- Chimera-users - RBVI Mailing Lists

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

1 0

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.

3 2

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

1 0

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 >

1 0

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

2 2

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

2 1

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

2 1

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

2 1

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.

2 1

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

2 1

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

2 1

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 -------

3 2

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

2 1

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

1 0

chimera vrml issues...
by Thomas Goddard 23 Feb '06

23 Feb '06

Janet Iwasa reports problems exporting ribbons and nucleotide renderings as x3d, problems converting x3d to vrml, and problems with POV and Renderman output. Tom ------- Start of forwarded message ------- Date: Wed, 22 Feb 2006 17:49:33 -0800 From: "Janet Iwasa" <jiwasa(a)gmail.com> To: "Thomas Goddard" <goddard(a)cgl.ucsf.edu> Subject: Re: chimera vrml issues... Hi Tom, Unfortunately, I still ran into a bunch of problems. The structure I had was a bunch of ribbons with some colored sphere residues. When I exported the scene as x3d and used the vrml converter (which did work but took forever on my home computer) it only appeared to export the sphere surfaces, not the ribbon. I ended up using a different program (called 'ribbons' - I think I talked to you about it before) to make a vrml of the ribbon structure. Then I took the colored spheres and superimposed it over the ribbon in Maya. It was pretty time consuming, but worked in the end. The structure (which was a nucleosome) also had some nice DNA representations using the depiction > nucleotide option, and those didn't seem to get exported to x3d either (could have been a problem with the x3d -> vrml conversion -- hard for me to tell where things went wrong). So I used multiscale models and exported the DNA as VRML that way, which worked perfectly, as always. I haven't tested it to see whether the x3d export only works with spheres or what. It took the better part of an hour to convert from x3d to vrml (and this for only 20 or so residues!), so I would love to find a better solution... Ideas? I think I'm pretty much done with that project for the time being, but it would be really nice to have the scene export stuff working. Any clue about what's up with the pov and renderman formats? Those may be easier to find converters for. thanks! Hope you're doing well, Janet ------- End of forwarded message -------

1 0

Re: [Chimera-users] Chimera on Intel macs
by Eric Pettersen 19 Feb '06

19 Feb '06

Having received no major bug reports for the 1.2199 release candidate, we are promoting it to production release status. We have figured out how to make a combined release for Mac Intel and PPC, 10.3 and 10.4, so the download page is a little shorter. :-) --Eric

1 0

Re: [Chimera-users] chimera vrml issues...
by Thomas Goddard 17 Feb '06

17 Feb '06

Hi Janet, The Chimera VRML export only exports surfaces (molecular surfaces, volume data surfaces, multiscale model surfaces). It does not export ribbons or atomic models. Some text in the Export Scene dialog describes this limitation when you select VRML as the File Type. The X3D export is probably the best option. It is a pain to convert but I would try the X3dToVrml97.xslt translator on a machine with more memory if you think that is the reason it is not working. If you don't have a machine available, we can try on one of our machines. Greg Couch here will need to look at the POV and Renderman failures. Tom

1 0

Chimera 1.2176: surfaces fail for some structures?
by Anna Feldman-Salit 13 Feb '06

13 Feb '06

Hello, I have noticed that for 1.2199 version there is a "know bug" of surface failure. We have been working with 1.2176 version (which is probably even not release version). Apparently, I have the same problem with some of molecules (working with 1.2176). Is it occasionally or there is a "known bug" for 1.2176 too? Can you maybe recommend some version that has not such a problem? Thank you in advance! Sincerely, Anna.

2 1

Chimera on Intel macs
by Eric Pettersen 10 Feb '06

10 Feb '06

The 1.2199 release candidate was compiled for PPC macs and fails on Intel macs despite Apple's emulation software. We are working on compiling natively for Intel macs and will send another mail when an Intel version is available. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

1 0

labels in Chimera
by Sergey Ryazantsev 09 Feb '06

09 Feb '06

Dear Chimera users I am new in this area, so my question may sound stupid, but anyway. I am using Chimera for 3D model visualization (nothing to do with PDB etc). It's 3D models of biological macromolecules obtained using EMAN 3D reconstruction software. Often I need to compare a bunch of the models at the same time and I need them to be labelled (like 1,2,3,4 etc). I did not find easy way to label multiple objects, so labels would sort of stick to particular object and be independent from the other labels. How also, I could place labels in 3D space, so labels would be at different depth? Any ideas? Many thanks, Sergey. _____________________________________ Sergey Ryazantsev Ph. D. Electron Microscopy Lab UCLA School of Medicine Department of Biological Chemistry 10833 Le Conte Ave, Room 33-080 Los Angeles, CA 90095 Phone: (310) 825-1144 (office) (310) 206-1029 (Lab) FAX (departmental): (310) 206-5272 mailto:sryazant@ucla.edu

