December 2013 - Chimera-users - RBVI Mailing Lists

Failure of energy miminization
by Ross KK Leung 30 Dec '13

30 Dec '13

In August there was a discussion entitled "Minimization and mystery nonstandard HIS atom name" and that's the exact problem supposed to have been solved last year. What I did is similar to Jason (http://www.cgl.ucsf.edu/pipermail/chimera-users/2013-August/009069.html) and unfortunately I'm unable to resolve the problem, giving that I'm using chimera 1.8.1 on a Win 7 32G RAM computer. I attach two files, one succeeded till completion while the other one failed early. What I did is simply "Structure editing", next, ok, next, .. Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log No MMTK name for atom "HC1" in standard residue "ALA" Any suggestions to fix the problem is highly appreciated because Chimera is so impressive and I've been using it for many good analyses already. A pity to give up and switch to other programs at this very last stage.

1 0

Sir, i donot want to recieve antomately letter from chimera, can you remove my email adress from your email list..
by 一波 28 Dec '13

28 Dec '13

2 1

How to get central cross section which pass through two asigned cross axis
by Jian Guan 27 Dec '13

27 Dec '13

Dear all, I have a density map of virus-Fab complex. I want to make a central cross section which pass through the Fab pseudo-symmetry 2-fold axis. I have measure the angle of Fab relative to the capsid. Hope someone can help me. Thank you so much. Sincerely yours, Jian -----Original Message----- From: chimera-users-bounces(a)cgl.ucsf.edu [mailto:chimera-users-bounces@cgl.ucsf.edu] On Behalf Of chimera-users-request(a)cgl.ucsf.edu Sent: 2013年12月24日 15:00 To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 128, Issue 25 Send Chimera-users mailing list submissions to chimera-users(a)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(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)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. Re: saving coords from script (Eric Pettersen) ---------------------------------------------------------------------- Message: 1 Date: Mon, 23 Dec 2013 15:59:16 -0800 From: Eric Pettersen <pett(a)cgl.ucsf.edu> To: Tetsuro Fujisawa <fujisawa(a)gifu-u.ac.jp> Cc: "chimera-users(a)cgl.ucsf.edu Mailing List" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] saving coords from script Message-ID: <04B15E0C-844B-4594-8AE6-760588744D85(a)cgl.ucsf.edu> Content-Type: text/plain; charset="windows-1252" On Dec 20, 2013, at 1:58 AM, Tetsuro Fujisawa wrote: > Hi, > > I found some strange behavior in saving pdb file by script file. > I tried to modify the orientation of pdb file ?tst.pdb? (#1) in reference to axis coordinate (#0), then save the atomic coordinates in pdb file. > When I typed in the commands through either command line window or IDLE, transformed coordinates were saved. It worked fine. However, the exact identical commands (inside the brancket) or lines (rc(?..?)) were run by script file shown in below, the untransformed coordinates were saved. This is also the case for ?Midas.write method?. > I wondered this might be a bug. > > Regards, > Tetsuro > > Sample.py: > ---------------------------------------------- > from chimera import runCommand as rc > > rc('open axis.bild') > rc('open tst.pdb') > rc('rock y 60 1 center #1 coord #0 models #1') # orientation of > tst.pdb was modified > rc('focus') > rc('write relative #0 #1 tstA.pdb') > # write current coordinates to tstA.pdb rc('open tstA.pdb') # opened > tstA has original untransformed orientation > ----------------------------------------------- Hi Tetsuro, The issue is that unlike using the command line or IDLE or running a chimera-command script, no frames get drawn during the execution of a Python script unless explicitly requested and therefore the "rock" command in your script doesn't actually do anything until after the entire script runs, and by that time your coordinate file has already been written. To get the rock command to complete before proceeding with the rest of the script you need to append "; wait" or "; wait 1" (since you are rocking for 1 frame) to the end of your rock command. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

