- Chimera-users - RBVI Mailing Lists

Read PDB file
by Eduardo Sanz Garcia 07 Apr '06

07 Apr '06

Hi, Is it possible to read the PDB file of the molecule directly from chimera? Thank you Eduardo Sanz

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Name selection
by Eduardo Sanz Garcia 06 Apr '06

06 Apr '06

Hi everybody, Is there any way to give a name to a selection from the command line? Same as: *Select... Name Selection...* <cid:part1.01070107.06060601@terra.es> but from the command line. Thank you.

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further levels of detail in low-res surface of a single chain Multiscale model
by Klinkhardt＠em.uni-frankfurt.de 05 Apr '06

05 Apr '06

Hello, I would like to divide/define the low-res structure of a multiscale model which contains only one chain. I need further levels of detail in this single chain (preferentially all single nucleotide bases as small podgy shapes and the backbone of phosphate-sugars as an irregular rope) so I can can animate the resulating smaller units later. In your online hept (documentation) there is written that a python script like #bluetongue.py# can create a multiscale model with further levels of (individual?) structure. I have opend the python script but unfortunately I am no programmer so I am not able to modify this script to my requirements. Is there a #more general# script which I can use for my chain or any other workaround?? Thanks a lot in advance, best regards Ute Klinkhardt

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question about CHIMERA
by Guy Nimrod 04 Apr '06

04 Apr '06

Hello, I am a PhD student in the department of Biochemistry of the Tel-Aviv University and often use your great application, CHIMERA. Is it possible to view on chimera the selected part only? Regarding this, is it possible to split a model to its units (so each chain/ligand) will be considered as a model? Thanks Guy Nimrod http://ashtoret.tau.ac.il/~nimrodg

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Please consider adding PyTables to Chimera
by David E. Konerding 04 Apr '06

04 Apr '06

Hello, Recently I have been converting most of my scientific data to the HDF5 format. HDF5 is a powerful, high performance data format library. I found an absolutely wonderful open source code, PyTables, which provides an HDF5 interface. It adds enormous value to HDF5 by making it much easier to use, and exposing a lot of the complex functionality that HDF5 supports (such as variable-length records). http://www.pytables.org/moin I would really appreciate it if you guys would consider adding PyTables. I would definitely convert a lot of my existing extensions and processing tools to use PyTables- for example, when I analyze trajectories to find hydrogen bond data and use that to render long movies, PyTables makes it a lot easier (I already used the Chimera headers to build my own copy of PyTables on Linux, but it would be a lot more painful to do on Windows). PyTables depends on numarray (although it also provides Numeric Python support). I'd like to see numarray in Chimera as well (although I could live with just Numeric support) Dave

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trigonometry
by jean-francois menetret 03 Apr '06

03 Apr '06

What is Chimera's trigonometry convention ? How can get angles out of the rotation matrix (saved with "matrixget") ? Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street

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Different colors for individual chains within a model
by Karpen, Saul J. 31 Mar '06

31 Mar '06

Dear Chimera group, Simple question from a new user--How do I distinctly color ribbon representations of different chains within the same model? Thanks, Saul J. Karpen, M.D., Ph.D. Baylor College of Medicine

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Re: [Chimera-users] Question about background transparency
by Weldon, Scott 28 Mar '06

28 Mar '06

Thanks to all for the help. I have transparent images now. Thanks, Scott Weldon, M.A. Supervisor, Medical Illustrator Division of Cardiothoracic Surgery Michael E. DeBakey Department of Surgery Baylor College of Medicine One Baylor Plaza, BCM 390 Houston, TX 77030 TEL: (832) 355-9941 FAX: (832) 355-9948 E-mail: sweldon(a)bcm.edu -----Original Message----- From: Thomas Goddard [mailto:goddard@cgl.ucsf.edu] Sent: Tuesday, March 28, 2006 11:43 AM To: Weldon, Scott Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Question about background transparency Hi Scott, You need 2 dashes in the background opacity option --bgopacity According to the Chimera manual that option should occur before input PDB files in the Chimera startup command. Here are the relevant pages of the Chimera User's Guide: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/startup.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html Tom

