March 2015 - Chimera-users - RBVI Mailing Lists

Rename models from command line
by Oliver Clarke 30 Mar '15

30 Mar '15

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

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MatchMaker-vs-MatchAlign
by Egor Tchesnokov 30 Mar '15

30 Mar '15

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

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on the section command
by Smith Liu 30 Mar '15

30 Mar '15

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

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Running graphical Chimera from remote server
by Hurt, Darrell (NIH/NIAID) [E] 29 Mar '15

29 Mar '15

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

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Tutorials
by Bobby Barnett 28 Mar '15

28 Mar '15

I was wondering if anyone had interactive tutorial session(s) that can be used to educate a small class of undergraduate students. Bobby Barnett Department of Chemistry University of Chemistry

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Problems with reproducing 'write relative' output
by Dan McNamara 25 Mar '15

25 Mar '15

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

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black bar in saved image
by sunyeping 25 Mar '15

25 Mar '15

Dear all,I find in the saved volume image (png file), there are some black bar whick mask the image? Please see the following link:https://www.dropbox.com/s/nvy3douvafymqxd/image.png?dl=0Do you know how to get rid of them?Thank you very much! Yeping Sun Institute of Microbiology, Chinese Academy of Sciences

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Creating MultiScale surface from a script
by Cruz, Phil (NIH/NIAID) [C] 24 Mar '15

24 Mar '15

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

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command related to the alignment of the ribbon form and the ball & stick form
by Smith Liu 24 Mar '15

24 Mar '15

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

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Sampling the density of a map in the vicinity of each atom in a model
by Mario J. Borgnia 23 Mar '15

23 Mar '15

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

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Chimera-users March 2015