
>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>>
>>>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>




From marek.basler at gmail.com  Tue Dec  7 12:36:06 2010
From: marek.basler at gmail.com (Marek Basler)
Date: Tue, 7 Dec 2010 15:36:06 -0500
Subject: [Chimera-users] Recommended HW for Chimera 3D
Message-ID: <AANLkTin0K+7Rf7+6Sy-fDi_6oqXgXd081zHFCLg3ZZMM@mail.gmail.com>

Hi,
what would be recommended HW and OS for trouble free 3D using glasses
with new 120Hz LCDs? Linux or Win? What is the best graphics card? I
don't care about money but nothing crazy either. Any suggestions?
Thanks a lot!
Marek


From gregc at cgl.ucsf.edu  Tue Dec  7 13:08:50 2010
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Tue, 07 Dec 2010 13:08:50 -0800
Subject: [Chimera-users] Recommended HW for Chimera 3D
In-Reply-To: <AANLkTin0K+7Rf7+6Sy-fDi_6oqXgXd081zHFCLg3ZZMM@mail.gmail.com>
References: <AANLkTin0K+7Rf7+6Sy-fDi_6oqXgXd081zHFCLg3ZZMM@mail.gmail.com>
Message-ID: <4CFEA262.2060903@cgl.ucsf.edu>

On 12/07/2010 12:36 PM, Marek Basler wrote:
> Hi,
> what would be recommended HW and OS for trouble free 3D using glasses
> with new 120Hz LCDs? Linux or Win? What is the best graphics card? I
> don't care about money but nothing crazy either. Any suggestions?
> Thanks a lot!
> Marek

NVIDIA appears to have temporarily cornered the market.  And Linux has 
the least overhead.  So my recommendation would be to use Linux (my 
current favorite is Ubuntu 10.10) with a NVIDIA Quadro card that has a 
3-pin stereo connector (so the 4000, 5000 or 6000, or an older FX 3800 
or better), and NVIDIA 3D Vision or 3D Vision Pro glasses.  The NVIDIA 
3D Vision web page has a list of supported 120Hz LCDs.  And be careful 
to size your system to handle the graphics card's power and cooling 
requirements and to handle the amount of data you wish to visualize.

See the chimera benchmarks page, 
http://plato.cgl.ucsf.edu/trac/chimera/wiki/benchmarks, for some help on 
choosing a graphic card.  As you can see, we need more benchmark results 
submissions.  So especially if you get one of the newer Quadro cards, 
please submit the benchmark results from the Tools / Utilities / 
Benchmark tool.

     -- Greg


From sabujp at gmail.com  Tue Dec  7 13:16:59 2010
From: sabujp at gmail.com (Sabuj Pattanayek)
Date: Tue, 7 Dec 2010 15:16:59 -0600
Subject: [Chimera-users] Recommended HW for Chimera 3D
In-Reply-To: <4CFEA262.2060903@cgl.ucsf.edu>
References: <AANLkTin0K+7Rf7+6Sy-fDi_6oqXgXd081zHFCLg3ZZMM@mail.gmail.com>
	<4CFEA262.2060903@cgl.ucsf.edu>
Message-ID: <AANLkTi=Cmkngb_7gk31Faz__PLSGmOEqAE3c1WqJV4HW@mail.gmail.com>

The oldest card that'll work in Linux is the Quadro 3700. Sharper
Technology will sell you the whole bundle for less than $900
(http://www.sharpertechnology.com/3d_vision_quadro.html) or in pieces,
e.g. the Quadro 3700 by itself (Note PNY warranties don't work through
Ebay if you don't purchase from a "store"), You can see if they'll
sell you one of the bigger ACERs (23 or 24" 120Hz 1920x1080 or x1200)
rather than the 1680x1050 22" samsung as well.

On Tue, Dec 7, 2010 at 3:08 PM, Greg Couch <gregc at cgl.ucsf.edu> wrote:
> On 12/07/2010 12:36 PM, Marek Basler wrote:
>> Hi,
>> what would be recommended HW and OS for trouble free 3D using glasses
>> with new 120Hz LCDs? Linux or Win? What is the best graphics card? I
>> don't care about money but nothing crazy either. Any suggestions?
>> Thanks a lot!
>> Marek
>
> NVIDIA appears to have temporarily cornered the market. ?And Linux has
> the least overhead. ?So my recommendation would be to use Linux (my
> current favorite is Ubuntu 10.10) with a NVIDIA Quadro card that has a
> 3-pin stereo connector (so the 4000, 5000 or 6000, or an older FX 3800
> or better), and NVIDIA 3D Vision or 3D Vision Pro glasses. ?The NVIDIA
> 3D Vision web page has a list of supported 120Hz LCDs. ?And be careful
> to size your system to handle the graphics card's power and cooling
> requirements and to handle the amount of data you wish to visualize.
>
> See the chimera benchmarks page,
> http://plato.cgl.ucsf.edu/trac/chimera/wiki/benchmarks, for some help on
> choosing a graphic card. ?As you can see, we need more benchmark results
> submissions. ?So especially if you get one of the newer Quadro cards,
> please submit the benchmark results from the Tools / Utilities /
> Benchmark tool.
>
> ? ? -- Greg
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>



From emailanindito at yahoo.co.in  Thu Dec  9 19:15:05 2010
From: emailanindito at yahoo.co.in (Anindito Sen)
Date: Fri, 10 Dec 2010 08:45:05 +0530 (IST)
Subject: [Chimera-users] Measuring the volume enclosed by a complex
Message-ID: <655997.52671.qm@web95605.mail.in.yahoo.com>


Dear All?
This question may have been answered before but will be helpful if you can let me know -?
How can I measure the volume enclosed by a protein
 complex.
Thanks
Andy


Dr. Anindito Sen (Ph.D)
School of Biological Sciences
University of Auckland
3A Symonds Street Room 420
Auckland City. New Zealand.
Tel: +64 -9- 373-7599 ext: 87593


      
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From sharjanto at i2r.a-star.edu.sg  Thu Dec  9 23:07:03 2010
From: sharjanto at i2r.a-star.edu.sg (Sumitro Harjanto)
Date: Fri, 10 Dec 2010 15:07:03 +0800
Subject: [Chimera-users] Calculating Solvent Accessible Surface of
	individual residue in a model
Message-ID: <162B8AFBFBBB2148A9A1B8F9C57534280BC9796C@mailbe01.teak.local.net>

Hi Meng,

 

I would like to find out if I can use Chimera to calculate the solvent
accessible surface(SAS) of each residue in a model..? I would like to
find out, basically, if I show the surface of the molecule, which are
the residues buried (SAS = 0) and which are the ones contributing to the
surface contour (SAS > 0).

 

Thanks! =]

 

Cheers,

Sumitro

 

 

Institute for Infocomm Research disclaimer:  "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."
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From meng at cgl.ucsf.edu  Fri Dec 10 09:49:00 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 10 Dec 2010 09:49:00 -0800
Subject: [Chimera-users] Calculating Solvent Accessible Surface of
	individual residue in a model
In-Reply-To: <162B8AFBFBBB2148A9A1B8F9C57534280BC9796C@mailbe01.teak.local.net>
References: <162B8AFBFBBB2148A9A1B8F9C57534280BC9796C@mailbe01.teak.local.net>
Message-ID: <D297D60B-02CB-4DA2-8B11-81F2DF5404AA@cgl.ucsf.edu>

Hi Harjanto,
Yes, it is automatically calculated as soon as you show a surface.  SAS and SES areas are "attributes" of atoms and residues.  After you show a surface, you can see histograms of the values and save them to a file using Render by Attribute (under Tools... Structure Analysis).
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render>

You can select just the residues with some range of SAS values using Select by Attribute, which is another part of that same tool.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#select>

Please see this previous post for more details:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-October/005693.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 Dec 9, 2010, at 11:07 PM, Sumitro Harjanto wrote:

> Hi Meng, 
> I would like to find out if I can use Chimera to calculate the solvent accessible surface(SAS) of each residue in a model..? I would like to find out, basically, if I show the surface of the molecule, which are the residues buried (SAS = 0) and which are the ones contributing to the surface contour (SAS > 0).
> Thanks! =] 
> Cheers,
> Sumitro
>  




From meng at cgl.ucsf.edu  Fri Dec 10 10:15:03 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 10 Dec 2010 10:15:03 -0800
Subject: [Chimera-users] Measuring the volume enclosed by a complex
In-Reply-To: <655997.52671.qm@web95605.mail.in.yahoo.com>
References: <655997.52671.qm@web95605.mail.in.yahoo.com>
Message-ID: <C0F22AA3-5478-44D0-96F1-8D61D9C68BAA@cgl.ucsf.edu>

Hi Andy,
I can't tell whether you are starting with a density map or an atomic structure.  The short answer in either case is to show a surface, then measure the volume enclosed in the surface.  Volume enclosed in the whole surface model is calculated with "Measure Volume and Area" whereas if a single model has multiple blobs and you only want the volume inside one of the blobs, you would use "Measure and Color Blobs."  Those are both under "Tools... Volume Data" in the menu.

If it is an atomic structure, there are a few additional issues. 
(A) whether you want the proteins as separate surfaces or the complex as one big surface.  If one big surface,  it is necessary to put all the proteins in one model (can be done with "copy/combine" function in the Model Panel) and it may also be necessary to specify they should be grouped together using the "surfcat" command
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/msms.html>

(B) surface calculation parameters, whether you want to allow molecular surfaces to have inside bubbles.
If you do not want to include these bubbles in subsequent surface calculations, use the Preferences (under Favorites menu), New Surface category, turn off "show disjoint surfaces" and click Save.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Surfaces>

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 Dec 9, 2010, at 7:15 PM, Anindito Sen wrote:
> 
> Dear All 
> This question may have been answered before but will be helpful if you can let me know - 
> How can I measure the volume enclosed by a protein complex.
> Thanks
> Andy
> 




From goddard at sonic.net  Fri Dec 10 11:41:35 2010
From: goddard at sonic.net (Tom Goddard)
Date: Fri, 10 Dec 2010 11:41:35 -0800
Subject: [Chimera-users] Calculating Solvent Accessible Surface
 of	individual residue in a model
In-Reply-To: <162B8AFBFBBB2148A9A1B8F9C57534280BC9796C@mailbe01.teak.local.net>
References: <162B8AFBFBBB2148A9A1B8F9C57534280BC9796C@mailbe01.teak.local.net>
Message-ID: <4D02826F.3010302@sonic.net>

Hi Sumitro,

   I made a Chimera video tutorial showing how to determine which 
residues are on the surface.

     http://www.cgl.ucsf.edu/chimera/videodoc/surfaceresidues/index.html

   Tom

> Hi Meng,
>
> I would like to find out if I can use Chimera to calculate the solvent 
> accessible surface(SAS) of each residue in a model..? I would like to 
> find out, basically, if I show the surface of the molecule, which are 
> the residues buried (SAS = 0) and which are the ones contributing to 
> the surface contour (SAS > 0).
>
> Thanks! =]
>
> Cheers,
>
> Sumitro
>
> Institute for Infocomm Research disclaimer: "This email is 
> confidential and may be privileged. If you are not the intended 
> recipient, please delete it and notify us immediately. Please do not 
> copy or use it for any purpose, or disclose its contents to any other 
> person. Thank you."
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users


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From s.molnar at sbcglobal.net  Sun Dec 12 06:30:27 2010
From: s.molnar at sbcglobal.net (Stephen P. Molnar)
Date: Sun, 12 Dec 2010 09:30:27 -0500
Subject: [Chimera-users] Inatallation Location
Message-ID: <20101212093027.2dfa9fb0.s.molnar@sbcglobal.net>

Chimera 1.5 (32-bit) on OpenSuSE 64-bit v11.2

I have just installed 1.5 on my syustem.. The installer insists on an installation in /home/computation/.local in spite of my attempts to install in a location of my choice.

This is rather annoying as I prefer to install software on a hard drive that will not be overwritten when I upgrade the OS.

Please advise.

Thanks in advance.
-- 
Stephen P. Molnar, Ph.D.			Life is a fuzzy set
Foundation for Chemistry			Stochastic and multivarate
http://www.FoundationForChemistry.com


From ybaime at gmail.com  Mon Dec 13 02:06:34 2010
From: ybaime at gmail.com (=?UTF-8?B?15nXldeb15HXkw==?=)
Date: Mon, 13 Dec 2010 12:06:34 +0200
Subject: [Chimera-users] Chimera Error
In-Reply-To: <AANLkTimygyJ5A_iL4a4yJ3RV2RetySc3c1qqXQu++zWS@mail.gmail.com>
References: <AANLkTimygyJ5A_iL4a4yJ3RV2RetySc3c1qqXQu++zWS@mail.gmail.com>
Message-ID: <AANLkTin=Xhj0Y9a8dMj6=vPvffVPC4Utu_SPaog4Z_vy@mail.gmail.com>

---------- Forwarded message ----------
From: ????? <ybaime at gmail.com>
Date: Mon, Dec 13, 2010 at 11:44 AM
Subject: Chimera Error
To: chimera-users at cgl.ucsf.edu


 Hi
I'm trying to open a density map file using chimera and for some reason the
file won't open. The opening is followed by an error message regarding the
file size being too small for the grid size.
The same error appears also in the old version (1.4.1) and also in the
newest version.
How can I solve this problem? How can I change the grid size?
The same file opens successfully on a friends computer with the 1.4.1
version and so I assume  the file is not corrupted.
Attached is an image of the error message.
I'd appreciate your response.
Thank you
Yocheved Baime
Bar-Ilan univ.
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From goddard at sonic.net  Mon Dec 13 09:16:47 2010
From: goddard at sonic.net (Tom Goddard)
Date: Mon, 13 Dec 2010 09:16:47 -0800
Subject: [Chimera-users] Chimera Error
In-Reply-To: <AANLkTin=Xhj0Y9a8dMj6=vPvffVPC4Utu_SPaog4Z_vy@mail.gmail.com>
References: <AANLkTimygyJ5A_iL4a4yJ3RV2RetySc3c1qqXQu++zWS@mail.gmail.com>
	<AANLkTin=Xhj0Y9a8dMj6=vPvffVPC4Utu_SPaog4Z_vy@mail.gmail.com>
Message-ID: <4D0654FF.2050204@sonic.net>

  Believe the error message!  It says the file is too small and it is.  
The grid size of 120 by 120 by 120 has over 1 million grid points but 
the file size is 0.5 million bytes.  The smallest value format used 
takes 1 byte per grid point.  You may have a truncated copy of the 
file.  If the file opens on another machine, then the copy on that 
machine must not be truncated.  Check the size of that file and make 
sure you get a full-size copy of it.

