October 2010 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Chimera surfaces
by Tom Goddard 28 Oct '10

28 Oct '10

Hi Vijay, The MSMS molecular surface calculation (Actions / Surface / show) fails on some molecular models. The mailing list describes some tricks that might make surface calculation work: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-January/004713.html An alternative is to use a Gaussian surface instead of the MSMS solvent excluded surface, using the command (Favorites / Command-Line) molmap #0 3 gridSpacing 0.5 to make a 3 Angstrom surface for molecular model #0. Then use the Color Zone dialog (menu Tools / Volume Data / Color Zone) to color the surface to match selected atoms within a specified distance from the atoms. You can select all the atoms with menu Select / Select All or use command "select #0". The Gaussian surface doesn't look much like a solvent excluded surface -- it puts a Gaussian at each atom position to compute a density map. If you prefer the solvent excluded surface then look at the above mailing list message for suggestions. Tom > Hi Tom, Greetings, Hope all is well > > I have a question about generating surfaces. When I load a simple PDB > and try to display surfaces... by selecting a molecule, > > Actions/Surface/Show > > I get the error Surface calculation failed, mscalc returned code 2 > > I could always generate a surface using multiscale models in HIgher > order structure... But how can I can color the surface corresponding > to different region of the protein surface (corresponding to few > residues) in selected colors. > > Many thanks, > > Kind regards > Vijay > > ======================================== > Vijay S. Reddy, Ph.D. > Associate Professor > Department of Molecular Biology, TPC6 > The Scripps Research Institute, > 10550 North Torrey Pines Road, > La Jolla, CA 92037 > > ======================================== > > > > > > > > > > > > > >

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misconfiguration error in just one user account
by Harry Kao 28 Oct '10

28 Oct '10

On a linux workstation, a particular user is receiving the following error message when starting up Chimera: Display misconfiguration. Please increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card. Also see chimera installation instructions. This error message happened after a previous Chimera session crashed. The user had about 10 models open. The display setting is already at 24bit, and the workstation has the correct Nvidia driver. Here is what we tried: 1. On the same workstation, under a different user account, Chimera starts up fine, no error message. 2. I created a new empty user directory, Chimera starts up fine the first time and the user can re-open models he was working on. However, the error message returns in the next Chimera session. Based on the observation, I am assuming there is a user-specific configuration/preference file that Chimera reads when starting up. Perhaps in that file, some display parameter is being corrupted? If so, where or how can I find and fix or delete such files? Thank you. Harry

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Selecting atoms
by Peter Baker 28 Oct '10

28 Oct '10

Good Morning. I am trying to display the H atoms in the para-position of the all the Phe residues. Could anyone offer me some advice on specific key commands which would help me out. I have tried da: phe@ cz but I was not successful . Thanks Peter.

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help with surfnet results
by saumyak＠ebi.ac.uk 27 Oct '10

27 Oct '10

Hello, Thanks for the reply. I was able to separate all the blobs. I have a new query now. I am trying to retrieve the residues that surround one of the predicted binding pockets by Surfnet. I tried the command #1: za<8.0, but it doesn't work as it needs specification of an atom from which it will calculate the zone. In my case, there is no small molecule that can be used as reference. I want to select and highlight all the residues that surround that predicted pocket. Please suggest how this can be carried out. Thanks, Saumya

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.dx file problem
by Greg Friedland 27 Oct '10

27 Oct '10

Hi, I'm trying to load an electrostatic potential file (.dx) that I created with the online APBS tools. Nothing displays however when I select "color" from the "surface color" dialog. Is this feature working in the current version? I'm using version 1.4.1. The potential file is http://dl.dropbox.com/u/5763765/pot.dx.gz Thanks, Greg

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Raytrace VDW surface with POV-RAY
by #MAZIAR SOLEYMANI ARDEJANI# 26 Oct '10

26 Oct '10

Hi All, Is there a way to have VDW surface in images being ray traced by POV-RAY? Right now, when I ray trace the image using POV-RAY the VDW surface disappears in the generated figure. So much thanks in advance, Maziar

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Waters of hydration in a protein
by Beale, John 26 Oct '10

26 Oct '10

I am conducting molecular dynamics simulations on a protein in explicit water. I would like to be able to determine the positions of waters of hydration of the protein at the beginning and then at various points along the MD trajectory. What I need to do is locate the position of a water molecule that is hydrogen bonded to a given amino acid and somehow tabulate the positional data. Is there a way to do this in Chimera? Thanks! John M. Beale, Jr., Ph.D. Professor of Medicinal Chemistry and Pharmacognosy Saint Louis College of Pharmacy 4588 Parkview Place Saint Louis, Missouri 63110 314-446-8461 Cell: 314-315-0409 FAX: 314-446-8460 jbeale(a)stlcop.edu<mailto:jbeale@stlcop.edu>

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help on virus visualization
by jh 26 Oct '10

26 Oct '10

Dear all, I want to mask area outside certain surface and to visualize the inner capsid of a virus by Chimera. Anyone would be kind to help me with that? C.J.

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Label all atoms except hydrogens
by Michael Day 21 Oct '10

21 Oct '10

How would I label all atoms in a structure without labeling hydrogen atoms? I'm trying to label a small molecule with about 60 non-hydrogen atoms. Cheers, Mike <<< ------------------------------------------------------------------------>>> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125 <>< <>< <>< <>< <>< <>< <>< <>< <>< <>< Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday(a)caltech.edu <<< ------------------------------------------------------------------------>>>

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Fwd: Re: GLXBadRenderRequest
by Greg Couch 21 Oct '10

21 Oct '10

(Forgot to reply to list.) -------- Original Message -------- On 10/18/2010 01:56 PM, Gough, Erik S wrote: > > Hello, > > I am receiving the following error when I try and open a structure > running chimera with Mesa 7.0 on Debian 5. > > X Error of failed request: GLXBadRenderRequest > > Major opcode of failed request: 148 (GLX) > > Minor opcode of failed request: 1 (X_GLXRender) > > Serial number of failed request: 5334 > > Current serial number in output stream: 5336 > > I am assuming that this is related to running an older version of the > Mesa driver, but I do not have root on the system and the > administrators are hesitant of upgrading the Mesa package in /usr/lib > to anything beyond the stable release. The servers do not have > access to any hardware based video so doing an updated hardware based > driver install won't help either. I am limited to what I can do and > only have access to my home directory. Would it be possible for me to > compile a newer version of the Mesa driver in my home directory and > then compile chimera to use that version of the driver instead of the > default in /usr/lib? > > Thanks! > If the Debian 5 system is a server, I would remote mount my home directory on my workstation with the hardware graphics driver, and run chimera locally. Or you might be able to copy libGL.so from your workstation to a directory in your home directory on the server and set the LD_LIBRARY_PATH environment variable to that directory. If the Debian 5 system is supposed to be a workstation, I would be very tempted to reboot it with a Ubuntu Live CD and when done, reboot it back to Debian 5, or maybe the administrators would be willing to make it a dual-boot system. Your idea, of compiling a software-only version of Mesa, should work if you set the LD_LIBRARY_PATH environment variable appropriately. In the LD_LIBRARY_PATH cases above you would need to start chimera from the command line after setting up the environment or start chimera after editing the CHIMERA/bin/chimera shell script. Hope this helps, Greg

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Chimera-users October 2010