October 2009 - Chimera-users - RBVI Mailing Lists

problem with SAXS profile
by Stefan Jehle 27 Oct '09

27 Oct '09

Hi, I have to finish very urgently a model of a big oligomer and the SAXS curve utility would be extremely helpfull for me if working properly. Here my problem: I get the following error message after pressing the "Profile" button: Wrote /var/folders/dP/dPWm0vEeFkG9xqa+tbipE++++TM/-Tmp-/tmprnvHi_.pdb Executing command: /Users/stefan/Downloads/Chimera.app/Contents/Resources/share/SAXS/ChimeraExtension.py /var/folders/dP/dPWm0vEeFkG9xqa+tbipE++++TM/-Tmp-/tmprnvHi_.pdb /Users/stefan/Documents/modelling/saxsprofile/abc30mer.dat Error 512 executing command "/Users/stefan/Downloads/Chimera.app/Contents/Resources/share/SAXS/ChimeraExtension.py /var/folders/dP/dPWm0vEeFkG9xqa+tbipE++++TM/-Tmp-/tmprnvHi_.pdb /Users/stefan/Documents/modelling/saxsprofile/abc30mer.dat" First I thought this may be because I have encrypted my cache (using MacOSX Leopard) but the same problem occurs using Win Vista or Windows XP or Windows Vista. I would appreciate your help, if you could provide me a saxs.py file working. Thanks a lot Best Regards Stefan __________________________________ Dr. Stefan Jehle Structural Biology Unit Leibniz Institute for Molecular Pharmacology, FMP Robert-Rössle-Str. 10 13125 Berlin Germany jehle(a)fmp-berlin.de Phone +49 30 94793232 Fax +49 30 94793169

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Error during PDB Fetch
by Bryan Krantz 27 Oct '09

27 Oct '09

Dear Chimera Users: Does anyone know how to resolve this bug. I tried to load a PDB file from the web using the ID 3hvd. Got this error back: Error reading 3hvd: Error during PDB fetch: [Errno socket error] (-2, 'Name or service not known') I am running this Chimera : Linux 64-bitchimera-1.4-linux_x86_64.exe<https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=linux_x86_64/chimera-1…> Size: 77850528 bytes MD5: 1e05f4607699c88467e81cc249aa4ad1 My OS is Debian Lenny AMD64. Thanks in advance for your help. Yours, bryan -- Bryan Krantz University of California, Berkeley Department of Molecular & Cell Biology Department of Chemistry 476 Stanley Hall #3220 Berkeley, CA 94720-3220 Phone: (510) 666-2788 Email: bakrantz(a)berkeley.edu Lab: 492 Stanley Hall Lab phone: (510) 666-2789 URL: http://mcb.berkeley.edu/labs/krantz/

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Re: [Chimera-users] Terminating Match-align without loosing reply log
by Eric Pettersen 27 Oct '09

27 Oct '09

Hi Mario, There is no guaranteed way. On the Mac or on Linux you may be able to stop the computation by sending Chimera's Python interpreter an INT signal (terminal interrupt) [I don't know of any such option on Windows]. Open a terminal window (on Mac: /Applications/Utilities/ Terminal.app). Find Chimera's Python process via: ps augxww | grep python You'll see something along the lines of: pett 86576 98.7 13.4 1218088 562256 ?? R 11:58AM 2:17.97 /Users/pett/Applications/Chimera-daily-x11.app/Contents/ Resources/bin/python2.5 /Users/pett/Applications/Chimera-daily-x11.app/ Contents/Resources/share/__main__.py The first number (86576) is the process ID of Chimera's Python interpreter. Send it an interrupt signal by: kill -INT 86576 If all goes well, Chimera will bring up an error dialog saying something about KeyboardInterrupt. The Match->Align computation will have stopped with the structures in the same position as they were at the end of the last iteration, the last alignment window will be up, and the Reply Log will be available. On Linux, if you started Chimera yourself from the command line you may be able to just hit control-C (or whatever your interrupt character is) instead of the rigamarole above. --Eric On Oct 27, 2009, at 11:46 AM, Mario Borgnia wrote: > Hi Eric, > > Thanks for the fast response. My other question is how to terminate > the process > in progress without compromising the output of previous iterations. > Thanks!!! > > Mario > > Eric Pettersen wrote: >> Hi Mario, >> The iterations are independent. So you could iterate twice, save a >> session, and then iterate further later. You could use the 'Save' >> button on the Reply Log to save info as needed. >> >> --Eric >> >> P.S. Sorry it's slow. It's all in Python and given how complex it >> is >> it's unlikely it's going to be recoded in C++ anytime soon. >> >> >> Eric Pettersen >> >> UCSF Computer Graphics Lab >> >> http://www.cgl.ucsf.edu >> >> >> >> On Oct 27, 2009, at 7:47 AM, Mario Borgnia wrote: >> >>> Hi, >>> I launched a massive match-align procedure with five iterations >>> without knowing >>> that it would take so long to complete. Is it possible to stop it at >>> iteration 2 >>> without loosing the information computed to that point? Also, is it >>> possible to >>> continue from that point on in a subsequent round? >>> Thanks! >>> >>> Mario