     Tom

>
> Hi
> I'm trying to open a density map file using chimera and for some 
> reason the file won't open. The opening is followed by an error 
> message regarding the file size being too small for the grid size.
> The same error appears also in the old version (1.4.1) and also in the 
> newest version.
> How can I solve this problem? How can I change the grid size?
> The same file opens successfully on a friends computer with the 1.4.1 
> version and so I assume  the file is not corrupted.
> Attached is an image of the error message.
> I'd appreciate your response.
> Thank you
> Yocheved Baime
> Bar-Ilan univ.
>
>
> _______________________________________________
> 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  Mon Dec 13 10:02:32 2010
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Mon, 13 Dec 2010 10:02:32 -0800
Subject: [Chimera-users] Inatallation Location
In-Reply-To: <20101212093027.2dfa9fb0.s.molnar@sbcglobal.net>
References: <20101212093027.2dfa9fb0.s.molnar@sbcglobal.net>
Message-ID: <4D065FB8.5020800@cgl.ucsf.edu>

On 12/12/2010 06:30 AM, Stephen P. Molnar wrote:
> Chimera 1.5 (32-bit) on OpenSuSE 64-bit v11.2
>
> I have just installed 1.5 on my syustem.. The installer insists on an installation in /home/computation/.local in spite of my attempts to install in a location of my choice.
>
> This is rather annoying as I prefer to install software on a hard drive that will not be overwritten when I upgrade the OS.
>
> Please advise.
>
> Thanks in advance.
The Linux installer did change, but it is only suggesting that chimera 
be put in ~/.local.  And if you install as root (e.g., via sudo), it 
will suggest that chimera be put in /opt/UCSF/Chimera.  To change were 
chimera is installed, use your terminal's character erase or line kill 
key to edit it (typically DEL and Control-U).  The gory details about 
character editing are found in the stty manual page.

The updated Linux installer also installs a desktop icon and will setup 
a symbolic link to the the chimera executable on your path so you don't 
need to put CHIMERA/bin on your path (in fact, we recommend not putting 
CHIMERA/bin on your path to avoid conflicts with system binaries).

     - Greg


From raj_sss at yahoo.com  Mon Dec 13 11:08:14 2010
From: raj_sss at yahoo.com (S. Shunmugasundararaj)
Date: Mon, 13 Dec 2010 11:08:14 -0800 (PST)
Subject: [Chimera-users] delete named selection
Message-ID: <58665.64070.qm@web33801.mail.mud.yahoo.com>

?Hi,

How do I delete the "Named selection"? from the? chimera file? I could not get the info from the archive or by searching the web.

Thanks in advance
Raj 






      
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From goddard at sonic.net  Mon Dec 13 18:08:11 2010
From: goddard at sonic.net (Tom Goddard)
Date: Mon, 13 Dec 2010 18:08:11 -0800
Subject: [Chimera-users] Maximum surface areas for each amino acid
In-Reply-To: <4D0681FE.2050207@psu.edu>
References: <162B8AFBFBBB2148A9A1B8F9C57534280BC9796C@mailbe01.teak.local.net>
	<4D02826F.3010302@sonic.net> <4D0681FE.2050207@psu.edu>
Message-ID: <4D06D18B.7040806@sonic.net>

Hi Ira,

   I don't know of any table of maximal solvent accessible surface areas 
for each residue type when bounded by glycines.  Maybe someone on the 
Chimera mailing list will know.

   A Chimera Python script could run through the PDB and accumulate 
per-residue surface area statistics.  One trouble with that would be 
that surface calculation fails in Chimera in some percentage of cases 
(~5%) due to numerical problems.

     Tom

> Hi Tom,
>
> Love the software. Do you have a table for calculating the maximum 
> available surface area for amino acids eg.(Gly-Xxx-Gly) so that I can 
> get a relative percentage exposed surface area from the calculations? 
> Do you know how to find one in the literature? Has anyone written a 
> program that describes the possible surface exposure for a residue in 
> a particular secondary structure and/or a particular sequence? This 
> maximal value would certainly be different depending on the local 
> sequence and structure. For example, a residue in the middle of a 
> helix would have to be shielded from the solvent by the i+4 and i-4 
> residues, and the size of those residues would matter.
>
> Thanks,
> Ira
>
>
> On 12/10/10 2:41 PM, Tom Goddard wrote:
>> Hi Sumitro,
>>
>>   I made a Chimera video tutorial showing how to determine which 
>> residues are on the surface.
>>
>> http://www.cgl.ucsf.edu/chimera/videodoc/surfaceresidues/index.html
>>
>>   Tom

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From goddard at sonic.net  Mon Dec 13 18:55:05 2010
From: goddard at sonic.net (Tom Goddard)
Date: Mon, 13 Dec 2010 18:55:05 -0800
Subject: [Chimera-users] Center of segmentation regions
Message-ID: <4D06DC89.40101@sonic.net>

Hi Tyler,

   The Chimera Segger segmentation tool currently doesn't report the 
geometric center of segmentation regions or the principal axes.  I've 
attached a Python script that will do that.  Select the regions in 
Chimera then open the script (File / Open).  The results will appear in 
the reply log (menu Favorites / Reply Log).  The results are in physical 
coordinates (taking account of volume grid spacing), not grid index units.

     Tom

> Dr. Meng,
>
> I am using Segger in Chimera and displaying the principal axes for 
> some of my segmentations.  I am wondering if there is a way to find 
> the XYZ coordinates of the origin of the principal axes for each of my 
> segments.  Is there a way to put the coordinates for these axes in a 
> text file?
>
> Thank you,
>
> Tyler Steele
>
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From kshatresh at gmail.com  Mon Dec 13 21:47:44 2010
From: kshatresh at gmail.com (Kshatresh Dutta Dubey)
Date: Tue, 14 Dec 2010 11:17:44 +0530
Subject: [Chimera-users] Chimera Error
Message-ID: <AANLkTin0BpYmzRNFCfax2t4AmJSE7k3oXg+0DufdEtpW@mail.gmail.com>

Dear All,
When i am trying to assign partial charge on a molecule, it is giving error
something like this-

AttributeError: '_chimera.Atom' object has no attribute 'gaffType'
File "/opt/UCSF/Chimera64-1.5rc/share/WriteMol2/__init__.py", line 289, in
writeMol2
atomType = atom.gaffType

I am using chimera 1.5 on linux 64-bit

Kindly help to resolve this problem
Thanks in advance
kshatresh
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From meng at cgl.ucsf.edu  Tue Dec 14 09:36:54 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 14 Dec 2010 09:36:54 -0800
Subject: [Chimera-users] Chimera Error
In-Reply-To: <AANLkTin0BpYmzRNFCfax2t4AmJSE7k3oXg+0DufdEtpW@mail.gmail.com>
References: <AANLkTin0BpYmzRNFCfax2t4AmJSE7k3oXg+0DufdEtpW@mail.gmail.com>
Message-ID: <11989EB7-CB47-4ADE-81D6-5196DCFB4D43@cgl.ucsf.edu>

Hi Kshatresh,
Please use "Help... Report a Bug" in the Chimera menu instead of sending mail to chimera-users.  This will automatically include information about what version of Chimera and type of computer you are using.  If you attach the molecule structure file, and enter a description of how to generate the error, we may be able to identify the problem.  Otherwise it is not enough information.  Also, if you want to hear back, please include your email address in the bugreport.
Thanks,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 13, 2010, at 9:47 PM, Kshatresh Dutta Dubey wrote:

> Dear All,
> When i am trying to assign partial charge on a molecule, it is giving error something like this-
> 
> AttributeError: '_chimera.Atom' object has no attribute 'gaffType'
> File "/opt/UCSF/Chimera64-1.5rc/share/WriteMol2/__init__.py", line 289, in writeMol2
> atomType = atom.gaffType
> 
> I am using chimera 1.5 on linux 64-bit
> 
> Kindly help to resolve this problem
> Thanks in advance 
> kshatresh




From meng at cgl.ucsf.edu  Tue Dec 14 09:55:14 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 14 Dec 2010 09:55:14 -0800
Subject: [Chimera-users] Maximum surface areas for each amino acid
In-Reply-To: <4D06D18B.7040806@sonic.net>
References: <162B8AFBFBBB2148A9A1B8F9C57534280BC9796C@mailbe01.teak.local.net>
	<4D02826F.3010302@sonic.net> <4D0681FE.2050207@psu.edu>
	<4D06D18B.7040806@sonic.net>
Message-ID: <B5A48344-3706-403C-8FA1-8DB7A5FC5830@cgl.ucsf.edu>

Hi Ira,
There is such a table in the Getarea online manual (about halfway down this page):

<http://curie.utmb.edu/area_man.html>

>From that page, 'The "random coil" value of a residue X is the average solvent-accessible surface area of X in the tripeptide Gly-X-Gly in an ensemble of 30 random conformations.'

Be aware, however, that various programs use different atomic radii and that those values will affect the surface areas.  Chimera likely uses different radii than Getarea, but I believe both programs use reasonable values and that it may still be useful to normalize by the Getarea random coil values as long as you are aware of these issues.  At least the default probe radius in Chimera and Getarea is the same, 1.4 Angstroms.  It is unclear if Getarea uses the same random coil values even if you specify a different probe radius.

Also be careful about solvent-excluded surface (which is what Chimera displays) versus solvent-accessible surface.  Chimera gives both kinds of areas, whereas the Getarea random coil values are SAS.  The SAS is farther out from the atomic centers and the values range much larger.

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 Dec 13, 2010, at 6:08 PM, Tom Goddard wrote:

> Hi Ira,
>   I don't know of any table of maximal solvent accessible surface areas for each residue type when bounded by glycines.  Maybe someone on the Chimera mailing list will know.
>   A Chimera Python script could run through the PDB and accumulate per-residue surface area statistics.  One trouble with that would be that surface calculation fails in Chimera in some percentage of cases (~5%) due to numerical problems.
>     Tom
> 
>> Hi Tom,
>> Love the software. Do you have a table for calculating the maximum available surface area for amino acids eg.(Gly-Xxx-Gly) so that I can get a relative percentage exposed surface area from the calculations? Do you know how to find one in the literature? Has anyone written a program that describes the possible surface exposure for a residue in a particular secondary structure and/or a particular sequence? This maximal value would certainly be different depending on the local sequence and structure. For example, a residue in the middle of a helix would have to be shielded from the solvent by the i+4 and i-4 residues, and the size of those residues would matter.
>> Thanks,
>> Ira
> 




From ayassin at wadsworth.org  Sun Dec 12 18:26:14 2010
From: ayassin at wadsworth.org (ayassin at wadsworth.org)
Date: Sun, 12 Dec 2010 21:26:14 -0500 (EST)
Subject: [Chimera-users] 3D-Stereo.
Message-ID: <5424fe290c060bb1af2e8af55521f253.squirrel@webmailz1.wadsworth.org>

Hello,

Will the sequential stereo work with the Nvidia 3D vision kit available
with the Toshiba 3DV series laptops? if not, What would be the best option
for sequential stereo?

Thank You.

Aymen Yassin.



IMPORTANT NOTICE: This e-mail and any attachments may contain
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privileged or otherwise protected by law from further disclosure.  It
is intended only for the addressee.  If you received this in error or
from someone who was not authorized to send it to you, please do not
distribute, copy or use it or any attachments.  Please notify the
sender immediately by reply e-mail and delete this from your
system. Thank you for your cooperation.




From Thomas.Marlovits at imba.oeaw.ac.at  Tue Dec 14 04:10:12 2010
From: Thomas.Marlovits at imba.oeaw.ac.at (Marlovits,Thomas)
Date: Tue, 14 Dec 2010 13:10:12 +0100
Subject: [Chimera-users] merging 3D volumes
Message-ID: <F5165B14-33C1-4055-A942-57B1B334F3E2@imp.ac.at>

Hi,

I was wondering, whether  a 3D map can be placed into a box with a user defined number or x/y/z planes ?  Ideally, I would like to place several 3D maps into boxes of the same dimensions and would like then to merge all maps into one 3D map file.  Is this possible ?

Tx for your fast answer,
Best,
-Thomas




Thomas C Marlovits
Research Group Leader
marlovits at imp.ac.at






From meng at cgl.ucsf.edu  Tue Dec 14 11:10:06 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 14 Dec 2010 11:10:06 -0800
Subject: [Chimera-users] merging 3D volumes
In-Reply-To: <F5165B14-33C1-4055-A942-57B1B334F3E2@imp.ac.at>
References: <F5165B14-33C1-4055-A942-57B1B334F3E2@imp.ac.at>
Message-ID: <9E99068D-40F3-4C06-B8C8-2FB752AAB4AB@cgl.ucsf.edu>

Hi Thomas,
The command "vop add" merges maps. (There is a similar "vop subtract" command too.)  If the maps are not on the same grid, this resamples as needed. It lets you specify a subregion (which planes to use) from the reference map.

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

I hope this is what you had in mind,
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 Dec 14, 2010, at 4:10 AM, Marlovits,Thomas wrote:

> Hi,
> I was wondering, whether  a 3D map can be placed into a box with a user defined number or x/y/z planes ?  Ideally, I would like to place several 3D maps into boxes of the same dimensions and would like then to merge all maps into one 3D map file.  Is this possible ?
> Tx for your fast answer,
> Best,
> -Thomas
> 



From pett at cgl.ucsf.edu  Tue Dec 14 11:10:44 2010
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 14 Dec 2010 11:10:44 -0800
Subject: [Chimera-users] Chimera Error
In-Reply-To: <AANLkTin0BpYmzRNFCfax2t4AmJSE7k3oXg+0DufdEtpW@mail.gmail.com>
References: <AANLkTin0BpYmzRNFCfax2t4AmJSE7k3oXg+0DufdEtpW@mail.gmail.com>
Message-ID: <0873A95E-C6E3-4968-A02C-F0C5EEBC76CD@cgl.ucsf.edu>

I guessing you were doing Minimize and one or more charge computations  
on non-standard residues failed (or some non-standard atoms in  
standard residues had zero charge assigned).  You tried to continue on  
and got this error.  Is this right?  Regardless, filing a bug report  
as Elaine suggests would be the best course.

--Eric

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

On Dec 13, 2010, at 9:47 PM, Kshatresh Dutta Dubey wrote:

> Dear All,
> When i am trying to assign partial charge on a molecule, it is  
> giving error something like this-
>
> AttributeError: '_chimera.Atom' object has no attribute 'gaffType'
> File "/opt/UCSF/Chimera64-1.5rc/share/WriteMol2/__init__.py", line  
> 289, in writeMol2
> atomType = atom.gaffType
>
> I am using chimera 1.5 on linux 64-bit
>
> Kindly help to resolve this problem
> Thanks in advance
> kshatresh
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



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From goddard at sonic.net  Tue Dec 14 11:10:54 2010
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 14 Dec 2010 11:10:54 -0800
Subject: [Chimera-users] merging 3D volumes
In-Reply-To: <F5165B14-33C1-4055-A942-57B1B334F3E2@imp.ac.at>
References: <F5165B14-33C1-4055-A942-57B1B334F3E2@imp.ac.at>
Message-ID: <4D07C13E.6040603@sonic.net>

  Hi Thomas,

   The command for this is "vop add" which allows you to add any number 
of maps on the grid defined by some map.

     vop add #1,2,5 onGrid #7

The problem comes when you don't already have a map with the desired 
resulting grid (number of planes, spacing, and location in space 
relative to other maps).  Unfortunately there is no simple way to 
produce an empty grid with your desired specifications.  I've been 
meaning to add a command to do this.  My current hack way to achieve 
this is to use the volume dialog Subregion Selection panel to drag a box 
for my new volume, rotate it, resize it as desired, and set the sample 
voxel size, and press Crop.  If I want the volume to contain all zeros I 
move the box to have no intersection with the original volume.