2 1

saving coords from script
by Tetsuro Fujisawa 23 Dec '13

23 Dec '13

The following bug report has been submitted: Platform: windows Chimera Version: 1.8.1 Description Hi, I found some strange behavior in saving pdb file by script file. I tried to modify the orientation of pdb file ‘tst.pdb’ (#1) in reference to axis coordinate (#0), then save the atomic coordinates in pdb file. When I typed in the commands through either command line window or IDLE, transformed coordinates were saved. It worked fine. However, the exact identical commands (inside the brancket) or lines (rc(’..’)) were run by script file shown in below, the untransformed coordinates were saved. This is also the case for “Midas.write method”. I wondered this might be a bug. Regards, Tetsuro Sample.py: ---------------------------------------------- from chimera import runCommand as rc rc('open axis.bild') rc('open tst.pdb') rc('rock y 60 1 center #1 coord #0 models #1') # orientation of tst.pdb was modified rc('focus') rc('write relative #0 #1 tstA.pdb') # write current coordinates to tstA.pdb rc('open tstA.pdb') # opened tstA has original untransformed orientation -----------------------------------------------

2 1

Color by ramachandran probability? Or molprobity overlap?
by Oliver Clarke 19 Dec '13

19 Dec '13

Hi all, Quick question, just wondering if there is any way to color a structure by Ramachandran probability? Or by steric overlap scores for each atom as generated by mol probity? Either of these would be very handy as a way of getting a quick graphical overview of trouble spots in a structure. It seems like Chimera “knows about” Ramachandran plot data, (as one can generate such plots from the model panel) but I can’t find any convenient way to display this data on the structure. Many thanks, Oliver.

2 3

Running Segger from a script
by Tom Goddard 19 Dec '13

19 Dec '13

Hi Rakesh, There is not Chimera command to run Segger, only a dialog. So you would have to use Python to run it and write out map files for each masked region if you wanted to script it. Segger uses several Chimera features such as Gaussian filtering, and watershed calculations that are in written in C++ and compiled against the Chimera Python. While you can get those to run in another Python if it has an identical version (e.g. 2.7.3), setting up the environment variables to find all the needed libraries is a difficult process. So I suggest using the Chimera Python. You can run Chimera scripts without the graphical interface by starting it from a shell "chimera --nogui myscript.py". The Segger Python functions are not documented so you would need to study the (complex and messy) code found in chimera/share/Segger or on Mac in Chimera.app/Contents/Resources/share/Segger Tom On Dec 18, 2013, at 5:54 PM, rakesh ramachandram wrote: > Hi, > > I would like to know if I can run Segger in a script in an automated fashion and then obtain the individual segmented regions as separate density maps. Is there a way to run chimera scripts from command line directly without using the chimera's python interpreter but using the default python interpreter after importing its libraries. > > Regards > Rakesh >

1 0

question
by wanxiaobo＠nibs.ac.cn 18 Dec '13

18 Dec '13

Dear chimera team / users, I was looking for a way to save the content of Axis/plane/centroid information, not only the radii via command line, because I want to analyze the structure movement from MD trajectory. It is not convenient to save the information manually for each frame. Thanks Xiaobo

2 1

Command line export to webgl
by Thomas Hrabe 17 Dec '13

17 Dec '13

Dear Chimera Team, I was curious if there was a functionality to export chimera scenes to webgl through the command line, without having to open the chimera window. Is there a set of python script commands that would do it? Thank you for your support, Thomas

2 1

Attribute Calculator by command line?
by Hurt, Darrell (NIH/NIAID) [E] 16 Dec '13

16 Dec '13

Hi Chimera friends, I'm trying to calculate convexity as demonstrated in the Attributes tutorial: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html I can do it with the graphical tools without a problem, but when I try to do it via the command line, I run into trouble. I cannot find any documentation on running the Attributes Calculator on the command line. I've tried using "setattr": setattr a convexity atom.areaSAS/atom.areaSES This command generates a new atom attribute called "convexity" for every atom, but the value of this attribute for every atom is literally "atom.areaSAS/atom.areaSES" instead of the calculated value. Is there a way to calculate a new attribute value on the command line within Chimera? Sorry to be so demanding… Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

3 4

Setting selection mode command line
by rswett＠chem.wayne.edu 16 Dec '13

16 Dec '13

Hi all, I'm interested in putting together a script that will open several large pdb files, select some very specific pieces of those files and save the output to another file. The problem is that they are large files and unwieldy in a graphics window. I have no problem generating the commands to select the regions I'm interested in, but I still need to be able to switch selection modes in between commands. Is there a way to change the selection mode at the command line without navigating the selection menu? Rebecca

3 5