October 2010 - Chimera-users - RBVI Mailing Lists

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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stereo LCD display
by Wu, Weimin (NIH/NIAMS) [E] 20 Oct '10

20 Oct '10

Dear All, 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? Thanks, weimin

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Converting EM map to SAXS bead model
by Tom Goddard 19 Oct '10

19 Oct '10

Hi Alexander, I have talked to someone (forgot name, at Grenoble EM fitting workshop a year ago) who was interested in computing SAXS profiles for EM blobs of unknown proteins and your EM2DAM program could make that possible. It might also have utility in analyzing EM maps. I wonder about details like how how far apart are the dummy atoms placed. Is documentation for the program available? About 9 months ago I added to Chimera the ability to compute a SAXS profile from an atomic model which is then plotted against an experimental profile. The idea is that you could test various atomic model conformations to see which is most compatible with SAXS data. Since then YZ in our lab has added new options and made it work using a web service in addition to the option of running a local program. This is in Chimera daily builds but not in the 1 year old Chimera 1.4 production release. We will have a Chimera 1.5 release soon that will have it. It uses FoXS (http://modbase.compbio.ucsf.edu/foxs/about.html) for the profile computation. Here's a description from the Chimera User's Guide of the Chimera user interface. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/saxs/saxs.html Tom > Hi Tom > > First of all, thank you very much for very helpful comments. > Although thanks for such a nice tool as Chimera! > > The reason I was asking all questions about volume viewing and MRC > file format is that I am developing a tool that converts > EM density maps to dummy atom models (EM2DAM). Bead models (PDB format) > can be used by other software to validate EM models for example. > > You can read more here: > http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg17870.html > > I like Chimera a lot. And if you be interested in integrating/using em2dam > (fortran90) in Chimera, let me know. > > Btw, could you comment on SAXS function in Chimera? > > Kind regards from Hamburg > Alexander >

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Problem adding charges to RNA
by Andrea L Edwards 19 Oct '10

19 Oct '10

When I try to add charge to the RNA molecule, I get a message that says "Please specify the net charges for the above residues so that their atomic partial charges can be computed." And above the message it lists every residue in my molecule. What do I do? I cannot find anyway to specify the net charges, and I though that this script was going to assign the charges anyway, so why do I need to specify them before hand? -A

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GLXBadRenderRequest
by Gough, Erik S 18 Oct '10

18 Oct '10

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!

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Molecule fusing
by Brian & Lanie Grech 16 Oct '10

16 Oct '10

Hi Sir/Madam I want to create models which consist of multiple protein molecules, in which the individual protein molecules are fused together to form a single structure. Something like the scanning 3D maps produced by electron microscopes. Is it possible to do this with the Muliscale Models tool or some other tool or method in Chimera? An example of what I want to do appears in the cutaway rotavirus illustration (Fig. 1A) in Chen and colleagues paper, titled, "Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM" (PNAS, vol. 106. no. 26, p. 10644). In this illustration the yellow triangular shaped structure are multiple VP7 molecules fused together. Regards Brian Grech

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Chimera-users October 2010