   I'll think about the command syntax, maybe a "vop zeros" command to 
make a new grid using typed parameters.  Maybe I can add this to the 
daily builds soon.  I'll let you know after some thinking.

     Tom

> Hi,
>
> I was wondering, whether  a 3D map can be placed into a box with a user defined number or x/y/z planes ?  Ideally, I would like to place several 3D maps into boxes of the same dimensions and would like then to merge all maps into one 3D map file.  Is this possible ?
>
> Tx for your fast answer,
> Best,
> -Thomas
>
>
>
>
> Thomas C Marlovits
> Research Group Leader
> marlovits at imp.ac.at
>
>
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>




From gregc at cgl.ucsf.edu  Tue Dec 14 11:43:51 2010
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Tue, 14 Dec 2010 11:43:51 -0800
Subject: [Chimera-users] 3D-Stereo.
In-Reply-To: <5424fe290c060bb1af2e8af55521f253.squirrel@webmailz1.wadsworth.org>
References: <5424fe290c060bb1af2e8af55521f253.squirrel@webmailz1.wadsworth.org>
Message-ID: <4D07C8F7.8060706@cgl.ucsf.edu>

On 12/12/2010 06:26 PM, ayassin at wadsworth.org wrote:
> Will the sequential stereo work with the Nvidia 3D vision kit available
> with the Toshiba 3DV series laptops? if not, What would be the best option
> for sequential stereo?

Unfortunately the Toshiba 3DV series will not work because it has NVIDIA 
GeForce  graphics.  With all of its dialogs, chimera needs the ability 
to do OpenGL stereo graphics within a window, and currently, only the 
NVIDIA Quadro graphics driver supports that.

The page may be out of date, but see 
<http://www.nvidia.com/object/quadro_pro_graphics_boards.html> for a 
list of possible Quadro graphics boards. The laptop versions have a 
capital M suffix.  My quick search did not find a laptop with both 
Quadro graphics and a 3D stereo screen, so you would need to connect the 
laptop to an external monitor to see sequential stereo.

     - Greg


From pett at cgl.ucsf.edu  Tue Dec 14 13:55:58 2010
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 14 Dec 2010 13:55:58 -0800
Subject: [Chimera-users] delete named selection
In-Reply-To: <58665.64070.qm@web33801.mail.mud.yahoo.com>
References: <58665.64070.qm@web33801.mail.mud.yahoo.com>
Message-ID: <621A2B47-2928-4889-8C12-F4FA898B28FB@cgl.ucsf.edu>

On Dec 13, 2010, at 11:08 AM, S. Shunmugasundararaj wrote:

>  Hi,
>
> How do I delete the "Named selection"  from the  chimera file? I  
> could not get the info from the archive or by searching the web.

I guess I've never run into a situation where someone wants to remove/ 
delete a named selection!  Can you describe why you want/need to do  
this?  I would consider making it easier to do if whatever situation  
you describe seems like it might be run into by others.

Anyway, I'm assuming that "chimera file" means a Chimera session  
file.  To remove named selections from a session file you would edit  
it with a text editor (that can handle long lines) and look for a line  
that looks like this:

savedSels = [[sel-name1, [bunch of numbers...], [sel-name2, [more  
numbers], etc.]

To remove sel-name1 from the save selection, change the line to:

savedSels = [[sel-name2, [more numbers], etc.]

To remove all selections:

saveSels = []

Don't just remove the line entirely.  You'll get an error restoring  
the session if you do that.

--Eric

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


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From bshaanan at bgu.ac.il  Wed Dec 15 01:02:17 2010
From: bshaanan at bgu.ac.il (Boaz Shaanan)
Date: Wed, 15 Dec 2010 09:02:17 GMT
Subject: [Chimera-users] Maximum surface areas for each amino acid
In-Reply-To: <mailman.40.1292353809.13958.chimera-users@cgl.ucsf.edu>
References: <mailman.40.1292353809.13958.chimera-users@cgl.ucsf.edu>
Message-ID: <f6cabdd1f46d9.4d088419@bgu.ac.il>

Hi Elaine,

The values in the table you mentioned seem to correspond to side-chain accessibility only, if I compare them to those for Gly-X-Gly peptide as in the classical paper by Miller et al. (1987), 196, 641-656. Their table can also be found in the book by Creighton: Proteins, 2nd edition, p. 142.

Best regards,

???????????????? Boaz

----- Original Message -----
From: chimera-users-request at cgl.ucsf.edu
Date: Tuesday, December 14, 2010 21:11
Subject: Chimera-users Digest, Vol 92, Issue 11
To: chimera-users at cgl.ucsf.edu

> Send Chimera-users mailing list submissions to
> 	chimera-users at cgl.ucsf.edu
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> or, via email, send a message with subject or body 'help' to
> 	chimera-users-request at cgl.ucsf.edu
> 
> You can reach the person managing the list at
> 	chimera-users-owner at cgl.ucsf.edu
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Chimera-users digest..."
> 
> 
> Today's Topics:
> 
> ?? 1. Maximum surface areas for each amino acid (Tom 
> Goddard)?? 2. Center of segmentation regions (Tom Goddard)
> ?? 3. Chimera Error (Kshatresh Dutta Dubey)
> ?? 4. Re: Chimera Error (Elaine Meng)
> ?? 5. Re: Maximum surface areas for each amino acid 
> (Elaine Meng)
> ?? 6. 3D-Stereo. (ayassin at wadsworth.org)
> ?? 7. merging 3D volumes (Marlovits,Thomas)
> ?? 8. Re: merging 3D volumes (Elaine Meng)
> 
> 
> -----------------------------------------------------------------
> -----
> 
> Message: 1
> Date: Mon, 13 Dec 2010 18:08:11 -0800
> From: Tom Goddard <goddard at sonic.net>
> Subject: [Chimera-users] Maximum surface areas for each amino acid
> To: iropson at psu.edu
> Cc: 'Chimera BB' <chimera-users at cgl.ucsf.edu>
> Message-ID: <4D06D18B.7040806 at sonic.net>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi Ira,
> 
> ?? I don't know of any table of maximal solvent 
> accessible surface areas 
> for each residue type when bounded by glycines.? Maybe 
> someone on the 
> Chimera mailing list will know.
> 
> ?? A Chimera Python script could run through the PDB 
> and accumulate 
> per-residue surface area statistics.? One trouble with that 
> would be 
> that surface calculation fails in Chimera in some percentage of 
> cases 
> (~5%) due to numerical problems.
> 
> ???? Tom
> 
> > Hi Tom,
> >
> > Love the software. Do you have a table for calculating the 
> maximum 
> > available surface area for amino acids eg.(Gly-Xxx-Gly) so 
> that I can 
> > get a relative percentage exposed surface area from the 
> calculations? 
> > Do you know how to find one in the literature? Has anyone 
> written a 
> > program that describes the possible surface exposure for a 
> residue in 
> > a particular secondary structure and/or a particular sequence? 
> This 
> > maximal value would certainly be different depending on the 
> local 
> > sequence and structure. For example, a residue in the middle 
> of a 
> > helix would have to be shielded from the solvent by the i+4 
> and i-4 
> > residues, and the size of those residues would matter.
> >
> > Thanks,
> > Ira
> >
> >
> > On 12/10/10 2:41 PM, Tom Goddard wrote:
> >> Hi Sumitro,
> >>
> >>?? I made a Chimera video tutorial showing how to 
> determine which 
> >> residues are on the surface.
> >>
> >> http://www.cgl.ucsf.edu/chimera/videodoc/surfaceresidues/index.html
> >>
> >>?? Tom
> 
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> 
> ------------------------------
> 
> Message: 2
> Date: Mon, 13 Dec 2010 18:55:05 -0800
> From: Tom Goddard <goddard at sonic.net>
> Subject: [Chimera-users] Center of segmentation regions
> To: twsteele2 at vcu.edu, "'Chimera BB'" <chimera-users at cgl.ucsf.edu>
> Message-ID: <4D06DC89.40101 at sonic.net>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi Tyler,
> 
> ?? The Chimera Segger segmentation tool currently 
> doesn't report the 
> geometric center of segmentation regions or the principal 
> axes.? I've 
> attached a Python script that will do that.? Select the 
> regions in 
> Chimera then open the script (File / Open).? The results 
> will appear in 
> the reply log (menu Favorites / Reply Log).? The results 
> are in physical 
> coordinates (taking account of volume grid spacing), not grid 
> index units.
> 
> ???? Tom
> 
> > Dr. Meng,
> >
> > I am using Segger in Chimera and displaying the principal axes 
> for 
> > some of my segmentations.? I am wondering if there is a 
> way to find 
> > the XYZ coordinates of the origin of the principal axes for 
> each of my 
> > segments.? Is there a way to put the coordinates for 
> these axes in a 
> > text file?
> >
> > Thank you,
> >
> > Tyler Steele
> >
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> 
> ------------------------------
> 
> Message: 3
> Date: Tue, 14 Dec 2010 11:17:44 +0530
> From: Kshatresh Dutta Dubey <kshatresh at gmail.com>
> Subject: [Chimera-users] Chimera Error
> To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Message-ID:
> 	<AANLkTin0BpYmzRNFCfax2t4AmJSE7k3oXg+0DufdEtpW at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Dear All,
> When i am trying to assign partial charge on a molecule, it is 
> giving error
> something like this-
> 
> AttributeError: '_chimera.Atom' object has no attribute 'gaffType'
> File "/opt/UCSF/Chimera64-1.5rc/share/WriteMol2/__init__.py", 
> line 289, in
> writeMol2
> atomType = atom.gaffType
> 
> I am using chimera 1.5 on linux 64-bit
> 
> Kindly help to resolve this problem
> Thanks in advance
> kshatresh
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> 
> ------------------------------
> 
> Message: 4
> Date: Tue, 14 Dec 2010 09:36:54 -0800
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Chimera Error
> To: Kshatresh Dutta Dubey <kshatresh at gmail.com>
> Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Message-ID: <11989EB7-CB47-4ADE-81D6-5196DCFB4D43 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=us-ascii
> 
> Hi Kshatresh,
> Please use "Help... Report a Bug" in the Chimera menu instead of 
> sending mail to chimera-users.? This will automatically 
> include information about what version of Chimera and type of 
> computer you are using.? If you attach the molecule 
> structure file, and enter a description of how to generate the 
> error, we may be able to identify the problem.? Otherwise 
> it is not enough information.? Also, if you want to hear 
> back, please include your email address in the bugreport.
> Thanks,
> Elaine
> -----
> Elaine C. Meng, 
> Ph.D.?????????????????????? 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Dec 13, 2010, at 9:47 PM, Kshatresh Dutta Dubey wrote:
> 
> > Dear All,
> > When i am trying to assign partial charge on a molecule, it is 
> giving error something like this-
> > 
> > AttributeError: '_chimera.Atom' object has no attribute 'gaffType'
> > File "/opt/UCSF/Chimera64-1.5rc/share/WriteMol2/__init__.py", 
> line 289, in writeMol2
> > atomType = atom.gaffType
> > 
> > I am using chimera 1.5 on linux 64-bit
> > 
> > Kindly help to resolve this problem
> > Thanks in advance 
> > kshatresh
> 
> 
> 
> 
> ------------------------------
> 
> Message: 5
> Date: Tue, 14 Dec 2010 09:55:14 -0800
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Maximum surface areas for each 
> amino acid
> To: iropson at psu.edu
> Cc: Chimera BB <chimera-users at cgl.ucsf.edu>
> Message-ID: <B5A48344-3706-403C-8FA1-8DB7A5FC5830 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=us-ascii
> 
> Hi Ira,
> There is such a table in the Getarea online manual (about 
> halfway down this page):
> 
> <http://curie.utmb.edu/area_man.html>
> 
> >From that page, 'The "random coil" value of a residue X is the 
> average solvent-accessible surface area of X in the tripeptide 
> Gly-X-Gly in an ensemble of 30 random conformations.'
> 
> Be aware, however, that various programs use different atomic 
> radii and that those values will affect the surface areas.? 
> Chimera likely uses different radii than Getarea, but I believe 
> both programs use reasonable values and that it may still be 
> useful to normalize by the Getarea random coil values as long as 
> you are aware of these issues.? At least the default probe 
> radius in Chimera and Getarea is the same, 1.4 Angstroms.? 
> It is unclear if Getarea uses the same random coil values even 
> if you specify a different probe radius.
> 
> Also be careful about solvent-excluded surface (which is what 
> Chimera displays) versus solvent-accessible surface.? 
> Chimera gives both kinds of areas, whereas the Getarea random 
> coil values are SAS.? The SAS is farther out from the 
> atomic centers and the values range much larger.
> 
> 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 Dec 13, 2010, at 6:08 PM, Tom Goddard wrote:
> 
> > Hi Ira,
> >?? I don't know of any table of maximal solvent 
> accessible surface areas for each residue type when bounded by 
> glycines.? Maybe someone on the Chimera mailing list will know.
> >?? A Chimera Python script could run through the PDB 
> and accumulate per-residue surface area statistics.? One 
> trouble with that would be that surface calculation fails in 
> Chimera in some percentage of cases (~5%) due to numerical problems.
> >???? Tom
> > 
> >> Hi Tom,
> >> Love the software. Do you have a table for calculating the 
> maximum available surface area for amino acids eg.(Gly-Xxx-Gly) 
> so that I can get a relative percentage exposed surface area 
> from the calculations? Do you know how to find one in the 
> literature? Has anyone written a program that describes the 
> possible surface exposure for a residue in a particular 
> secondary structure and/or a particular sequence? This maximal 
> value would certainly be different depending on the local 
> sequence and structure. For example, a residue in the middle of 
> a helix would have to be shielded from the solvent by the i+4 
> and i-4 residues, and the size of those residues would matter.
> >> Thanks,
> >> Ira
> > 
> 
> 
> 
> 
> ------------------------------
> 
> Message: 6
> Date: Sun, 12 Dec 2010 21:26:14 -0500 (EST)
> From: ayassin at wadsworth.org
> Subject: [Chimera-users] 3D-Stereo.
> To: chimera-users at cgl.ucsf.edu
> Message-ID:
> 	<5424fe290c060bb1af2e8af55521f253.squirrel at webmailz1.wadsworth.org>
> Content-Type: text/plain;charset=iso-8859-1
> 
> Hello,
> 
> Will the sequential stereo work with the Nvidia 3D vision kit 
> availablewith the Toshiba 3DV series laptops? if not, What would 
> be the best option
> for sequential stereo?
> 
> Thank You.
> 
> Aymen Yassin.
> 
> 
> 
> IMPORTANT NOTICE: This e-mail and any attachments may contain
> confidential or sensitive information which is, or may be, legally
> privileged or otherwise protected by law from further 
> disclosure.? It
> is intended only for the addressee.? If you received this 
> in error or
> from someone who was not authorized to send it to you, please do not
> distribute, copy or use it or any attachments.? Please 
> notify the
> sender immediately by reply e-mail and delete this from your
> system. Thank you for your cooperation.
> 
> 
> 
> 
> ------------------------------
> 
> Message: 7
> Date: Tue, 14 Dec 2010 13:10:12 +0100
> From: "Marlovits,Thomas" <Thomas.Marlovits at imba.oeaw.ac.at>
> Subject: [Chimera-users] merging 3D volumes
> To: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
> Message-ID: <F5165B14-33C1-4055-A942-57B1B334F3E2 at imp.ac.at>
> Content-Type: text/plain; charset="us-ascii"
> 
> Hi,
> 
> I was wondering, whether? a 3D map can be placed into a box 
> with a user defined number or x/y/z planes ?? Ideally, I 
> would like to place several 3D maps into boxes of the same 
> dimensions and would like then to merge all maps into one 3D map 
> file.? Is this possible ?
> 
> Tx for your fast answer,
> Best,
> -Thomas
> 
> 
> 
> 
> Thomas C Marlovits
> Research Group Leader
> marlovits at imp.ac.at
> 
> 
> 
> 
> 
> 
> ------------------------------
> 
> Message: 8
> Date: Tue, 14 Dec 2010 11:10:06 -0800
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] merging 3D volumes
> To: "Marlovits,Thomas" <Thomas.Marlovits at imba.oeaw.ac.at>
> Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
> Message-ID: <9E99068D-40F3-4C06-B8C8-2FB752AAB4AB at cgl.ucsf.edu>
> Content-Type: text/plain; charset=us-ascii
> 
> Hi Thomas,
> The command "vop add" merges maps. (There is a similar "vop 
> subtract" command too.)? If the maps are not on the same 
> grid, this resamples as needed. It lets you specify a subregion 
> (which planes to use) from the reference map.
> 
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#add>
> 
> I hope this is what you had in mind,
> 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 Dec 14, 2010, at 4:10 AM, Marlovits,Thomas wrote:
> 
> > Hi,
> > I was wondering, whether? a 3D map can be placed into a 
> box with a user defined number or x/y/z planes ?? Ideally, 
> I would like to place several 3D maps into boxes of the same 
> dimensions and would like then to merge all maps into one 3D map 
> file.? Is this possible ?
> > Tx for your fast answer,
> > Best,
> > -Thomas
> > 
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
> End of Chimera-users Digest, Vol 92, Issue 11
> *********************************************
> 

Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone: 972-8-647-2220 ; Fax: 646-1710
Skype: boaz.shaanan?
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From danielgurnon at depauw.edu  Wed Dec 15 06:44:35 2010
From: danielgurnon at depauw.edu (Daniel Gurnon)
Date: Wed, 15 Dec 2010 09:44:35 -0500
Subject: [Chimera-users] selection line-width
Message-ID: <AANLkTikVy3Y_Zxij7EmHoEcTv5LaUYazb0K2Ft=yv_Mu@mail.gmail.com>

Hi everyone,
Two requests that would help with interactive demonstrations to large
audiences:
In preferences/background, the selection mode can be "fill" or "outline". Is
it possible to add a line-width option for outline? I want to increase the
thickness of a selection outline to make it easier for my students to see
when I'm projecting an image, but I don't want to use the fill option and
lose residue color information.

I suspect that's an easy fix, but this one might be more difficult:
Transparent surfaces are very informative when combined with underlying
ribbons or stick representations of atoms. But if a residue is visible
beneath a transparent surface, selecting it (via the command line) does not
show the selection outline. Is it possible to make that work?
Thanks,
Dan

-- 
____________________________

Daniel Gurnon, Ph. D.
Assistant Professor of Chemistry
DePauw University
Greencastle, IN 46135

p: 765-658-6279
e: danielgurnon at depauw.edu
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From meng at cgl.ucsf.edu  Wed Dec 15 09:46:31 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 15 Dec 2010 09:46:31 -0800
Subject: [Chimera-users] [Chimera-announce] Chimera 1.5 release
In-Reply-To: <DF90167B87B34343BA82EB7EFEFEFDD61154D8EAC2@EXCHANGE1.utmb.edu>
References: <582D41C5-6731-4B65-8686-28EB2E4190E0@cgl.ucsf.edu>
	<DF90167B87B34343BA82EB7EFEFEFDD61154D8EAC2@EXCHANGE1.utmb.edu>
Message-ID: <70BD0310-367B-4111-AC71-89DC703AA059@cgl.ucsf.edu>

Hi Surendra,
Yes, if you are doing map-in-map fitting, it calculates the correlation values, in 1.5 and also in earlier versions.  You have the choice of calculating the correlation about zero or about the mean.  If you are doing atoms-in-map fitting, it does not give correlation values UNLESS you turn on the "Use map simulated from atoms" option, and in that case you also need to enter a resolution value for the simulated map.

If you click the Help button on the dialog it will show the manual page with more detailed explanations,
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.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 Dec 15, 2010, at 9:33 AM, Negi, Surendra S. wrote:

> Hi Elaine, 
> In EM fit, Is it possible to calculate the Correlation? I am using current version 1.5 of UCSF chimera.
> Thank you.
> Surendra
> ps: the snapshot is available at : http://img221.imageshack.us/img221/2492/screenshotpt.png




From goddard at sonic.net  Wed Dec 15 10:14:45 2010
From: goddard at sonic.net (Tom Goddard)
Date: Wed, 15 Dec 2010 10:14:45 -0800
Subject: [Chimera-users] selection line-width
In-Reply-To: <AANLkTikVy3Y_Zxij7EmHoEcTv5LaUYazb0K2Ft=yv_Mu@mail.gmail.com>
References: <AANLkTikVy3Y_Zxij7EmHoEcTv5LaUYazb0K2Ft=yv_Mu@mail.gmail.com>
Message-ID: <4D090595.5070406@sonic.net>

  Hi Daniel,

   Looking at the code I think it would not  be too hard to thicken the 
green selection outline.  We can test the appearance with a one line 
modification of the C++ code.  I've added this to the feature request list.

     http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests

The fact that selected objects don't show a green outline when they are 
under a transparent surface is bug 7777 reported over a year ago.

     http://plato.cgl.ucsf.edu/trac/chimera/ticket/7777

The technical problem is that the depth buffer is being written when 
drawing transparent surfaces.  This is needed for one-layer transparent 
surfaces (the default for molecular surfaces) but is not required for 
multi-layer transparent surfaces (the default a few years ago).  Even 
for multi-layer transparent surfaces it is desirable to write the depth 
buffer when multiple transparent models are used to minimize incorrect 
transparent object rendering (depth order wrong).

   Here's one idea for a solution.  Green selection outlines could be 
shown even for objects hidden behind opaque surfaces and models.  It 
would be like x-ray vision.  I think this may be nice because when 
selected items are not seen because they are covered it is hard to know 
what is selected.  But it may be confusing to see these x-ray 
silhouettes -- would have to try to know.  I think it is easy to try.

     Tom

> Hi everyone,
> Two requests that would help with interactive demonstrations to large 
> audiences:
> In preferences/background, the selection mode can be "fill" or 
> "outline". Is it possible to add a line-width option for outline? I 
> want to increase the thickness of a selection outline to make it 
> easier for my students to see when I'm projecting an image, but I 
> don't want to use the fill option and lose residue color information.
>
> I suspect that's an easy fix, but this one might be more difficult:
> Transparent surfaces are very informative when combined with 
> underlying ribbons or stick representations of atoms. But if a residue 
> is visible beneath a transparent surface, selecting it (via the 
> command line) does not show the selection outline. Is it possible to 
> make that work?
> Thanks,
> Dan
>
> -- 
> ____________________________
>
> Daniel Gurnon, Ph. D.
> Assistant Professor of Chemistry
> DePauw University
> Greencastle, IN 46135
>
> p: 765-658-6279
> e: danielgurnon at depauw.edu <mailto:danielgurnon at depauw.edu>
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users


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From danielgurnon at depauw.edu  Wed Dec 15 10:57:41 2010
From: danielgurnon at depauw.edu (Daniel Gurnon)
Date: Wed, 15 Dec 2010 13:57:41 -0500
Subject: [Chimera-users] selection line-width
In-Reply-To: <4D090595.5070406@sonic.net>
References: <AANLkTikVy3Y_Zxij7EmHoEcTv5LaUYazb0K2Ft=yv_Mu@mail.gmail.com>
	<4D090595.5070406@sonic.net>
Message-ID: <AANLkTimQ-oYbi1yerVBLOcvCa6SPhPq=h8Ab3hP0Yurp@mail.gmail.com>

The X-ray vision is a good idea, and would be useful in thinking about
interfaces as well as surfaces. But I can imagine some situations where
'x-ray' would be problematic- you would lose some sense of depth if the
green silhouette was always visible as you rotated a model, and multiple
selections would get messy. If transparency is the problem here, would it be
easier to make selections visible through a surface *regardless *of
transparency, but not visible through other objects (i.e., ribbons and bonds
underlying the surface and other models in front of the selection would
conceal the green outline)?

Also, I'm not advocating a permanent increase in the thickness of the
selection outline- I want control over it, so I can thicken it for
presentations to large audiences.

Dan

On Wed, Dec 15, 2010 at 1:14 PM, Tom Goddard <goddard at sonic.net> wrote:

>  Hi Daniel,
>
>   Looking at the code I think it would not  be too hard to thicken the
> green selection outline.  We can test the appearance with a one line
> modification of the C++ code.  I've added this to the feature request list.
>
>     http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests
>
> The fact that selected objects don't show a green outline when they are
> under a transparent surface is bug 7777 reported over a year ago.
>
>     http://plato.cgl.ucsf.edu/trac/chimera/ticket/7777
>
> The technical problem is that the depth buffer is being written when
> drawing transparent surfaces.  This is needed for one-layer transparent
> surfaces (the default for molecular surfaces) but is not required for
> multi-layer transparent surfaces (the default a few years ago).  Even for
> multi-layer transparent surfaces it is desirable to write the depth buffer
> when multiple transparent models are used to minimize incorrect transparent
> object rendering (depth order wrong).
>
>   Here's one idea for a solution.  Green selection outlines could be shown
> even for objects hidden behind opaque surfaces and models.  It would be like
> x-ray vision.  I think this may be nice because when selected items are not
> seen because they are covered it is hard to know what is selected.  But it
> may be confusing to see these x-ray silhouettes -- would have to try to
> know.  I think it is easy to try.
>
>     Tom
>
> Hi everyone,
> Two requests that would help with interactive demonstrations to large
> audiences:
> In preferences/background, the selection mode can be "fill" or "outline".
> Is it possible to add a line-width option for outline? I want to increase
> the thickness of a selection outline to make it easier for my students to
> see when I'm projecting an image, but I don't want to use the fill option
> and lose residue color information.
>
> I suspect that's an easy fix, but this one might be more difficult:
> Transparent surfaces are very informative when combined with underlying
> ribbons or stick representations of atoms. But if a residue is visible
> beneath a transparent surface, selecting it (via the command line) does not
> show the selection outline. Is it possible to make that work?
> Thanks,
> Dan
>
> --
> ____________________________
>
> Daniel Gurnon, Ph. D.
> Assistant Professor of Chemistry
> DePauw University
> Greencastle, IN 46135
>
> p: 765-658-6279
> e: danielgurnon at depauw.edu
>
>
> _______________________________________________
> Chimera-users mailing listChimera-users at cgl.ucsf.eduhttp://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>
>


-- 
____________________________

Daniel Gurnon, Ph. D.
Assistant Professor of Chemistry
DePauw University
Greencastle, IN 46135

p: 765-658-6279
e: danielgurnon at depauw.edu
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From biocjh at gmail.com  Wed Dec 15 18:36:03 2010
From: biocjh at gmail.com (C.J.)
Date: Thu, 16 Dec 2010 10:36:03 +0800
Subject: [Chimera-users] [chimera-users]about "color key"
Message-ID: <AANLkTik3Ky=6G5kddF9DhMqED+DeCyoY9bEN+sjP6jZd@mail.gmail.com>

Dear all,

I seek for help that how to change the unit of "color key" to angstrom.
As the default value displaied in "color key" is just number, I wonder
what it means.
Any reply will be greatly appreciated.

-- 
Regards!
C.J.


From meng at cgl.ucsf.edu  Wed Dec 15 18:47:40 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 15 Dec 2010 18:47:40 -0800
Subject: [Chimera-users] [chimera-users]about "color key"
In-Reply-To: <AANLkTik3Ky=6G5kddF9DhMqED+DeCyoY9bEN+sjP6jZd@mail.gmail.com>
References: <AANLkTik3Ky=6G5kddF9DhMqED+DeCyoY9bEN+sjP6jZd@mail.gmail.com>
Message-ID: <18A8BC5F-E576-4283-8690-B6CCD336DBAB@cgl.ucsf.edu>

Dear CJ,
The units depend on what you are trying to show with color.  If you started Color Key with the button in the Surface Color tool and in that tool, you were coloring by distance (radius, cylinder radius, or height), the units are whatever distance units are in your structure data.  That is usually angstroms, but it could be nanometers for some density maps.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html#colorkey>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>

If you mean you want to display an angstrom symbol, that can be done with the 2D Labels tool, which is another tab on the same dialog as Color Key.  You can just make a symbol label and then drag it to wherever you want.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html#2dlabels>

There is an example of putting an angstrom symbol over a color key in this image tutorial:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.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 Dec 15, 2010, at 6:36 PM, C.J. wrote:

> Dear all,
> I seek for help that how to change the unit of "color key" to angstrom.
> As the default value displaied in "color key" is just number, I wonder
> what it means.
> Any reply will be greatly appreciated.
> -- 
> Regards!
> C.J.




From biocjh at gmail.com  Wed Dec 15 19:21:51 2010
From: biocjh at gmail.com (C.J.)
Date: Thu, 16 Dec 2010 11:21:51 +0800
Subject: [Chimera-users] [chimera-users]about "color key"
In-Reply-To: <18A8BC5F-E576-4283-8690-B6CCD336DBAB@cgl.ucsf.edu>
References: <AANLkTik3Ky=6G5kddF9DhMqED+DeCyoY9bEN+sjP6jZd@mail.gmail.com>
	<18A8BC5F-E576-4283-8690-B6CCD336DBAB@cgl.ucsf.edu>
Message-ID: <AANLkTikHpfhKN5e4TSViyvqjzAw3k1XSVvzMBX2Y=CQU@mail.gmail.com>

Thanks.

But I don't know clearlly how to set these paremeters to creat a
color key with unit of "Angstrom" automatically.
More help will be appreciated.

2010/12/16 Elaine Meng <meng at cgl.ucsf.edu>:
> Dear CJ,
> The units depend on what you are trying to show with color. ?If you started Color Key with the button in the Surface Color tool and in that tool, you were coloring by distance (radius, cylinder radius, or height), the units are whatever distance units are in your structure data. ?That is usually angstroms, but it could be nanometers for some density maps.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html#colorkey>
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>
>
> If you mean you want to display an angstrom symbol, that can be done with the 2D Labels tool, which is another tab on the same dialog as Color Key. ?You can just make a symbol label and then drag it to wherever you want.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html#2dlabels>
>
> There is an example of putting an angstrom symbol over a color key in this image tutorial:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.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 Dec 15, 2010, at 6:36 PM, C.J. wrote:
>
>> Dear all,
>> I seek for help that how to change the unit of "color key" to angstrom.
>> As the default value displaied in "color key" is just number, I wonder
>> what it means.
>> Any reply will be greatly appreciated.
>> --
>> Regards!
>> C.J.
>
>



-- 
Regards!
C.J.