2 1

chimera: gnuplot.py
by John Robinson 09 Feb '06

09 Feb '06

Dear chimera power-users: I can use the gnuplot.py library from the python command line without issue. However, when I try to do the same in IDLE under chimera, I get a broken pipe error. Any suggestions? --John -------------------------------------------- John M. Robinson, M.D., Ph.D. mailto:johnmrobinson@mac.com

3 3

Chimera for 64-bit Linux machines
by jbrown 09 Feb '06

09 Feb '06

I'm curious - which production/snapshot release runs best on a 64-bit Linux machine? Also, if the current production releases don't run on such a machine, will there b onee in the near future? Thanks a lot. - Jesse Brown

2 1

Stereo on Mac OS X, 10.4
by David Belnap 08 Feb '06

08 Feb '06

Almost a year ago, I asked if there were plans to support stereo on Mac OS X. Greg replied that Chimera could only when Mac OS X supported stereo-in-a-window (see my question and Greg Couch's answer below). There seems to have been some progress on this by Apple. Their "scientific visualization" page (http://www.apple.com/science/ researchsolutions/visualization.html) says: Thanks to its PCI Express architecture, the Power Mac G5 with the optional NVIDIA Quadro FX 4500 graphics card gives researchers 3D stereo-in-a-window capabilities using a CRT display and Stereographics CrystalEyes liquid crystal shutter eyewear and E2Mac emitter. See also http://www.stereographics.com/apple.html. If I buy the NVIDIA Quadro FX 4500 graphics card, will I now be able to run Chimera in stereo on a Mac? Thanks. David On Wed, 16 Mar 2005, David Belnap wrote: > As a follow-up to the discussion about stereo by Virginia and > Sabuj, will > Chimera currently, or in the future, work in stereo on a Mac > running OS X? > Only if Mac OS X supports stereo-in-a-window. That appears to be unlikely because stereo-in-a-window is a feature that is only supported on workstation-class graphics cards (NVidia Quadro, ATI FireGL, 3DLabs Wildcat), and Apple only sells consumer-class graphics cards (NVidia GeForce, ATI Radeon). chimera needs stereo-in-a-window, instead of full-screen stereo, so the scientist can still use the dialogs to control chimera. If we figure out a reasonable way to keep the (mono) dialogs working in full-screen stereo, then we will support stereo on the Mac. (This also presupposes that most of the Tcl/Tk on Aqua bugs are fixed.) For some other thoughts about stereo hardware, see: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2004-September/ 000197.html> Greg Couch UCSF Computer Graphics Lab gregc(a)cgl.ucsf.edu ============================================ David M. Belnap Department of Chemistry and Biochemistry Brigham Young University Provo, Utah 84602 USA Phone: 801-422-9163 FAX: 801-422-0153 David_Belnap(a)byu.edu ============================================

2 1

release candidate
by Eric Pettersen 07 Feb '06

07 Feb '06

Hi all, We've put a release candidate (1.2199) on the web. Here's a list of changes and new features: http://www.cgl.ucsf.edu/chimera/docs/ relnotes/1.2199.html . If any of them appeal to you, please download the candidate and give it a whirl and let us know if you find any problems. The main motivation for getting this release out is so that web-fetching PDB files doesn't break in a few months (the previous release is using a legacy URL to the RCSB web site that will likely go away). --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

1 0

DMS installation
by Steven Finckbeiner 06 Feb '06

06 Feb '06

The Dockprep and WriteMol2 files worked like a charm. Could anyone give me any pointers on installing DMS? I have spent the better part of a day following the instructions on the web site and I can't get the damn thing to work. I've gotten this far: 2187 atoms usr/local/lib/dms/radii: no such file or directory Thanks again! "Sometimes, life hits you in the head with a brick." Steve Jobs ---------------------------------------------------------------- Steve Finckbeiner 132 Grace Cancer Drug Center Roswell Park Cancer Institute Elm and Carlton Streets Buffalo, NY 14263-0001 (716)845-5818 --------------------------------- Brings words and photos together (easily) with PhotoMail - it's free and works with Yahoo! Mail.

3 5