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Question about background transparency
by Weldon, Scott 28 Mar '06

28 Mar '06

Hello, I'm not having any luck using command line to change the background to transparent. I've tried "-bgopacity" and "bgopacity" and both say it is not a valid command. Would you please provide the exact syntax that should be entered to achieve this? Does this need to be entered before the PDB file is opened? Thank you for your help, Scott Weldon, M.A. Supervisor, Medical Illustrator Division of Cardiothoracic Surgery Michael E. DeBakey Department of Surgery Baylor College of Medicine One Baylor Plaza, BCM 390 Houston, TX 77030 TEL: (832) 355-9941 FAX: (832) 355-9948 E-mail: sweldon(a)bcm.edu

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ses volume
by Charles Spink 21 Mar '06

21 Mar '06

Is it possible to get a calculated volume for the solvent excluded area for a protein or dna? I know the volume for a solvent accessible surface is possible through "measure volume" command. What about SES volumes? Thanks, Charlie Spink

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superimposing proteins on co-factor
by Boaz Shaanan 08 Mar '06

08 Mar '06

Hi Chimera prople, If I want to superimpose proteins on their co-factors (or part of them), is ensembleMatch the way to go or are there other ways to do this ? I'd appreciate your advice. Regards, Boaz -- ************************************************************* Boaz Shaanan, Ph.D. Associate Prof. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 e-mail:bshaanan@bgu.ac.il Fax: 972-8-647-2992 or 972-8-646-1710 *************************************************************

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Re: [Chimera-users] (no subject)
by Eric Pettersen 08 Mar '06

08 Mar '06

On Mar 8, 2006, at 2:22 PM, Todd T Talley wrote: > Hay, > Sorry to bother you, but you were so helpful last week > I thought that I would try again. Is there a way to show the > carbonyl of the backbone of a specific residue? I would like to > show the H bond between my ligand and a specific Trp. Well, the vanilla answer is (if we're talking about residue 12.A for example) "disp :12.a@c,o". However, I'm guessing that the reason you've undisplayed the carbonyl in the first place is because you're showing a ribbon -- in which case there are a few more useful things to know. By default the ribbon depiction replaces the backbone atoms (including the carbonyl oxygen) so even if you turn the display of specific backbone atoms back on (e.g. with the above "disp" command), no atoms will be shown. However, Chimera will know that these atoms are now "displayed" and will begin to show things such as H-bonds that involve those atoms (drawing the end of the H-bond to the interpolated ribbon position of the backbone atom). You can force backbone atoms to be explicitly depicted even in the presence of a ribbon with the "ribbackbone" command (e.g. "ribbackbone :12.a") -- they will be shown at their normal non-interpolated positions. --Eric

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Question on Chimera
by Seiha Thorng 06 Mar '06

06 Mar '06

To whom it may concern, My name is Seiha Thorng and I work for BioMarin Pharmaceuticals, Inc. I'm looking into UCSF Chimera as a promising software for our research purposes. I would like to ask you what equipment you would recommend for optimal performance of this software. The answer I'm looking for is in terms of ram, platform, processor, disc space ....etc. We would like very much to be able to run this program at the best possible performance. Thank you. Seiha This message is intended only for the confidential use of the intended recipient(s). If you have received this communication in error, please notify the sender by reply e-mail, and delete the original message and any attachments. Any unauthorized disclosure, copying, or distribution of this message (including the attachments), or the taking of any action based on it, is strictly prohibited.

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Re: [Chimera-users] Show me the disulfides!
by Eric Pettersen 03 Mar '06

03 Mar '06

Todd Talley writes: > Hay, > > I am sure that this is a dumb problem BUT I am unable > to “turn on” the disulfide bonds in my structures. They are a > crucial part of the structures that I am publishing and I really > would like to use Chimera to render the images for our publication > but I am not a code guy and none of the combos I have tried > worked. If anyone is out there with the answer please let me know! > > Thanks! Deposited PDB structures specify disulfide linkages using CONECT records, which Chimera honors. So one way to go is to add such CONECT records to your structures. CONECT records are documented here: http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/part_69.html You can also add the linkages directly in Chimera. If you select a pair of sulfurs that should have the linkage, then the command "bond sel" (Favorites->Command Line) will add the linkage. Sessions and PDB files that you save thereafter will have the linkage information (i.e. a saved PDB file will have the appropriate CONECT record). If you have a lot of disulfide bonds or a lot of structures, I could send you a short Python script to add the linkages automatically. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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delphi in chimera
by Thomas Goddard 02 Mar '06