From chiendarret at gmail.com  Wed Dec 15 22:45:57 2010
From: chiendarret at gmail.com (Francesco Pietra)
Date: Thu, 16 Dec 2010 07:45:57 +0100
Subject: [Chimera-users] changing HIS to HIP
Message-ID: <AANLkTimvTB1SktboLNo6WAvu-BMrGNxAdfwKE58iQ0mP@mail.gmail.com>

Hello:
I need to change several histidine residues (both HIS and HIE,
although both called HIS) to HIP. I tried manually. In case of
monoprotonation at NE2:

modify structure
element N
bonds 3
geom trigonal
connect to preex atoms
color by element
change modified residue's name to HIP
set atom names to ND1
or
retain current atom names

In both cases the proton attached to ND1 takes the name "H1" instead
of the expected HD1.


Is that error in the above procedure or chimera bug? (chimera alpha
version 1.5 (build 30702) on GNU/LINUX 32bit)

Addendum: is there any other method of accomplishing the task with
chimera? It is rather troublesome to go through all monoprotonated
histidines of this large homomer (in different chains HIS of the same
number have been differently protonated by reduce). A problem with
reduce (if not my misuse of reduce) is that all histidines become
monoprotonated, while the experimental pH is such that all should be
diprotonated. I must add that I  am bound to reduce because the
program that I use subsequently goes through reduce.

thanks for help
francesco pietra


From meng at cgl.ucsf.edu  Thu Dec 16 09:03:00 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 16 Dec 2010 09:03:00 -0800
Subject: [Chimera-users] [chimera-users]about "color key"
In-Reply-To: <AANLkTikHpfhKN5e4TSViyvqjzAw3k1XSVvzMBX2Y=CQU@mail.gmail.com>
References: <AANLkTik3Ky=6G5kddF9DhMqED+DeCyoY9bEN+sjP6jZd@mail.gmail.com>
	<18A8BC5F-E576-4283-8690-B6CCD336DBAB@cgl.ucsf.edu>
	<AANLkTikHpfhKN5e4TSViyvqjzAw3k1XSVvzMBX2Y=CQU@mail.gmail.com>
Message-ID: <E60B4EE8-CC4B-4AAF-AE7E-AC4C1E27460C@cgl.ucsf.edu>

Hi CJ,
If your structure and/or map data is in angstrom cooordinates, and you are coloring by distance in Surface Color, and you start Color Key from the button in Surface Color, it is already automatically in angstrom units.
Elaine

On Dec 15, 2010, at 7:21 PM, C.J. wrote:

> Thanks.
> 
> But I don't know clearlly how to set these paremeters to creat a
> color key with unit of "Angstrom" automatically.
> More help will be appreciated.
> 
> 2010/12/16 Elaine Meng <meng at cgl.ucsf.edu>:
>> Dear CJ,
>> The units depend on what you are trying to show with color.  If you started Color Key with the button in the Surface Color tool and in that tool, you were coloring by distance (radius, cylinder radius, or height), the units are whatever distance units are in your structure data.  That is usually angstroms, but it could be nanometers for some density maps.
>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html#colorkey>
>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>
>> 
>> If you mean you want to display an angstrom symbol, that can be done with the 2D Labels tool, which is another tab on the same dialog as Color Key.  You can just make a symbol label and then drag it to wherever you want.
>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html#2dlabels>
>> 
>> There is an example of putting an angstrom symbol over a color key in this image tutorial:
>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.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 Dec 15, 2010, at 6:36 PM, C.J. wrote:
>> 
>>> Dear all,
>>> I seek for help that how to change the unit of "color key" to angstrom.
>>> As the default value displaied in "color key" is just number, I wonder
>>> what it means.
>>> Any reply will be greatly appreciated.
>>> --
>>> Regards!
>>> C.J.
>> 
>> 
> 
> 
> 
> -- 
> Regards!
> C.J.
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From meng at cgl.ucsf.edu  Thu Dec 16 09:46:27 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 16 Dec 2010 09:46:27 -0800
Subject: [Chimera-users] changing HIS to HIP
In-Reply-To: <AANLkTimvTB1SktboLNo6WAvu-BMrGNxAdfwKE58iQ0mP@mail.gmail.com>
References: <AANLkTimvTB1SktboLNo6WAvu-BMrGNxAdfwKE58iQ0mP@mail.gmail.com>
Message-ID: <2130DE72-6D62-4264-927A-0DACD36EC271@cgl.ucsf.edu>

Hi Francesco,
Your procedure is unnecessary.   Here are two much easier approaches:

Just use a text-editor to edit the PDB file and change the names of those residues to HIP, then open in Chimera and use AddH with default settings (histidine protonation "Residue-name-based")

- OR -

If it is OK if the residues are still named HIS, but you want certain ones protonated like HIP (positively charged sidechain, hydrogens on both nitrogens) you can avoid the text-editing part.  Just open the PDB file and use AddH with the histidine protonation option "Specified individually..." and then simply indicate with checkboxes all the histidine sidechain nitrogens you want protonated.

I recommend getting version 1.5 of Chimera if you are using something older.

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 Dec 15, 2010, at 10:45 PM, Francesco Pietra wrote:

> Hello:
> I need to change several histidine residues (both HIS and HIE,
> although both called HIS) to HIP. I tried manually. In case of
> monoprotonation at NE2:
> 
> modify structure
> element N
> bonds 3
> geom trigonal
> connect to preex atoms
> color by element
> change modified residue's name to HIP
> set atom names to ND1
> or
> retain current atom names
> 
> In both cases the proton attached to ND1 takes the name "H1" instead
> of the expected HD1.
> 
> 
> Is that error in the above procedure or chimera bug? (chimera alpha
> version 1.5 (build 30702) on GNU/LINUX 32bit)
> 
> Addendum: is there any other method of accomplishing the task with
> chimera? It is rather troublesome to go through all monoprotonated
> histidines of this large homomer (in different chains HIS of the same
> number have been differently protonated by reduce). A problem with
> reduce (if not my misuse of reduce) is that all histidines become
> monoprotonated, while the experimental pH is such that all should be
> diprotonated. I must add that I  am bound to reduce because the
> program that I use subsequently goes through reduce.
> 
> thanks for help
> francesco pietra




From biocjh at gmail.com  Thu Dec 16 17:17:42 2010
From: biocjh at gmail.com (C.J.)
Date: Fri, 17 Dec 2010 09:17:42 +0800
Subject: [Chimera-users] [chimera-users]about "color key"
In-Reply-To: <E60B4EE8-CC4B-4AAF-AE7E-AC4C1E27460C@cgl.ucsf.edu>
References: <AANLkTik3Ky=6G5kddF9DhMqED+DeCyoY9bEN+sjP6jZd@mail.gmail.com>
	<18A8BC5F-E576-4283-8690-B6CCD336DBAB@cgl.ucsf.edu>
	<AANLkTikHpfhKN5e4TSViyvqjzAw3k1XSVvzMBX2Y=CQU@mail.gmail.com>
	<E60B4EE8-CC4B-4AAF-AE7E-AC4C1E27460C@cgl.ucsf.edu>
Message-ID: <AANLkTimDEv4cjCkExPtRZH5b_VmWkKUapPX1Lg8-Lr1+@mail.gmail.com>

Dear Dr. Elaine,

I am afraid that my structure is not in angstrom coordinates.
So, any way to change the color key?
Thanks all the same.

2010/12/17 Elaine Meng <meng at cgl.ucsf.edu>:
> Hi CJ,
> If your structure and/or map data is in angstrom cooordinates, and you are coloring by distance in Surface Color, and you start Color Key from the button in Surface Color, it is already automatically in angstrom units.
> Elaine
>
> On Dec 15, 2010, at 7:21 PM, C.J. wrote:
>
>> Thanks.
>>
>> But I don't know clearlly how to set these paremeters to creat a
>> color key with unit of "Angstrom" automatically.
>> More help will be appreciated.
>>
>> 2010/12/16 Elaine Meng <meng at cgl.ucsf.edu>:
>>> Dear CJ,
>>> The units depend on what you are trying to show with color. ?If you started Color Key with the button in the Surface Color tool and in that tool, you were coloring by distance (radius, cylinder radius, or height), the units are whatever distance units are in your structure data. ?That is usually angstroms, but it could be nanometers for some density maps.
>>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html#colorkey>
>>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>
>>>
>>> If you mean you want to display an angstrom symbol, that can be done with the 2D Labels tool, which is another tab on the same dialog as Color Key. ?You can just make a symbol label and then drag it to wherever you want.
>>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html#2dlabels>
>>>
>>> There is an example of putting an angstrom symbol over a color key in this image tutorial:
>>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.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 Dec 15, 2010, at 6:36 PM, C.J. wrote:
>>>
>>>> Dear all,
>>>> I seek for help that how to change the unit of "color key" to angstrom.
>>>> As the default value displaied in "color key" is just number, I wonder
>>>> what it means.
>>>> Any reply will be greatly appreciated.
>>>> --
>>>> Regards!
>>>> C.J.
>>>
>>>
>>
>>
>>
>> --
>> Regards!
>> C.J.
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>
>



-- 
Regards!
C.J.



From meng at cgl.ucsf.edu  Fri Dec 17 09:12:51 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 17 Dec 2010 09:12:51 -0800
Subject: [Chimera-users] [chimera-users]about "color key"
In-Reply-To: <AANLkTimDEv4cjCkExPtRZH5b_VmWkKUapPX1Lg8-Lr1+@mail.gmail.com>
References: <AANLkTik3Ky=6G5kddF9DhMqED+DeCyoY9bEN+sjP6jZd@mail.gmail.com>
	<18A8BC5F-E576-4283-8690-B6CCD336DBAB@cgl.ucsf.edu>
	<AANLkTikHpfhKN5e4TSViyvqjzAw3k1XSVvzMBX2Y=CQU@mail.gmail.com>
	<E60B4EE8-CC4B-4AAF-AE7E-AC4C1E27460C@cgl.ucsf.edu>
	<AANLkTimDEv4cjCkExPtRZH5b_VmWkKUapPX1Lg8-Lr1+@mail.gmail.com>
Message-ID: <85E02101-EF73-4495-A122-F95B70792F3C@cgl.ucsf.edu>

Hi CJ,
If you know what distance units are in your structure, you can simply apply the conversion factor to the values in the Color Key dialog.  In other words, if your structure is in nanometer units, you can just manually type new values into the Color Key dialog that are 10x the values that were there initially.  If the values from the structure are 10 and 50 (nanometers), you can just manually edit the values in the Color Key dialog to 100 and 500, then they will be in angstroms.  If your structure is in grid units where the grid points are spaced 1.582 angstroms apart, then you would multiply by 1.582 instead.  (etc.)
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 Dec 16, 2010, at 5:17 PM, C.J. wrote:

> Dear Dr. Elaine,
> 
> I am afraid that my structure is not in angstrom coordinates.
> So, any way to change the color key?
> Thanks all the same.
> 
> 2010/12/17 Elaine Meng <meng at cgl.ucsf.edu>:
>> Hi CJ,
>> If your structure and/or map data is in angstrom cooordinates, and you are coloring by distance in Surface Color, and you start Color Key from the button in Surface Color, it is already automatically in angstrom units.
>> Elaine
> 




From biocjh at gmail.com  Mon Dec 20 19:44:34 2010
From: biocjh at gmail.com (C.J.)
Date: Tue, 21 Dec 2010 11:44:34 +0800
Subject: [Chimera-users] [chimera-users]about "color key"
In-Reply-To: <85E02101-EF73-4495-A122-F95B70792F3C@cgl.ucsf.edu>
References: <AANLkTik3Ky=6G5kddF9DhMqED+DeCyoY9bEN+sjP6jZd@mail.gmail.com>
	<18A8BC5F-E576-4283-8690-B6CCD336DBAB@cgl.ucsf.edu>
	<AANLkTikHpfhKN5e4TSViyvqjzAw3k1XSVvzMBX2Y=CQU@mail.gmail.com>
	<E60B4EE8-CC4B-4AAF-AE7E-AC4C1E27460C@cgl.ucsf.edu>
	<AANLkTimDEv4cjCkExPtRZH5b_VmWkKUapPX1Lg8-Lr1+@mail.gmail.com>
	<85E02101-EF73-4495-A122-F95B70792F3C@cgl.ucsf.edu>
Message-ID: <AANLkTi=7-u6B9EOSfkBkHGmo0xu4eDzaryr09pXMOk0O@mail.gmail.com>

Thanks, but can I change the distance unit of color key in Chimera? Or
I have to modify the pdb structure file to change that?

2010/12/18 Elaine Meng <meng at cgl.ucsf.edu>:
> Hi CJ,
> If you know what distance units are in your structure, you can simply apply the conversion factor to the values in the Color Key dialog. ?In other words, if your structure is in nanometer units, you can just manually type new values into the Color Key dialog that are 10x the values that were there initially. ?If the values from the structure are 10 and 50 (nanometers), you can just manually edit the values in the Color Key dialog to 100 and 500, then they will be in angstroms. ?If your structure is in grid units where the grid points are spaced 1.582 angstroms apart, then you would multiply by 1.582 instead. ?(etc.)
> 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 Dec 16, 2010, at 5:17 PM, C.J. wrote:
>
>> Dear Dr. Elaine,
>>
>> I am afraid that my structure is not in angstrom coordinates.
>> So, any way to change the color key?
>> Thanks all the same.
>>
>> 2010/12/17 Elaine Meng <meng at cgl.ucsf.edu>:
>>> Hi CJ,
>>> If your structure and/or map data is in angstrom cooordinates, and you are coloring by distance in Surface Color, and you start Color Key from the button in Surface Color, it is already automatically in angstrom units.
>>> Elaine
>>
>
>



-- 
Regards!
C.J.