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Chimera slow on Win 7 64-bit system
by Thomas Goddard 27 Oct '09

27 Oct '09

Hi Wen, The slow ribbon and atom rendering must be a graphics driver issue. Surfaces use different OpenGL calls for rendering allowing them to be fast. You can try updating your graphics driver. If you have the most recent you could try poking around with graphics driver settings that trade of speed and quality. We don't have a 64-bit Windows Chimera. Only 64-bit Linux Chimera is available. We'll probably put out a 64-bit Mac Chimera in about 6 months and 64-bit Windows Chimera in about 1 year. Tom -------- Original Message -------- Subject: chimera question From: Wen Jiang To: Tom Goddard Date: 10/15/09 7:54 PM > Hi Tom. > I recently set up a Windows 7 64bit system for Nvision stereo display > and ran into some problems with Chimera. First, the performance for > pdb molecules (ribbon and atoms) is very slow. It seems fine with > volume data (surface). Do you have any clue? Second, there is only > 32bit version for Chimera and it cannot deal with large map. Do you > have a 64bit version for Windows? > Thanks, > > Wen > > Wen Jiang, Ph.D. > Assistant Professor > Department of Biological Sciences > Lilly Hall, B-402A > Purdue University > West Lafayette, IN 47907

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Terminating Match-align without loosing reply log
by Mario Borgnia 27 Oct '09

27 Oct '09

Hi, I launched a massive match-align procedure with five iterations without knowing that it would take so long to complete. Is it possible to stop it at iteration 2 without loosing the information computed to that point? Also, is it possible to continue from that point on in a subsequent round? 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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[Fwd: creating more memory]
by Lori Nyland 24 Oct '09

24 Oct '09

Ooops forgot attachment. Here it is.

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problem with chimera 1.4
by lionel nauton 23 Oct '09

23 Oct '09

Hi everyone, I'm using chimera 1.4 since few days on Fedora 11 (leonidas) with a nvidia card (8600 gts), and it's working very fine. but just one problem, when we have more than one model displaying, every informations like distances, H-bond, labels, doesn't move with models during rotation or translation. this problem don't exist with just one model. best regards, ____________________________________ Mr NAUTON Lionel Ingénieur d'étude CNRS Laboratoire SEESIB UMR6504 Université Blaise Pascal Campus des Cézeaux Bâtiment Chimie 4 et Chimie 3 RDC 24 avenue des Landais 63177 AUBIERE Cedex France Tel : 0473405506 http://seesib.univ-bpclermont.fr/Nouveau_site/pages/

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creating more memory
by Lori Nyland 23 Oct '09

23 Oct '09

Hello, I have attached an image that shows the command line and the command where I am trying to save an image map of one volume relative to another. I received an error when the operation was executed. The error code is in the image. I noticed that there was an error in memory allocation (toward bottom of error script). So I think I need to allocate more memory. How do I do that? Thanks so much! Lori

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problem with chimera 1.4
by lionel nauton 23 Oct '09

23 Oct '09

thank's for your answer Victor Sure that the Action Mark is active, my problem is for the distance, label or H-bond printing, they stay fixed when the models are moving.

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trying to process 1000 proteins via Chimera
by Bisn 21 Oct '09

21 Oct '09

Hello, We are Chimera users trying to process 1000 proteins, e.g., add hydrogen and charge. We want to do this via a Chimera for DOCK preparation. I know that Chimera accepts command line, but this is not realizable for processing 10000 molecules. Have you any idea of the task? Thanks! Jian Chen

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Chimera-users October 2009