- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] multalignviewer/4650 (associations dialog problem)
by Eric Pettersen 12 Oct '07

12 Oct '07

Hi Roberta, The bug you ran into is that the associations dialog wasn't handling non-polymer models correctly (some of your models had had all the protein removed, leaving just ligand). I've just put in enough of a fix so that your session can be used. If you get tomorrow's test build (following the "Test Builds" link off www.cgl.ucsf.edu/chimera) that will have the fix in it. It's not yet a complete fix because it only handles the case where you open the associations dialog _after_ the protein deletion has occurred (which is okay for you). I need to put in more work to make it handle the case where the deletion occurs after the associations dialog is open. When that fix is done you will get an automated mail about it as I change the bug report from "open" to "internal-fix" -- and then it will be available in the next test build. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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molecular modelization softwares
by DESPLAT Nelly 11 Oct '07

11 Oct '07

Dear sir or madam, I am currently studying at the Université Paul Sabatier of Toulouse (France), in a Bioinformatics program (master degree) and I have a report to write, concerning molecular modelization softwares. Could it possible to obtain additional informations about your software Chimera? I would like to know its price, the price of an additionial module, and also how its maintenance work. I thank you ahead of time for your help. Sincerely. Nelly DESPLAT _____________________________________________________________________________ Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail

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Visualizing an ion channel
by Francesco Pietra 11 Oct '07

11 Oct '07

Hi Elaine: Perhaps trivial, though new for me: How to assemble reliably the essentials (to get the teepee) of the four alpha subunits of an ion channel when the Protein Data Bank gives the pdb file for one on the subunits? For example 2A79, a mammalian Kv1.2 ion channel. Thanks francesco pietra ____________________________________________________________________________________ Check out the hottest 2008 models today at Yahoo! Autos. http://autos.yahoo.com/new_cars.html

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Chimera POVRAY and Vista?
by Frank Neese 09 Oct '07

09 Oct '07

Dear Chimera team, First of all congratulations for a really nice program and thank you very much for making it available to the community! I like it a lot. I was nevertheless running into a problem when trying to create povray pictures on a windows vista PC. Is there anything i can do about it? With my best regards, sincerely yours, Frank Neese The output is below: running "C:\Program Files\Chimera\bin\povray.exe" "d:\HomeD\Research\Bonn\COLLAB - Gross\image.ini" "+Id:\HomeD\Research\Bonn\COLLAB - Gross\image.pov" "+Od:\HomeD\Research\Bonn\COLLAB - Gross\image.png" "+V" povray: cannot open the user configuration file C:\Users\neese\AppData\Roaming/.povray/3.6/povray.conf: No such file or directory povray: I/O restrictions are disabled. povray: cannot open an INI file, creating a temporary file 'C:\Users\Public\Desktop/pov36.ini'. povray: cannot write to C:\Users\Public\Desktop/pov36.ini: Permission denied Persistence of Vision(tm) Ray Tracer Version 3.6.1 (cl /nologo /Zc:forScope /Op- /GRX /EHc- /GF /G7 /MD /Zl /O2i) This is an unofficial version compiled by: UCSF Chimera <chimera(a)cgl.ucsf.edu> The POV-Ray Team(tm) is not responsible for supporting this version. POV-Ray is based on DKBTrace 2.12 by David K. Buck & Aaron A. Collins Copyright 1991-2003 Persistence of Vision Team Copyright 2003-2004 Persistence of Vision Raytracer Pty. Ltd. Primary POV-Ray 3.5/3.6 Developers: (Alphabetically) Chris Cason Thorsten Froehlich Nathan Kopp Ron Parker Contributing Authors: (Alphabetically) Steve Anger Eric Barish Dieter Bayer Steve A. Bennett David K. Buck Nicolas Calimet Aaron A. Collins Chris Dailey Steve Demlow Andreas Dilger Alexander Enzmann Dan Farmer Mark Gordon Christoph Hormann Mike Hough Chris Huff Kari Kivisalo Lutz Kretzschmar Jochen Lippert Pascal Massimino Jim McElhiney Douglas Muir Juha Nieminen Bill Pulver Eduard Schwan Wlodzimierz Skiba Robert Skinner Yvo Smellenbergh Zsolt Szalavari Scott Taylor Massimo Valentini Timothy Wegner Drew Wells Chris Young Other contributors are listed in the documentation. Support libraries used by POV-Ray: ZLib 1.2.3, Copyright 1995-1998 Jean-loup Gailly and Mark Adler LibPNG 1.2.16, Copyright 1998-2002 Glenn Randers-Pehrson LibJPEG 6b, Copyright 1998 Thomas G. Lane LibTIFF 3.8.0, Copyright 1988-1997 Sam Leffler, 1991-1997 SGI Redirecting Options All Streams to console..........On Debug Stream to console.........On Fatal Stream to console.........On Render Stream to console........On Statistics Stream to console....On Warning Stream to console.......On Parsing Options Input file: d:\HomeD\Research\Bonn\COLLAB - Gross\image.pov (compatible to version 3.61) Remove bounds........On Split unions.........On Library paths: C:\Program Files\Chimera\share\fonts Output Options Image resolution 512 by 384 (rows 1 to 384, columns 1 to 512). Output file: d:\HomeD\Research\Bonn\COLLAB - Gross/image.png, 24 bpp PNG Graphic display......On (gamma: 2.2) Mosaic preview.......Off CPU usage histogram..Off Continued trace......Off Tracing Options Quality: 9 Bounding boxes.......On Bounding threshold: 1 Light Buffer.........On Vista Buffer.........On Draw Vista Buffer....Off Antialiasing.........On (Method 1, Threshold 0.300, Depth 3, Jitter 1.00) Clock value: 0.000 (Animation off) 0:00:00 Parsing File: d:\HomeD\Research\Bonn\COLLAB - Gross\image.pov Line: 6 Possible Parse Error: Could not find file 'transforms.inc' File: d:\HomeD\Research\Bonn\COLLAB - Gross\image.pov Line: 6 File Context (5 lines): #include "transforms.inc" global_settings { charset utf8 max_trace_level 10 } Parse Error: Cannot open include file transforms.inc. File: d:\HomeD\Research\Bonn\COLLAB - Gross\image.pov Line: 6 Parse Warning: Check that the file is in a directory specifed with a +L switch or 'Library_Path=' .INI item. Standard include files are in the include directory or folder. Please read your documentation carefully. Total Scene Processing Times Parse Time: 0 hours 0 minutes 0 seconds (0 seconds) Photon Time: 0 hours 0 minutes 0 seconds (0 seconds) Render Time: 0 hours 0 minutes 0 seconds (0 seconds) Total Time: 0 hours 0 minutes 0 seconds (0 seconds)