From meng at cgl.ucsf.edu  Tue Dec 21 08:35:56 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 21 Dec 2010 08:35:56 -0800
Subject: [Chimera-users] [chimera-users]about "color key"
In-Reply-To: <AANLkTi=7-u6B9EOSfkBkHGmo0xu4eDzaryr09pXMOk0O@mail.gmail.com>
References: <AANLkTik3Ky=6G5kddF9DhMqED+DeCyoY9bEN+sjP6jZd@mail.gmail.com>
	<18A8BC5F-E576-4283-8690-B6CCD336DBAB@cgl.ucsf.edu>
	<AANLkTikHpfhKN5e4TSViyvqjzAw3k1XSVvzMBX2Y=CQU@mail.gmail.com>
	<E60B4EE8-CC4B-4AAF-AE7E-AC4C1E27460C@cgl.ucsf.edu>
	<AANLkTimDEv4cjCkExPtRZH5b_VmWkKUapPX1Lg8-Lr1+@mail.gmail.com>
	<85E02101-EF73-4495-A122-F95B70792F3C@cgl.ucsf.edu>
	<AANLkTi=7-u6B9EOSfkBkHGmo0xu4eDzaryr09pXMOk0O@mail.gmail.com>
Message-ID: <7FA5612D-E508-46BF-811D-FFBB4F75D1BF@cgl.ucsf.edu>

Hi CJ,
My previous reply (12/18 below) already explained how to change the units in the color key.  I can' t think of any other way to explain this, sorry.  If your structure is from the PDB, however, it is already in angstrom units.
Elaine

On Dec 20, 2010, at 7:44 PM, C.J. wrote:

> Thanks, but can I change the distance unit of color key in Chimera? Or
> I have to modify the pdb structure file to change that?
> 
> 2010/12/18 Elaine Meng <meng at cgl.ucsf.edu>:
>> Hi CJ,
>> If you know what distance units are in your structure, you can simply apply the conversion factor to the values in the Color Key dialog.  In other words, if your structure is in nanometer units, you can just manually type new values into the Color Key dialog that are 10x the values that were there initially.  If the values from the structure are 10 and 50 (nanometers), you can just manually edit the values in the Color Key dialog to 100 and 500, then they will be in angstroms.  If your structure is in grid units where the grid points are spaced 1.582 angstroms apart, then you would multiply by 1.582 instead.  (etc.)
>> 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 Dec 16, 2010, at 5:17 PM, C.J. wrote:
>> 
>>> Dear Dr. Elaine,
>>> 
>>> I am afraid that my structure is not in angstrom coordinates.
>>> So, any way to change the color key?
>>> Thanks all the same.
>>> 
>>> 2010/12/17 Elaine Meng <meng at cgl.ucsf.edu>:
>>>> Hi CJ,
>>>> If your structure and/or map data is in angstrom cooordinates, and you are coloring by distance in Surface Color, and you start Color Key from the button in Surface Color, it is already automatically in angstrom units.
>>>> Elaine
>>> 
>> 
>> 
> 
> 
> 
> -- 
> Regards!
> C.J.
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From richard.lavery at ibcp.fr  Tue Dec 21 06:42:17 2010
From: richard.lavery at ibcp.fr (Richard LAVERY)
Date: Tue, 21 Dec 2010 15:42:17 +0100
Subject: [Chimera-users] Curves+ graphics of DNA
Message-ID: <D8F62545-FFBF-44EC-B2CF-F312E73B3898@ibcp.fr>

I am trying to visualize the graphic output from the Curves+ of a DNA duplex, which consists of two smooth backbone traces linked by vectors indicating the measured widths of the minor and major grooves. In the test case shown, adding two atoms defining one such vector and a single CONECT line linking them together (see attached PDB file) leads to three new bond vectors in the representation shown below. Am I making a mistake, or is this a problem with Chimera?

Richard LAVERY
richard.lavery at ibcp.fr
http://web.mac.com/laveryr/Homepage

Institut de Biologie et Chimie des Prot?ines
7 passage du Vercors, Lyon 69367, France
Tel:  +33 (0)4 72 72 26 37, Cell 06 62 76 84 47

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From pett at cgl.ucsf.edu  Tue Dec 21 10:21:09 2010
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 21 Dec 2010 10:21:09 -0800
Subject: [Chimera-users] Curves+ graphics of DNA
In-Reply-To: <D8F62545-FFBF-44EC-B2CF-F312E73B3898@ibcp.fr>
References: <D8F62545-FFBF-44EC-B2CF-F312E73B3898@ibcp.fr>
Message-ID: <052C8010-045C-4419-A0D9-B7E936997651@cgl.ucsf.edu>

On Dec 21, 2010, at 6:42 AM, Richard LAVERY wrote:

> I am trying to visualize the graphic output from the Curves+ of a  
> DNA duplex, which consists of two smooth backbone traces linked by  
> vectors indicating the measured widths of the minor and major  
> grooves. In the test case shown, adding two atoms defining one such  
> vector and a single CONECT line linking them together (see attached  
> PDB file) leads to three new bond vectors in the representation  
> shown below. Am I making a mistake, or is this a problem with Chimera?

Hi Richard,
	The trick here is that Chimera will always connect consecutive  
residues contained in ATOM records unless there is an intervening TER  
record.  That's where the two extra bonds are coming from:  one  
between BACAD 1 and BACBD 2 and one between BACBD 2 and GRVAD 1.   
Ironically, the CONECT record you added was superfluous since Chimera  
would have automatically added a bond between GRVAD 1 and GRVAD 2!
	Your options to correct this are:

1) Add TER records between the residues
2) Use HETATM records instead of ATOM records.  Chimera won't  
automatically join consecutive HETATM residues.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab




From meng at cgl.ucsf.edu  Tue Dec 21 10:24:32 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 21 Dec 2010 10:24:32 -0800
Subject: [Chimera-users] Curves+ graphics of DNA
In-Reply-To: <D8F62545-FFBF-44EC-B2CF-F312E73B3898@ibcp.fr>
References: <D8F62545-FFBF-44EC-B2CF-F312E73B3898@ibcp.fr>
Message-ID: <3FD5501D-8D42-46CB-AB2A-1BA864EF6D2C@cgl.ucsf.edu>

Hi Richard, 
It is a format problem -- compared to "standard" PDB,  the discrepancies are that the residue names are too long, multiple atoms in the same residue have the same name, and the atom names (unless 4 characters) should start one column later.  However, these are not why you are getting connections...  there will be an attempt to connect atoms within the same residue (having the same residue number), as well as successive-in-the-file ATOM residues that are not separated by TER.  I believe you will get the expected result by either changing "ATOM  " to "HETATM" or by putting a TER between the residues (both alternatives attached).

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

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On Dec 21, 2010, at 6:42 AM, Richard LAVERY wrote:

> I am trying to visualize the graphic output from the Curves+ of a DNA duplex, which consists of two smooth backbone traces linked by vectors indicating the measured widths of the minor and major grooves. In the test case shown, adding two atoms defining one such vector and a single CONECT line linking them together (see attached PDB file) leads to three new bond vectors in the representation shown below. Am I making a mistake, or is this a problem with Chimera?
> 
> Richard LAVERY
> richard.lavery at ibcp.fr
> http://web.mac.com/laveryr/Homepage
> 
> Institut de Biologie et Chimie des Prot?ines
> 7 passage du Vercors, Lyon 69367, France
> Tel:  +33 (0)4 72 72 26 37, Cell 06 62 76 84 47


From meng at cgl.ucsf.edu  Tue Dec 21 10:41:22 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 21 Dec 2010 10:41:22 -0800
Subject: [Chimera-users] [chimera-dev] Coloring
In-Reply-To: <C933748B.90B4%hajpark@scripps.edu>
References: <C933748B.90B4%hajpark@scripps.edu>
Message-ID: <809B7EC2-1790-44E9-9698-CEB55183EE0F@cgl.ucsf.edu>

Hi Hajeung,
To color all carbons green the command would simply be

color green,a C

whereas "byatom" means to use the built-in element coloring scheme, not a specific color

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortables.html#byelement>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/color.html>

and @ means atom name, not element, so "@C" would only get the atoms named C (not CA,CB, etc.).

General user questions should probably go to chimera-users at cgl.ucsf.edu (chimera-dev is for development/programming questions).   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 Dec 19, 2010, at 5:36 AM, Hajeung Park wrote:

> Hello, I want to color ?C? to a certain color. The manual is not very clear bout it.
> My understanding is
> 
> Color green byatom ,a @C
> 
> But it give me error.
> 
> Thanks.




From biocjh at gmail.com  Wed Dec 22 02:17:52 2010
From: biocjh at gmail.com (C.J.)
Date: Wed, 22 Dec 2010 18:17:52 +0800
Subject: [Chimera-users] [chimera-users]about "color key"
In-Reply-To: <7FA5612D-E508-46BF-811D-FFBB4F75D1BF@cgl.ucsf.edu>
References: <AANLkTik3Ky=6G5kddF9DhMqED+DeCyoY9bEN+sjP6jZd@mail.gmail.com>
	<18A8BC5F-E576-4283-8690-B6CCD336DBAB@cgl.ucsf.edu>
	<AANLkTikHpfhKN5e4TSViyvqjzAw3k1XSVvzMBX2Y=CQU@mail.gmail.com>
	<E60B4EE8-CC4B-4AAF-AE7E-AC4C1E27460C@cgl.ucsf.edu>
	<AANLkTimDEv4cjCkExPtRZH5b_VmWkKUapPX1Lg8-Lr1+@mail.gmail.com>
	<85E02101-EF73-4495-A122-F95B70792F3C@cgl.ucsf.edu>
	<AANLkTi=7-u6B9EOSfkBkHGmo0xu4eDzaryr09pXMOk0O@mail.gmail.com>
	<7FA5612D-E508-46BF-811D-FFBB4F75D1BF@cgl.ucsf.edu>
Message-ID: <AANLkTikfz0RrYvwnNcp-O552d4NbcbLksSQPeuxDsAw4@mail.gmail.com>

Dear Elaine,

Thanks for explaining that for many times

Regards!
CJ

2010/12/22 Elaine Meng <meng at cgl.ucsf.edu>:
> Hi CJ,
> My previous reply (12/18 below) already explained how to change the units in the color key. ?I can' t think of any other way to explain this, sorry. ?If your structure is from the PDB, however, it is already in angstrom units.
> Elaine
>
> On Dec 20, 2010, at 7:44 PM, C.J. wrote:
>
>> Thanks, but can I change the distance unit of color key in Chimera? Or
>> I have to modify the pdb structure file to change that?
>>
>> 2010/12/18 Elaine Meng <meng at cgl.ucsf.edu>:
>>> Hi CJ,
>>> If you know what distance units are in your structure, you can simply apply the conversion factor to the values in the Color Key dialog. ?In other words, if your structure is in nanometer units, you can just manually type new values into the Color Key dialog that are 10x the values that were there initially. ?If the values from the structure are 10 and 50 (nanometers), you can just manually edit the values in the Color Key dialog to 100 and 500, then they will be in angstroms. ?If your structure is in grid units where the grid points are spaced 1.582 angstroms apart, then you would multiply by 1.582 instead. ?(etc.)
>>> 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 Dec 16, 2010, at 5:17 PM, C.J. wrote:
>>>
>>>> Dear Dr. Elaine,
>>>>
>>>> I am afraid that my structure is not in angstrom coordinates.
>>>> So, any way to change the color key?
>>>> Thanks all the same.
>>>>
>>>> 2010/12/17 Elaine Meng <meng at cgl.ucsf.edu>:
>>>>> Hi CJ,
>>>>> If your structure and/or map data is in angstrom cooordinates, and you are coloring by distance in Surface Color, and you start Color Key from the button in Surface Color, it is already automatically in angstrom units.
>>>>> Elaine
>>>>
>>>
>>>
>>
>>
>>
>> --
>> Regards!
>> C.J.
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>
>



-- 
Regards!
C.J.



From meng at cgl.ucsf.edu  Wed Dec 22 08:52:46 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 22 Dec 2010 08:52:46 -0800
Subject: [Chimera-users] [chimera-users]about "color key"
In-Reply-To: <AANLkTikfz0RrYvwnNcp-O552d4NbcbLksSQPeuxDsAw4@mail.gmail.com>
References: <AANLkTik3Ky=6G5kddF9DhMqED+DeCyoY9bEN+sjP6jZd@mail.gmail.com>
	<18A8BC5F-E576-4283-8690-B6CCD336DBAB@cgl.ucsf.edu>
	<AANLkTikHpfhKN5e4TSViyvqjzAw3k1XSVvzMBX2Y=CQU@mail.gmail.com>
	<E60B4EE8-CC4B-4AAF-AE7E-AC4C1E27460C@cgl.ucsf.edu>
	<AANLkTimDEv4cjCkExPtRZH5b_VmWkKUapPX1Lg8-Lr1+@mail.gmail.com>
	<85E02101-EF73-4495-A122-F95B70792F3C@cgl.ucsf.edu>
	<AANLkTi=7-u6B9EOSfkBkHGmo0xu4eDzaryr09pXMOk0O@mail.gmail.com>
	<7FA5612D-E508-46BF-811D-FFBB4F75D1BF@cgl.ucsf.edu>
	<AANLkTikfz0RrYvwnNcp-O552d4NbcbLksSQPeuxDsAw4@mail.gmail.com>
Message-ID: <4B49A35B-0B74-45A4-806D-9E72D7F3E5E2@cgl.ucsf.edu>

Hi CJ,
One more idea:  maybe you want Scale Bar (under "Tools... Higher-Order Structure" in the menu) instead of Color Key.

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/scalebar/scalebar.html>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html#colorkey>

Scale Bar is just a stick with measured length, without any relationship to color.

Color Key shows what colors are used for what values, which could be distances or some other thing like B-factors.  If you start it from some other tool (Surface Color, Render by Attribute) the values will be the same thing that is shown in that other tool.
Best,
Elaine

On Dec 22, 2010, at 2:17 AM, C.J. wrote:

> Dear Elaine,
> 
> Thanks for explaining that for many times
> 
> Regards!
> CJ
> 
> 2010/12/22 Elaine Meng <meng at cgl.ucsf.edu>:
>> Hi CJ,
>> My previous reply (12/18 below) already explained how to change the units in the color key.  I can' t think of any other way to explain this, sorry.  If your structure is from the PDB, however, it is already in angstrom units.
>> Elaine
>> 
>> On Dec 20, 2010, at 7:44 PM, C.J. wrote:
>> 
>>> Thanks, but can I change the distance unit of color key in Chimera? Or
>>> I have to modify the pdb structure file to change that?
>>> 
>>> 2010/12/18 Elaine Meng <meng at cgl.ucsf.edu>:
>>>> Hi CJ,
>>>> If you know what distance units are in your structure, you can simply apply the conversion factor to the values in the Color Key dialog.  In other words, if your structure is in nanometer units, you can just manually type new values into the Color Key dialog that are 10x the values that were there initially.  If the values from the structure are 10 and 50 (nanometers), you can just manually edit the values in the Color Key dialog to 100 and 500, then they will be in angstroms.  If your structure is in grid units where the grid points are spaced 1.582 angstroms apart, then you would multiply by 1.582 instead.  (etc.)
>>>> 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 Dec 16, 2010, at 5:17 PM, C.J. wrote:
>>>> 
>>>>> Dear Dr. Elaine,
>>>>> 
>>>>> I am afraid that my structure is not in angstrom coordinates.
>>>>> So, any way to change the color key?
>>>>> Thanks all the same.
>>>>> 
>>>>> 2010/12/17 Elaine Meng <meng at cgl.ucsf.edu>:
>>>>>> Hi CJ,
>>>>>> If your structure and/or map data is in angstrom cooordinates, and you are coloring by distance in Surface Color, and you start Color Key from the button in Surface Color, it is already automatically in angstrom units.
>>>>>> Elaine
>>>>> 




From hajpark at scripps.edu  Tue Dec 21 14:46:01 2010
From: hajpark at scripps.edu (Hajeung Park)
Date: Tue, 21 Dec 2010 17:46:01 -0500
Subject: [Chimera-users] [chimera-dev] Coloring
In-Reply-To: <809B7EC2-1790-44E9-9698-CEB55183EE0F@cgl.ucsf.edu>
Message-ID: <C9369859.520B%hajpark@scripps.edu>

THANKS. THAT WORKED WELL. HaJeung


On 12/21/10 1:41 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

Hi Hajeung,
To color all carbons green the command would simply be

color green,a C

whereas "byatom" means to use the built-in element coloring scheme, not a specific color

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortables.html#byelement>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/color.html>

and @ means atom name, not element, so "@C" would only get the atoms named C (not CA,CB, etc.).