02 Mar '06

Hi Damien, Chimera Delphi Controller tries to execute the command-line program "delphi" so it must be in your shell executable search path. On Linux you need it in the directory containing the delphi executable in the PATH environment variable. On the Mac I'm not sure how to set the search path when you start Chimera by double clicking on it. You can still set the shell PATH variable and start Chimera from a terminal like: % path-to-chimera/Chimera.app/Contents/MacOS/chimera The Chimera User's Guide (under Tools / Delphi Controller) says that Delphi Controller does not work on Windows. Maybe it is easier to just edit the line in Delphi Controller code that starts delphi. Just edit line 97 in chimera/share/DelphiViewer/DelphiExecutor.py changing from cmd = "delphi %s > %s" % (self.prmFileName, self.outputFileName) to for example cmd = "/usr/local/bin/delphi %s > %s" % (self.prmFileName, self.outputFileName) giving an explicit path to the Delphi executable. On the Mac this file would be Chimera.app/Contents/Resources/share/DelphiViewer/DelphiExecutor.py Keep the indentation of the Python line the same as this is important. All that said, I would suggest just running Delphi yourself then opening the resulting *.phi file in Chimera. The Delphi Controller Chimera tool was written by a summer intern 5 years ago and has not been worked on much since then. The electrostatic potential file produced by MolMol is not in Delphi format. It uses a MolMol specific format (described at the end of this email) that Chimera does not read. You could hand convert it to another text file format by changing the header, to say the one used by APBS (called OpenDX). But I'd suggest calculating the electrostatic potential with APBS instead. Tom ------- Manual page for MolMol potential file format. NAME ReadPot - read potentials for surface coloring SYNOPSIS ReadPot fileName DESCRIPTION Read a file with potentials, these are used for coloring surfaces. The file must contain values on a grid, the format is: x0 xSize xInc y0 ySize yInc z0 zSize zInc val val val .... where x0, y0, z0 (float) are the coordinates of the grid origin, xSize, ySize and zSize (int) are the sizes of the grid in each dimension, and xInc, yInc and zInc (float) the spacing between two grid points in each dimention. This must be followed by xSize * ySize * zSize values (float), where the x-coordinate is the one that is running the fastest. The potentials will be set for all selected surfaces, but the PaintSurface command has to be given to update the colors. EXAMPLE ReadPot /home/joe/struct/my_pot.dat SEE ALSO CalcPot, AddSurface, SelectPrim, PaintSurface DATE 960509 > From: Damien Devos <damien(a)salilab.org> > Date: March 2, 2006 4:04:02 PM PST > To: "Eric Pettersen (chimera)" <pett(a)cgl.ucsf.edu> > Subject: delphi in chimera > > hi Eric, > i'm trying to use delphi in chimera, but couldn't get the delphi > controller to help me. > alternatively, i used molmol to generate the .phi file and tried to > open > it in chimera, but i got this message on the reply log: > > > Done opening /viol1/damien/fgf/molmol/1nuna.pdb > Opening /viol1/damien/fgf/molmol/1nuna.phi > /viol1/damien/fgf/molmol/1nuna.phi: Record size 539833144 > file size > 2725332 > Done opening /viol1/damien/fgf/molmol/1nuna.phi > > it seems that my .phi file is too big? does this make sense? > on the other side, if i could get the delphi controller to work on > chimera, that would solve all problems. we have delphi installed > localy, > but i don't know where to put the path of it and how so that chimera > could locate it. > > thanks > d > > -- > Damien Devos > Andrej Sali Lab > California Institute for Quantitative Biomedical Research > University of California at San Francisco > QB3, Box 2552 > 1700 4th Street, Room 501 > San Francisco, CA 94143-2552 (CA 94158 for courier delivery), USA > Phone: +1 (415) 514-4258 > Fax: +1 (415) 514-4231 > Email: damien(a)salilab.org > URL: http://www.salilab.org >