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Re: [Chimera-users] surface/4623 (Chimera surfacing failure)
by Eric Pettersen 09 Oct '07

09 Oct '07

Hi Jeff, Chimera doesn't communicate depth-cuing/fog info to POV-Ray yet. I will open a bug report about it with you included on the recipient list. What you may want to do in the interim to get a better looking image is to reposition the lights in the scene to reduce the shadows. You use Tools->Viewing->Lights to bring up the interface for position the key (bright) and fill (dim) lights. I've attached two images where I've done that. In both the key light is just slightly overhead and centered. The fill light in one is coming from slightly below and centered, and in the other the fill light is off (you have to go to the "advanced" section of the lighting interface to turn off lights). --Eric

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Re: [Chimera-users] dock-prep problem with Zn and K ions
by Eric Pettersen 08 Oct '07

08 Oct '07

Hi Joe, If you care about the protonation of the SHH ligand in that structure then I would actually recommend you use one of the new test builds (follow the "Test Builds" link off the Chimera home page). There have been improvements since the 1.2422 release in protonating atoms involved in coordination complexes, and in protonating ring nitrogens in non-standard residues (though the latter isn't directly relevant in your case). --Eric On Oct 8, 2007, at 12:17 PM, zzj wrote: > Hi Eric, > Sorry for the mess. The old Chimera version is 1.2259. > I just downloaded the latest version (1.2422). It works perfectly fine > the same PDB. Guess I'll stick to this version. > thanks a lot. > -Joe > > On 10/8/07, zzj <zzjsail(a)gmail.com> wrote: >> Hi Eric, >> thanks for your reply. I am using PDB 2PQO. The Chimera version is >> beta version 1 build 2259 2006/07/11 >> platform: darwin >> windowing system: aqua >> I am working on a Mac OS X 10.4.10 (G5). It seems Chimera works fine >> other than the problem I mentioned. >> -Joe >> >> On 10/8/07, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: >>> I can run Dock Prep on a PDB file containing zinc (1zip) without >>> the problem >>> you're getting. Can you tell me what PDB you're using, and what >>> version of >>> Chimera? >>> >>> --Eric >>> >>> >>> >>> Eric Pettersen >>> >>> UCSF Computer Graphics Lab >>> >>> pett(a)cgl.ucsf.edu >>> >>> http://www.cgl.ucsf.edu >>> >>> On Oct 8, 2007, at 10:54 AM, zzj wrote: >>> >>> Hi there, >>> I am preparing dock6 files in Chimera using the Dockprep option. The >>> Zn and K ions in the PDB files are giving me problems at the >>> point of >>> adding hydrogen. Everthing works fine if I remove these ion atoms. >>> Here is the Chimera Error message: >>> AttributeError: addHinfoDialog instance has no attribute >>> "cancerlCB". >>> I can select and highlight these ions without problem. I tried to >>> give >>> different names for the ions. Nothing worked. >>> Any suggestion is highly appreciated! >>> -Joe >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >>