General user questions should probably go to chimera-users at cgl.ucsf.edu (chimera-dev is for development/programming questions).   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 Dec 19, 2010, at 5:36 AM, Hajeung Park wrote:

> Hello, I want to color "C" to a certain color. The manual is not very clear bout it.
> My understanding is
>
> Color green byatom ,a @C
>
> But it give me error.
>
> Thanks.


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From g.tzotzos at unido.org  Wed Dec 22 09:41:00 2010
From: g.tzotzos at unido.org (George Tzotzos)
Date: Wed, 22 Dec 2010 18:41:00 +0100
Subject: [Chimera-users] File conversion: strange behaviour
Message-ID: <39A40299-80E0-4296-AB8A-82C0FF1B54F7@unido.org>

Hi everybody,

I'm attaching a  pdb file <3og.pdb>. This file on conversion from amber11 (ANTECHAMBER) yields 3og.mol2 which Chimera renders as per snapshot below. The two big blue spheres should be oxygen atoms. Selecting the molecule and trying to colour by atom has no effect other than colouring the atoms that are adjacent to the blue spheres.

Any explanation for this behaviour?

Many thanks and best regards

George
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From meng at cgl.ucsf.edu  Wed Dec 22 10:16:24 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 22 Dec 2010 10:16:24 -0800
Subject: [Chimera-users] File conversion: strange behaviour
In-Reply-To: <39A40299-80E0-4296-AB8A-82C0FF1B54F7@unido.org>
References: <39A40299-80E0-4296-AB8A-82C0FF1B54F7@unido.org>
Message-ID: <93FF8C0D-59B5-4597-BA59-6E65CA3007B3@cgl.ucsf.edu>

Hi George,
If you want Chimera to understand the atom types when you read the Mol2 file back in, when saving the Mol2 do *not* use the option to "Write Amber/GAFF atom types instead of Sybyl atom types".  If you use the default settings in the "save Mol2" dialog, it will write a standard Mol2 file with Sybyl atom types, and you can read the file back in without problems.  The Amber/GAFF type option is for people who wanted to know the force field type assignments, but is not suitable for reading back into Chimera.

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#mol2>

I hope this clarifies what is going on,
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 Dec 22, 2010, at 9:41 AM, George Tzotzos wrote:

> Hi everybody,
> 
> I'm attaching a  pdb file <3og.pdb>. This file on conversion from amber11 (ANTECHAMBER) yields 3og.mol2 which Chimera renders as per snapshot below. The two big blue spheres should be oxygen atoms. Selecting the molecule and trying to colour by atom has no effect other than colouring the atoms that are adjacent to the blue spheres.
> 
> Any explanation for this behaviour?
> 
> Many thanks and best regards
> 
> George




From pett at cgl.ucsf.edu  Wed Dec 22 10:20:32 2010
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 22 Dec 2010 10:20:32 -0800
Subject: [Chimera-users] File conversion: strange behaviour
In-Reply-To: <93FF8C0D-59B5-4597-BA59-6E65CA3007B3@cgl.ucsf.edu>
References: <39A40299-80E0-4296-AB8A-82C0FF1B54F7@unido.org>
	<93FF8C0D-59B5-4597-BA59-6E65CA3007B3@cgl.ucsf.edu>
Message-ID: <79F66D03-E32A-4E46-A620-77EE7488CEC3@cgl.ucsf.edu>

...and if you are getting the Mol2 file from Amber, try to get a PDB  
file instead.

--Eric

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

On Dec 22, 2010, at 10:16 AM, Elaine Meng wrote:

> Hi George,
> If you want Chimera to understand the atom types when you read the  
> Mol2 file back in, when saving the Mol2 do *not* use the option to  
> "Write Amber/GAFF atom types instead of Sybyl atom types".  If you  
> use the default settings in the "save Mol2" dialog, it will write a  
> standard Mol2 file with Sybyl atom types, and you can read the file  
> back in without problems.  The Amber/GAFF type option is for people  
> who wanted to know the force field type assignments, but is not  
> suitable for reading back into Chimera.
>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#mol2>
>
> I hope this clarifies what is going on,
> 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 Dec 22, 2010, at 9:41 AM, George Tzotzos wrote:
>
>> Hi everybody,
>>
>> I'm attaching a  pdb file <3og.pdb>. This file on conversion from  
>> amber11 (ANTECHAMBER) yields 3og.mol2 which Chimera renders as per  
>> snapshot below. The two big blue spheres should be oxygen atoms.  
>> Selecting the molecule and trying to colour by atom has no effect  
>> other than colouring the atoms that are adjacent to the blue spheres.
>>
>> Any explanation for this behaviour?
>>
>> Many thanks and best regards
>>
>> George
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



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From gtzotzos at me.com  Wed Dec 22 09:47:45 2010
From: gtzotzos at me.com (George Tzotzos)
Date: Wed, 22 Dec 2010 18:47:45 +0100
Subject: [Chimera-users] File conversion: strange behaviour
Message-ID: <12CF6B25-22A4-42F1-A853-DBF405483685@me.com>

Hi everybody,

I'm attaching a  pdb file <3og.pdb>. This file on conversion from amber11 (ANTECHAMBER) yields 3og.mol2 which Chimera renders as per snapshot below. The two big blue spheres should be oxygen atoms. Selecting the molecule and trying to colour by atom has no effect other than colouring the atoms that are adjacent to the blue spheres.

Any explanation for this behaviour?

Many thanks and best regards

George
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From raj_sss at yahoo.com  Wed Dec 22 12:54:02 2010
From: raj_sss at yahoo.com (S. Shunmugasundararaj)
Date: Wed, 22 Dec 2010 12:54:02 -0800 (PST)
Subject: [Chimera-users] CASTp .poc
Message-ID: <118125.98012.qm@web33805.mail.mud.yahoo.com>

Hi Everybody,

I? loaded the CASTp *.poc file in Chimera and saved as a *.py file.? When I open the .py file later, I do not see the .poc details. Is it hidden somewhere or how do I get that details? I do not see the "instance" item in the Tools menu.

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html page does not seem to have the details about that.

Thanks
Raj



      
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From meng at cgl.ucsf.edu  Wed Dec 22 13:02:20 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 22 Dec 2010 13:02:20 -0800
Subject: [Chimera-users] CASTp .poc
In-Reply-To: <118125.98012.qm@web33805.mail.mud.yahoo.com>
References: <118125.98012.qm@web33805.mail.mud.yahoo.com>
Message-ID: <55C5D1CB-23DE-448D-A672-B137E5282D42@cgl.ucsf.edu>

Hi Raj,
Sorry, currently the CASTp dialog and info are not saved in sessions.
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 Dec 22, 2010, at 12:54 PM, S. Shunmugasundararaj wrote:

> Hi Everybody,
> I  loaded the CASTp *.poc file in Chimera and saved as a *.py file.  When I open the .py file later, I do not see the .poc details. Is it hidden somewhere or how do I get that details? I do not see the "instance" item in the Tools menu.
> 
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html page does not seem to have the details about that.
> Thanks
> Raj




From biocjh at gmail.com  Wed Dec 22 23:26:03 2010
From: biocjh at gmail.com (C.J.)
Date: Thu, 23 Dec 2010 15:26:03 +0800
Subject: [Chimera-users] [chimera-users]about "color key"
In-Reply-To: <4B49A35B-0B74-45A4-806D-9E72D7F3E5E2@cgl.ucsf.edu>
References: <AANLkTik3Ky=6G5kddF9DhMqED+DeCyoY9bEN+sjP6jZd@mail.gmail.com>
	<18A8BC5F-E576-4283-8690-B6CCD336DBAB@cgl.ucsf.edu>
	<AANLkTikHpfhKN5e4TSViyvqjzAw3k1XSVvzMBX2Y=CQU@mail.gmail.com>
	<E60B4EE8-CC4B-4AAF-AE7E-AC4C1E27460C@cgl.ucsf.edu>
	<AANLkTimDEv4cjCkExPtRZH5b_VmWkKUapPX1Lg8-Lr1+@mail.gmail.com>
	<85E02101-EF73-4495-A122-F95B70792F3C@cgl.ucsf.edu>
	<AANLkTi=7-u6B9EOSfkBkHGmo0xu4eDzaryr09pXMOk0O@mail.gmail.com>
	<7FA5612D-E508-46BF-811D-FFBB4F75D1BF@cgl.ucsf.edu>
	<AANLkTikfz0RrYvwnNcp-O552d4NbcbLksSQPeuxDsAw4@mail.gmail.com>
	<4B49A35B-0B74-45A4-806D-9E72D7F3E5E2@cgl.ucsf.edu>
Message-ID: <AANLkTimA22uFNE7PiRSnO23FD6yZNpsO09F8h=xffm_7@mail.gmail.com>

Dear Elaine,

Thank you against!

Regards!
CJ

2010/12/23 Elaine Meng <meng at cgl.ucsf.edu>:
> Hi CJ,
> One more idea: ?maybe you want Scale Bar (under "Tools... Higher-Order Structure" in the menu) instead of Color Key.
>
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/scalebar/scalebar.html>
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html#colorkey>
>
> Scale Bar is just a stick with measured length, without any relationship to color.
>
> Color Key shows what colors are used for what values, which could be distances or some other thing like B-factors. ?If you start it from some other tool (Surface Color, Render by Attribute) the values will be the same thing that is shown in that other tool.
> Best,
> Elaine
>
> On Dec 22, 2010, at 2:17 AM, C.J. wrote:
>
>> Dear Elaine,
>>
>> Thanks for explaining that for many times
>>
>> Regards!
>> CJ
>>
>> 2010/12/22 Elaine Meng <meng at cgl.ucsf.edu>:
>>> Hi CJ,
>>> My previous reply (12/18 below) already explained how to change the units in the color key. ?I can' t think of any other way to explain this, sorry. ?If your structure is from the PDB, however, it is already in angstrom units.
>>> Elaine
>>>
>>> On Dec 20, 2010, at 7:44 PM, C.J. wrote:
>>>
>>>> Thanks, but can I change the distance unit of color key in Chimera? Or
>>>> I have to modify the pdb structure file to change that?
>>>>
>>>> 2010/12/18 Elaine Meng <meng at cgl.ucsf.edu>:
>>>>> Hi CJ,
>>>>> If you know what distance units are in your structure, you can simply apply the conversion factor to the values in the Color Key dialog. ?In other words, if your structure is in nanometer units, you can just manually type new values into the Color Key dialog that are 10x the values that were there initially. ?If the values from the structure are 10 and 50 (nanometers), you can just manually edit the values in the Color Key dialog to 100 and 500, then they will be in angstroms. ?If your structure is in grid units where the grid points are spaced 1.582 angstroms apart, then you would multiply by 1.582 instead. ?(etc.)
>>>>> 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 Dec 16, 2010, at 5:17 PM, C.J. wrote:
>>>>>
>>>>>> Dear Dr. Elaine,
>>>>>>
>>>>>> I am afraid that my structure is not in angstrom coordinates.
>>>>>> So, any way to change the color key?
>>>>>> Thanks all the same.
>>>>>>
>>>>>> 2010/12/17 Elaine Meng <meng at cgl.ucsf.edu>:
>>>>>>> Hi CJ,
>>>>>>> If your structure and/or map data is in angstrom cooordinates, and you are coloring by distance in Surface Color, and you start Color Key from the button in Surface Color, it is already automatically in angstrom units.
>>>>>>> Elaine
>>>>>>
>
>



-- 
Regards!
C.J.



From sharjanto at i2r.a-star.edu.sg  Thu Dec 23 00:00:06 2010
From: sharjanto at i2r.a-star.edu.sg (Sumitro Harjanto)
Date: Thu, 23 Dec 2010 16:00:06 +0800
Subject: [Chimera-users] average structure of superimposed models
Message-ID: <162B8AFBFBBB2148A9A1B8F9C57534280BE759D6@mailbe01.teak.local.net>

Hi Elaine,

 

I have superimposed a few highly similar models of the same protein
family. They are >80% identical in sequences. I would like to find an
'average' structure as a  representative model of these proteins. Can I
achieve this through Chimera..?

 

Cheers,

Sum

Institute for Infocomm Research disclaimer:  "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."
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From meng at cgl.ucsf.edu  Thu Dec 23 09:58:40 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 23 Dec 2010 09:58:40 -0800
Subject: [Chimera-users] average structure of superimposed models
In-Reply-To: <162B8AFBFBBB2148A9A1B8F9C57534280BE759D6@mailbe01.teak.local.net>
References: <162B8AFBFBBB2148A9A1B8F9C57534280BE759D6@mailbe01.teak.local.net>
Message-ID: <7BCC85E1-FF91-4DFE-803A-67B897EDBA01@cgl.ucsf.edu>

Hi Sum,
Sorry, Chimera does not calculate average structures.   

According to the publication describing the Superpose web server, it can generate an average backbone, but only if all the structures have the same atoms (e.g. different conformations of the same protein).

Superpose server:
<http://wishart.biology.ualberta.ca/SuperPose/>
Publication describing it:
<http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441615/>

A long time ago I used a program named MPOSE to make a consensus CA "template" from a set of related structures, but I don't have that program anymore and don't know if it is available.  It is described in this paper:

T.D. Wu, S.C. Schmidler, T. Hastie, and D.L. Brutlag, "Modeling and Superposition of Multiple Protein Structures Using Affine Transformations: Analysis of the Globins" Pac Symp Biocomput 3:509 (1998).
<http://psb.stanford.edu/psb-online/proceedings/psb98/abstracts/p509.html>

One should be aware that an average or consensus structure can be very distorted and energetically unreasonable, depending on how it was computed.  There are many issues such as whether to average coordinates for each atom or  internal coordinates such as angles.

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 Dec 23, 2010, at 12:00 AM, Sumitro Harjanto wrote:

> Hi Elaine,
> I have superimposed a few highly similar models of the same protein family. They are >80% identical in sequences. I would like to find an ?average? structure as a  representative model of these proteins. Can I achieve this through Chimera..?
> Cheers,
> Sum




From sette at uniroma2.it  Thu Dec 23 13:57:48 2010
From: sette at uniroma2.it (sette at uniroma2.it)
Date: Thu, 23 Dec 2010 22:57:48 +0100
Subject: [Chimera-users] average structure of superimposed models
In-Reply-To: <7BCC85E1-FF91-4DFE-803A-67B897EDBA01@cgl.ucsf.edu>
References: <162B8AFBFBBB2148A9A1B8F9C57534280BE759D6@mailbe01.teak.local.net>
	<7BCC85E1-FF91-4DFE-803A-67B897EDBA01@cgl.ucsf.edu>
Message-ID: <20101223225748.14986l7hwtrc97fg@webmail.uniroma2.it>


And if your models have the same sequence you should try to use suppose

http://structbio.vanderbilt.edu/~jsmith/suppose/

bye
Marco



Def. Quota "Elaine Meng" <meng at cgl.ucsf.edu>:

> Hi Sum,
> Sorry, Chimera does not calculate average structures.
>
> According to the publication describing the Superpose web server, it  
> can generate an average backbone, but only if all the structures  
> have the same atoms (e.g. different conformations of the same  
> protein).
>
> Superpose server:
> <http://wishart.biology.ualberta.ca/SuperPose/>
> Publication describing it:
> <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441615/>
>
> A long time ago I used a program named MPOSE to make a consensus CA  
> "template" from a set of related structures, but I don't have that  
> program anymore and don't know if it is available.  It is described  
> in this paper:
>
> T.D. Wu, S.C. Schmidler, T. Hastie, and D.L. Brutlag, "Modeling and  
> Superposition of Multiple Protein Structures Using Affine  
> Transformations: Analysis of the Globins" Pac Symp Biocomput 3:509  
> (1998).
> <http://psb.stanford.edu/psb-online/proceedings/psb98/abstracts/p509.html>
>
> One should be aware that an average or consensus structure can be  
> very distorted and energetically unreasonable, depending on how it  
> was computed.  There are many issues such as whether to average  
> coordinates for each atom or  internal coordinates such as angles.
>
> 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 Dec 23, 2010, at 12:00 AM, Sumitro Harjanto wrote:
>
>> Hi Elaine,
>> I have superimposed a few highly similar models of the same protein  
>> family. They are >80% identical in sequences. I would like to find  
>> an ?average? structure as a  representative model of these  
>> proteins. Can I achieve this through Chimera..?
>> Cheers,
>> Sum
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>



Dr.Marco Sette, Ph.D.