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plotting RMSD vs Residue number
by Isherwood, James 02 Mar '06

02 Mar '06

Hi, I was wondering if there was a way to use chimera to calculate Root Mean Squared Deviations for individual residues or backbone atoms. In order to produce a graph showing the relative freedom of different areas of a protein. James Isherwood

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3D Graph
by Jake Chrzanowski 02 Mar '06

02 Mar '06

Hi, I've been reading about the program your working on,Chimera, and was wondering if it had the functions I need for a project I'm working on: I'm trying to create a 3D graph to represent an image and the distance that image is away from a source. I was looking at your Chimera program to do this. I was wondering if your Chimeraprogram had the necessary functions I needed to do this? If so, can you point me in the right direction on what the functions I need would be? Below I described a little more in depth of what I'm trying to do. First, I'll give you a little detail on our overall project so you have a better idea of what I'm dealing with. We're trying to measure the distance of an object using two cameras. Two identical cameras are positioned near each other with a separation distance and focusing angle. The Image-Processing Computer applies filters to conform the images so that meaningful features stand out in contrast to non-meaningful features (i.e. shadows, textures, glare, and reflections). The computer uses a vast array of image-processing algorithms to find key features in the images. Cross-correlation is performed between the features in both images to determine the line-of-site angle and separation distance. With that found, triangulation is performed to determine the distance that an object(s) is away from the cameras. ------------------------------------- Now, once we have determined the distance, we want to have a 3D graph display the object's distance away from the camera (part where I'd like to use Chimera), as they come into focus. (i.e. The graph will be continually updating at 10 frames/sec along with the cameras) I have attached a general 3D graph .bmp file to show you kinda what I'm looking for. (Obviously, the graph won''t portrude negative as the .bmp file since the camera only look in one direction) What I'm thinking is I will basically take in two parameters. 1) The coordinates of the edge detected (horizontal and vertical pixel location). Edges won't be detected in the entire area ( i.e. a wall focused in too closely will ideally show no edges). The graph will only be concerned with areas that edges were detected. 2) The other parameter that needs to be taken in is the computed distance from the cameras of the detected edge. This is the parameter that will determine how far the graph protrudes out in the z direction. Ideally, I would like for portions of the graph to change colors corresponding to a certain distance detected (i.e. 0-1 feet red, 1-2 feet orange, etc...). Also, something that isn't needed (but would make the graph look a lot better), is if I could use some interpolation functions so areas that were encompassed by edges would protrude out, too, instead of just the edges. Sorry about the length of this email. I just wanted to give you a good idea of what I'm looking for. I also attached a picture (" picture2.bmp") that had gone through an edge detection program. The white lines are detected edges. Everywhere else in the image now has a pixel intensity of 0. I'm looking for a library to help me accomplish all or most of these things listed with the 3D graph. I am an amateur at computer programming , so the simpler the better (I'm an electrical engineering major, we don't get a chance to learn too much about how to program). Anything you can help me with I would really appreciate. Thanks a lot for your time and I'll look forward to your response. -- Sincerely, Jacob Chrzanowski Electrical Engineering Student, NDSU jmchrz(a)gmail.com (701) 866-3120

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movies of gromos files
by John Robinson 01 Mar '06

01 Mar '06

Trying to visualize gromos trajectories. The Tk popup is asking for three files: Topology, Coordinates, and PROMD. I don't seem to be giving it the files it needs. What are the file extensions corresponding to these file types? (.top, .trr, .tpr)? Thx, -------------------------------------------- John M. Robinson, M.D., Ph.D. mailto:johnmrobinson@mac.com

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selection of atoms on the surface of a molecule
by kovzany＠go.com 28 Feb '06

28 Feb '06

Dear All, Is there an easy way to select and save set of atoms (with their names and coordinates) representing VdW or solvent accessible surface of the given molecule? thanks, PK

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MTZ files
by Eran Shacham 28 Feb '06

28 Feb '06

Hey there, I am not sure if this question should go into users or developers but I will first try here. Accept my apologies if this does not concern you and maybe you could fwd this email to someone who could help me out. I am looking to convert MTZ files into ccp4 map files (using Python). Is there an extension of Chimera that allows that? Can you please point out some documentations about the issue? Thanks in advance for your help and time, Eran.

