- Chimera-users - RBVI Mailing Lists

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 25 Oct '10

25 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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Fwd: Re: stereo LCD display
by Greg Couch 21 Oct '10

21 Oct '10

(Forgot to reply to list.) On 10/20/2010 09:02 AM, Wu, Weimin (NIH/NIAMS) [E] wrote: > We are planning to buy a stereo LCD display system. Most of time we will use it to visualize the density map and PDB structure in Chimera. We want a LINUX 64bit system. Has anybody got experience on it? Would you please tell me the specifications of your hardwares? How about Miracube G240? The Miracube is a good product, see our tech note about the Miracube at <http://www.cgl.ucsf.edu/Outreach/technotes/miracube.html>. A Zalman display is an excellent, inexpensive, alternative, and both will work with gaming graphics cards (NVIDIA GeForce and AMD/ATI Radeon). But I would recommend a display where you don't lose half of the vertical resolution, that way the 2D dialogs are readable when you are looking at the 3D stereo image. For that, you will need a workstation graphics card, a NVIDIA Quadro/Quadro FX or a AMD/ATI FirePro/FireGL, and a suitable display: (1) The Planar 3D/Stereoscopic displays use passive glasses, like those that movie theater's use, and will work with both NVIDIA and AMD/ATI workstation graphics cards. (2) 120Hz LCD displays, with active glasses, like what many 3D televisions use, work well too (we have a Samsung 2233RZ that we like). NVIDIA has temporarily cornered this market. For a list of displays, see <http://www.nvidia.com/object/3d-vision-requirements.html>, but for a list of compatible workstation graphics cards, see <http://www.nvidia.com/object/quadro_pro_graphics_boards.html> (and in your case, click on the "Linux customers" link). NVIDIA has just released a "Pro" version of its stereo glasses, and the supported displays are slightly different, see <http://www.nvidia.com/object/3d-vision-pro-requirements.html> for details. I believe that option 2 is currently cheaper, but look at the total cost of the graphics card, glasses, and display for comparison. Planar claims that "flicker from active glasses can cause eye fatigue, headaches and other discomfort", but I have not experienced that, but I have not looked at a stereo display all day either. Hope this helps, Greg

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Chimera on iPad?
by Claire Birone 21 Oct '10

21 Oct '10

Hi all, I'm wondering if anyone has been running Chimera on an iPad. I'm a high school teacher using the software to help students build 3D protein models, and my class has access to iPads. Unfortunately, I haven't had success trying to get Chimera to run on the iPad. Is anyone running it on an iPad? And if so, how do you feel it compares to using it on a computer? Thanks! Claire

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help with Surfnet results
by saumyak＠ebi.ac.uk 20 Oct '10

20 Oct '10

Hello, I am using Chimera to identify binding sites in a protein structure using Surfnet, but I am unable to save the Surfnet results. Is there a way to save the Surfnet results (the density maps). Also please can you suggest a method to generate a list of all the disconnected blobs with their respective volume information that is implemented in Chimera. Many Thanks, Saumya

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Error: no molecule for surface
by Andrea L Edwards 20 Oct '10

20 Oct '10

I am trying the "Write DMS" tool for my molecule, and I get an error that says "no molecule for surface". I followed Actions->Surface->Show then I followed Tools->Structure Editing->Write DMS. -A

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Fusing or bonding two protein chains?!
by #MAZIAR SOLEYMANI ARDEJANI# 20 Oct '10

20 Oct '10

Hello, All! I have created a pdb file by putting two protein structures close to each other through rotation and translation; so that N-terminus of one is close to the C-terminus of the other. I would like to link one protein's C-terminus to the other protein's N-terminus, i.e. to create a peptide bond between two protein chains and then save the fused protein structure as a pdb file with a single chain. Is there a way to do this in chimera? Can Chemira reset atom numbers and the residue and chain names? Thanks in advance and best regards, Maziar S. Ardejani SPMS-CBC-04-37, The Orner Lab Division of Chemistry and Biological Chemistry School of Physical and Mathematical Sciences 21 Nanyang Link Nanyang Technological University Singapore 637371

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