Department of Chemical Sciences and Technology
University of Rome, "Tor Vergata"
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail:        sette at uniroma2.it
e-mail:        m77it at yahoo.it
Tel.:          +39-0672594424
Fax:           +39-0672594328


----------------------------------------------------------------
Invito da parte dell'Ateneo:
Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del
tuo aiuto. Dona il  5 x mille all'Universita' di Roma Tor Vergata
codice fiscale: 80213750583 http://5x1000.uniroma2.it




From sergio.alberto.garay at gmail.com  Mon Dec 27 02:05:44 2010
From: sergio.alberto.garay at gmail.com (Sergio Garay)
Date: Mon, 27 Dec 2010 03:05:44 -0700
Subject: [Chimera-users] =?utf-8?q?Quiero_ser_tu_amigo_en_Quepasa=2Ecom?=
Message-ID: <20101227100732.23544.344946221.swift@CHA-ME-003>

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From montfort at email.arizona.edu  Wed Dec 29 15:55:23 2010
From: montfort at email.arizona.edu (Bill Montfort)
Date: Wed, 29 Dec 2010 16:55:23 -0700
Subject: [Chimera-users] center of rotation
Message-ID: <5A8A8BCA-6EE5-43CF-8E45-4D5943C4A477@email.arizona.edu>

I'm returning to chimera after many years away and am quite impressed with the program, save for one issue: rotating about the screen center. My favorite way of viewing structures is for the rotation to be about a center of my choosing, as is common in many graphics programs (e.g. COOT). I would prefer to pick an atom on the screen and have this become the rotation center.  Is there a simple way to accomplish this in chimera? A small point perhaps, but one that is frustrating for me.......

Bill Montfort




From meng at cgl.ucsf.edu  Thu Dec 30 09:51:53 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 30 Dec 2010 09:51:53 -0800
Subject: [Chimera-users] center of rotation
In-Reply-To: <5A8A8BCA-6EE5-43CF-8E45-4D5943C4A477@email.arizona.edu>
References: <5A8A8BCA-6EE5-43CF-8E45-4D5943C4A477@email.arizona.edu>
Message-ID: <EDB3BDD8-AFA3-4440-BDBD-CAC89B8713CC@cgl.ucsf.edu>

Hi Bill,
You can use the command "cofr" with specified atoms (including "sel" as the specification if the atom or atoms are selected).
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/cofr.html>

There are several different rotation modes, and you can switch among them using either "cofr" or the Rotation tool (under Tools... Movement in the menu).
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sideview.html#rotation>

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 Dec 29, 2010, at 3:55 PM, Bill Montfort wrote:

> I'm returning to chimera after many years away and am quite impressed with the program, save for one issue: rotating about the screen center. My favorite way of viewing structures is for the rotation to be about a center of my choosing, as is common in many graphics programs (e.g. COOT). I would prefer to pick an atom on the screen and have this become the rotation center.  Is there a simple way to accomplish this in chimera? A small point perhaps, but one that is frustrating for me.......
> 
> Bill Montfort




From pett at cgl.ucsf.edu  Thu Dec 30 10:18:57 2010
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 30 Dec 2010 10:18:57 -0800
Subject: [Chimera-users] center of rotation
In-Reply-To: <EDB3BDD8-AFA3-4440-BDBD-CAC89B8713CC@cgl.ucsf.edu>
References: <5A8A8BCA-6EE5-43CF-8E45-4D5943C4A477@email.arizona.edu>
	<EDB3BDD8-AFA3-4440-BDBD-CAC89B8713CC@cgl.ucsf.edu>
Message-ID: <0223E384-AE27-4584-BB7C-F69AA4F7EFBA@cgl.ucsf.edu>

Alternatively, you can control-click on the atom to select it and then  
choose Actions->Set Pivot in the menus to make it the center of  
rotation.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

On Dec 30, 2010, at 9:51 AM, Elaine Meng wrote:

> Hi Bill,
> You can use the command "cofr" with specified atoms (including "sel"  
> as the specification if the atom or atoms are selected).
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/cofr.html>
>
> There are several different rotation modes, and you can switch among  
> them using either "cofr" or the Rotation tool (under Tools...  
> Movement in the menu).
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sideview.html#rotation 
> >
>
> 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 Dec 29, 2010, at 3:55 PM, Bill Montfort wrote:
>
>> I'm returning to chimera after many years away and am quite  
>> impressed with the program, save for one issue: rotating about the  
>> screen center. My favorite way of viewing structures is for the  
>> rotation to be about a center of my choosing, as is common in many  
>> graphics programs (e.g. COOT). I would prefer to pick an atom on  
>> the screen and have this become the rotation center.  Is there a  
>> simple way to accomplish this in chimera? A small point perhaps,  
>> but one that is frustrating for me.......
>>
>> Bill Montfort
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



From meng at cgl.ucsf.edu  Thu Dec 30 15:17:44 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 30 Dec 2010 15:17:44 -0800
Subject: [Chimera-users] center of rotation
In-Reply-To: <49AB8B71-BEE4-43ED-86F0-9B6BBFF4AEE6@email.arizona.edu>
References: <5A8A8BCA-6EE5-43CF-8E45-4D5943C4A477@email.arizona.edu>
	<EDB3BDD8-AFA3-4440-BDBD-CAC89B8713CC@cgl.ucsf.edu>
	<0223E384-AE27-4584-BB7C-F69AA4F7EFBA@cgl.ucsf.edu>
	<49AB8B71-BEE4-43ED-86F0-9B6BBFF4AEE6@email.arizona.edu>
Message-ID: <6F74FFAE-EE9F-49AD-95BE-ABA4F0D865F2@cgl.ucsf.edu>

Hi Bill,
If command "cofr sel" is too long, you could

(a) use the command "alias" to alias it to a shorter command, e.g.

alias ^blah cofr sel

which would then allow you to use the command "blah" 

or if you don't use the Command Line, (b) define your own keyboard shortcut
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/accelerators.html>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/accelerators.html#adding>

However, the latter requires some Python, on which I cannot advise.
Elaine


On Dec 30, 2010, at 11:02 AM, Bill Montfort wrote:

> Thanks! This works well. If there were a quicker means for activating Set Pivot, this would be even better (e.g. keyboard or mouse combination). Cheers!
> 
> On Dec 30, 2010, at 11:18 AM, Eric Pettersen wrote:
> 
>> Alternatively, you can control-click on the atom to select it and then  
>> choose Actions->Set Pivot in the menus to make it the center of  
>> rotation.
>> 
>> On Dec 30, 2010, at 9:51 AM, Elaine Meng wrote:
>> 
>>> Hi Bill,
>>> You can use the command "cofr" with specified atoms (including "sel"  
>>> as the specification if the atom or atoms are selected).
>>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/cofr.html>
>>> 
>>> There are several different rotation modes, and you can switch among  
>>> them using either "cofr" or the Rotation tool (under Tools...  
>>> Movement in the menu).
>>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sideview.html#rotation 
>>>> 
>>> On Dec 29, 2010, at 3:55 PM, Bill Montfort wrote:
>>> 
>>>> I'm returning to chimera after many years away and am quite  
>>>> impressed with the program, save for one issue: rotating about the  
>>>> screen center. My favorite way of viewing structures is for the  
>>>> rotation to be about a center of my choosing, as is common in many  
>>>> graphics programs (e.g. COOT). I would prefer to pick an atom on  
>>>> the screen and have this become the rotation center.  Is there a  
>>>> simple way to accomplish this in chimera? A small point perhaps,  
>>>> but one that is frustrating for me.......
>>>> 
>>>> Bill Montfort




From meng at cgl.ucsf.edu  Thu Dec 30 16:05:14 2010
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 30 Dec 2010 16:05:14 -0800
Subject: [Chimera-users] center of rotation
In-Reply-To: <6F74FFAE-EE9F-49AD-95BE-ABA4F0D865F2@cgl.ucsf.edu>
References: <5A8A8BCA-6EE5-43CF-8E45-4D5943C4A477@email.arizona.edu>
	<EDB3BDD8-AFA3-4440-BDBD-CAC89B8713CC@cgl.ucsf.edu>
	<0223E384-AE27-4584-BB7C-F69AA4F7EFBA@cgl.ucsf.edu>
	<49AB8B71-BEE4-43ED-86F0-9B6BBFF4AEE6@email.arizona.edu>
	<6F74FFAE-EE9F-49AD-95BE-ABA4F0D865F2@cgl.ucsf.edu>
Message-ID: <F4846FDF-48D3-4AD9-B722-C8E5CB676DD4@cgl.ucsf.edu>

Silly me, there is already a keyboard shortcut "cr" to set center of rotation at the selected atom(s):
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/alist.html#move.

Elaine

On Dec 30, 2010, at 3:17 PM, Elaine Meng wrote:

> Hi Bill,
> If command "cofr sel" is too long, you could
> 
> (a) use the command "alias" to alias it to a shorter command, e.g.
> 
> alias ^blah cofr sel
> 
> which would then allow you to use the command "blah" 
> 
> or if you don't use the Command Line, (b) define your own keyboard shortcut
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/accelerators.html>
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/accelerators.html#adding>
> 
> However, the latter requires some Python, on which I cannot advise.
> Elaine
> 
> 
> On Dec 30, 2010, at 11:02 AM, Bill Montfort wrote:
> 
>> Thanks! This works well. If there were a quicker means for activating Set Pivot, this would be even better (e.g. keyboard or mouse combination). Cheers!
>> 
>> On Dec 30, 2010, at 11:18 AM, Eric Pettersen wrote:
>> 
>>> Alternatively, you can control-click on the atom to select it and then  
>>> choose Actions->Set Pivot in the menus to make it the center of  
>>> rotation.
>>> 
>>> On Dec 30, 2010, at 9:51 AM, Elaine Meng wrote:
>>> 
>>>> Hi Bill,
>>>> You can use the command "cofr" with specified atoms (including "sel"  
>>>> as the specification if the atom or atoms are selected).
>>>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/cofr.html>
>>>> 
>>>> There are several different rotation modes, and you can switch among  
>>>> them using either "cofr" or the Rotation tool (under Tools...  
>>>> Movement in the menu).
>>>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sideview.html#rotation 
>>>>> 
>>>> On Dec 29, 2010, at 3:55 PM, Bill Montfort wrote:
>>>> 
>>>>> I'm returning to chimera after many years away and am quite  
>>>>> impressed with the program, save for one issue: rotating about the  
>>>>> screen center. My favorite way of viewing structures is for the  
>>>>> rotation to be about a center of my choosing, as is common in many  
>>>>> graphics programs (e.g. COOT). I would prefer to pick an atom on  
>>>>> the screen and have this become the rotation center.  Is there a  
>>>>> simple way to accomplish this in chimera? A small point perhaps,  
>>>>> but one that is frustrating for me.......
>>>>> 
>>>>> Bill Montfort
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From montfort at email.arizona.edu  Thu Dec 30 10:59:50 2010
From: montfort at email.arizona.edu (Bill Montfort)
Date: Thu, 30 Dec 2010 11:59:50 -0700
Subject: [Chimera-users] center of rotation
In-Reply-To: <EDB3BDD8-AFA3-4440-BDBD-CAC89B8713CC@cgl.ucsf.edu>
References: <5A8A8BCA-6EE5-43CF-8E45-4D5943C4A477@email.arizona.edu>
	<EDB3BDD8-AFA3-4440-BDBD-CAC89B8713CC@cgl.ucsf.edu>
Message-ID: <A912ABBD-A41D-4E8B-9C8C-A081FBE3F15B@email.arizona.edu>

thanks - set pivot works (see other messages).....Cheers!
__________________________
William R. Montfort
Professor, Chemistry and Biochemistry
BSW 533, 1041 E. Lowell St.
University of Arizona
Tucson, AZ 85721-0088
phone: 520 621-1884 fax: 520-626-9204
montfort at email.arizona.edu











On Dec 30, 2010, at 10:51 AM, Elaine Meng wrote:

> Hi Bill,
> You can use the command "cofr" with specified atoms (including "sel" as the specification if the atom or atoms are selected).
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/cofr.html>
> 
> There are several different rotation modes, and you can switch among them using either "cofr" or the Rotation tool (under Tools... Movement in the menu).
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sideview.html#rotation>
> 
> 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 Dec 29, 2010, at 3:55 PM, Bill Montfort wrote:
> 
>> I'm returning to chimera after many years away and am quite impressed with the program, save for one issue: rotating about the screen center. My favorite way of viewing structures is for the rotation to be about a center of my choosing, as is common in many graphics programs (e.g. COOT). I would prefer to pick an atom on the screen and have this become the rotation center.  Is there a simple way to accomplish this in chimera? A small point perhaps, but one that is frustrating for me.......
>> 
>> Bill Montfort
> 
> 




From skent at uchicago.edu  Thu Dec 30 14:15:18 2010
From: skent at uchicago.edu (Stephen B.H. Kent)
Date: Thu, 30 Dec 2010 16:15:18 -0600 (CST)
Subject: [Chimera-users] Mirror image proteins
Message-ID: <20101230161518.AGL17173@mstore02.uchicago.edu>

How can I invert the configuration of a pdb file to create the mirror image model 
of the protein molecule?

Thanks,

Steve Kent

Stephen Kent
Professor of Chemistry
Professor of Biochemistry & Molecular Biology
Institute for Biophysical Dynamics

Mail: 
Gordon Center for Integrative Science, Room W204
University of Chicago
929 East 57th Street
Chicago, IL 60637, USA
Tel: +1 773 702 4912
Email: skent at uchicago.edu


From sureshbioe at gmail.com  Fri Dec 31 04:40:29 2010
From: sureshbioe at gmail.com (SURESH KUMAR)
Date: Fri, 31 Dec 2010 18:10:29 +0530
Subject: [Chimera-users] query
Message-ID: <AANLkTimyzQf7xz2ERZSoWEgbMYS-MTSgO2B9g2+qr0VU@mail.gmail.com>

hello sir,

              I need to find electron density of protein, i am planning to
use UCSF Chimera software for that... so please help me how to find protein
electron density using UCSF Chimera


                     thank you


A.Suresh Kumar,
M.Tech Biomedical Engineering,
Amrita School of Engineering,
Ettimadai,
Coimbatore.
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