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Ribbon path smoothing
by Jakob Toudahl Nielsen 28 Feb '06

28 Feb '06

Dear Chimera users, I trying to create a ribbon model drawing of a DNA structure containting several abrupt chain-reversals in the DNA-backbone. By default the ribbon path is smoothed over five successive residues. This resuls in the ribbon path supressing the chain-reversals by oversmoothing the path. Is there any way to overide the default value of the FIVE succesive residues to a smaller number (e.g. TWO). Regards, Jakob Jakob Toudahl Nielsen Dep. of Chemistry University of Southern Denmark

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Making a new covalent bond
by Goel, Manisha 27 Feb '06

27 Feb '06

Hi, I have often come across detailed answers from chimera group for a variety of modelling problems on pdb-l or bioinformatics mailing lists. My problem should relatively easy to solve except that I havn't been able to figure it out myslef on chimera. I just need to make a covalent bond between a sugar molecule and an aminoacid (aa-COOH + sugar-OH --> H2O + aa-sugar). Is there an easy way of doing this manipulation in Chimera ? Please advice ? Thanks a lot for your time and effort. -Manisha Goel Post-doc associate Bioinformatics Lab Stowers Institute for Medical Research Kansas city-66210

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chimera vrml issues...
by Thomas Goddard 27 Feb '06

27 Feb '06

------- Start of forwarded message ------- Date: Thu, 16 Feb 2006 23:47:38 -0800 From: Janet Iwasa <jiwasa(a)gmail.com> To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Subject: chimera vrml issues... Hi Tom, I was trying out some of those new scene export functions in Chimera that you showed me a while back, and I've been running into some issues. I've got a large ribbon structure that I wanted to export as VRML, but Chimera only wrote a small file that couldn't be opened. Using notepad, all the file included was the following: #VRML V2.0 utf8 Transform { children [ ] } Saving as a X3d file seemed to work (seemed like a reasonable size at 10 MB) but I couldn't use the translator (X3dToVrml97.xslt) to change to VRML since it appeared to run into memory issues. Trying to save as POV or Renderman either failed or crashed Chimera. Any suggestions? Janet ------- End of forwarded message -------

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question
by Stefano Ciurli 23 Feb '06

23 Feb '06

Hello, I am a new user of Chimera and I need to ask a question: let's say that I am loading several PDB files from the RCSB, all of them belonging to the same protein, the latter having 3 subunits A, B, and C. I need a way to operate on single PDB files (select and manipulate features of each PDB file at once). How do I do it? I can easily find the select->chain option, but it would operate on all chains of that type in all PDB files. Regards, Stefano

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Re: [Chimera-users] chimera vrml issues...
by Greg Couch 23 Feb '06

23 Feb '06

Forgot to cc the list. So to summarize: There some major bugs fixed with the X3D ribbon output in chimera version 1.2180 that affected the Renderman and POV-ray output as well. So please upgrade your chimera. I think I have fixed all of the problems, so if it still fails, please submit a bug report (ideally with enough data to reproduce the problem). As for vrml output, the xslt technology is slow, but works. In the X3dToVrml97.xslt file, it suggests using saxon.sourceforge.net's java-based converter, and I second that recommendation (it was the fastest of the alternatives I tested). Even when the X3dToVrml97.xslt method works, it has problems -- it outputs VRML 3.0 and most VRML importers expect VRML97 aka VRML 2.0. This is especially problematic for ribbons because ribbons use triangle strips for their geometry and 3.0 supports triangle strips while 2.0 doesn't. VRML97 doesn't support translucent colors either. Consequently, I have put improving the VRML output on my list of things to do. And if you have the option of using the Renderman output, use it, because it reproduces what you see in the chimera window the best of the various export formats. Greg Couch UCSF Computer Graphics Lab

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