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dock-prep problem with Zn and K ions
by zzj 08 Oct '07

08 Oct '07

Hi there, I am preparing dock6 files in Chimera using the Dockprep option. The Zn and K ions in the PDB files are giving me problems at the point of adding hydrogen. Everthing works fine if I remove these ion atoms. Here is the Chimera Error message: AttributeError: addHinfoDialog instance has no attribute "cancerlCB". I can select and highlight these ions without problem. I tried to give different names for the ions. Nothing worked. Any suggestion is highly appreciated! -Joe

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End graphical representation from Dock tutorials
by Francesco Pietra 08 Oct '07

08 Oct '07

I carried out all Dock6.1 tutorials with the aid of Chimera 1.2422 and DMS. The relevant files used for, and got from, the flexible-ligand docking tutorial are attached. I believe I used defaults. The out file attached is the one of the four out files (from mpirun -np 4 ....) that seems to me to be relevant. How to view graphically the best scored ligand from flex_scored.mole2 in the protein? Just combine flex_scored.mole2 with the ligand-deprived receptor? This in view of my project of looking for docking between a family of lypophilic natural products (conformationally studied in vacuum with Amber9 simulated annealing) and a complex, large protein. I.e., by carrying out a process of the type illustrated by the docking tutorial for each pocket of the protein. I know there is interaction between the two (though a mere disassembling of the lipid bilayer can't be rigorously ruled out yet) but no idea where. Thanks francesco pietra ____________________________________________________________________________________ Catch up on fall's hot new shows on Yahoo! TV. Watch previews, get listings, and more! http://tv.yahoo.com/collections/3658

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Protein RMSD
by Elaine Meng 05 Oct '07

05 Oct '07

Hi John and everybody, I forgot to mention the following additional ways to calculate RMSD in Chimera if you are working with a conformational ensemble (different conformations/configurations of the same set of atoms): - if the ensemble is opened as a trajectory in MD Movie, you can calculate an all-by-all RMSD map http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ framemovie.html (go to the "RMSD Analysis" section) ... also covered in a tutorial http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ ensembles2.html#part2 - if the ensemble is present as multiple MODELs within a single PDB file opened the normal way in Chimera, you could use the EnsembleMatch tool http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ ensemblematch/ensemblematch.html ... also covered in a tutorial http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ ensembletut.html I don't know if these pertain to the original question, but I mention them for completeness. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Generating Spheres tutorial
by Francesco Pietra 05 Oct '07

05 Oct '07

I am running Chimera 1.2422 on a Linux desktop and DOCK6.1 and DMS on a scp-linked Linux parallel machine. Following the "Generating Spheres" tutorial of dock, I verified that DMS works correctly. Though, I am unable with Chimera to visualize properly the rec.ms and sphere_cluster.pdb (the files I have generated are identical to those downloaded). With rec.ms I am unable to visualize the small molecule inside the protein. With sphgen_cluster.pdb I can only see disconnected pieces, thogh placed as expected from the tutorial. Clearly, I need to pass to a Chimera tutorial. Which one(s) for the case in point? I apologize for the pedestrian questions. Though, coming from organic chemistry and ab initio calculations, I am finding Amber9, DOCK6.1, DMS, and Chimera no minor burden. Quite interesting, however. Thanks francesco pietra ____________________________________________________________________________________ Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos & more. http://mobile.yahoo.com/go?refer=1GNXIC

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