- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] CCL: trimer from monomer
by Elaine Meng 01 Nov '10

01 Nov '10

Hi Kshatresh, In Chimera there are several ways to get the trimer from the monomer. It depends what information is included in the PDB file. The "biological unit" is supposed to be described in BIOMT records, but many PDB files do not have useful BIOMT records, only an identity matrix. If the PDB file does contain useful BIOMT records (example: 1hxx), you can use the command sym or the "Multiscale Models" tool. For example, if the structure is open as model 0 you can simply use the command: sym #0 A PDB file can also contain various other matrices that describe crystallographic symmetry and the unit cell, which may or may not bear any relationship to the biological unit. These other matrices can also be used by the sym command (it has options), the Multiscale Models tool, and the Unit Cell tool in Chimera. If none of the information in the PDB file makes the trimer, you might also try fetching the predicted biological unit for that PDB entry from the PQS database. That can be done using Fetch by ID in Chimera (see the File menu). Documentation... http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemu… http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.… http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/fetch.html I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 1, 2010, at 2:07 AM, Kshatresh Dutta Dubey kshatresh#,#gmail.com wrote: > Dear all, > I want to model a simulate a protein which is found in trimeric form, but unfortunately i have only monomer of that protein. Can anyone suggest me how to model a trimer from a monomer. Kindly also suggest me modelling software which can do this. I have maestro, chiemera and VMD. > Thanks in advance > Regards > Kshatresh Dutta Dubey

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viewing of trajectory
by atila petrosian 01 Nov '10

01 Nov '10

Hi chimera users I did simulation of protein by gromacs. I want to see my trajectory during simulation by a viewr other than vmd, such as chimera. How and what files is needed for that? -- Atila Petrosian Ph.D. student of BioPhysical Chemistry University of Oulu,Finland

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Fwd: ribbon causes coordinates changing
by Francesco Oteri 30 Oct '10

30 Oct '10

Dear chimera users, I've a problem with ribbon. I've a DNA molecule where the two last base pair is an uncommon T-T pair. When I select these bases to display the ribbon, the coordinateds of the last atoms are changed. Seem that the new position are the end of the ribbon. The chimera version I'm using is 1.5rc1 on a windows7 PC. I attacch the session that represent my problem. The session is saved such to visualize the problem: look at the end of the blue and red ribbons to detect it.

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ribbon causes coordinates changing
by Francesco Oteri 30 Oct '10

30 Oct '10

Dear chimera users, I've a problem with ribbon. I've a DNA molecule where the two last base pair is an uncommon T-T pair. When I select these bases to display the ribbon, the coordinateds of the last atoms are changed. Seem that the new position are the end of the ribbon. The chimera version I'm using is 1.5rc1 on a windows7 PC. I attacch the session that represent my problem. The session is saved such to visualize the problem: look at the end of the blue and red ribbons to detect it.

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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 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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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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Relax H-bond constraints
by Joern Lenz 15 Oct '10

15 Oct '10

Hi, I used the automated H-bond detection of Chimera to detect H-bonds between an target protein and its docked lignds. On your webpages (http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbon…) I found the following: "[...] Relax H-bond constraints indicates that tolerances to Relax constraints by should be applied to the precise geometric criteria [...]; empirically, tolerances of 0.4 angstroms and 20.0 degrees work well for most macromolecular structures." Can you lease tell me if there is a literature which discusses this relaxation in more detail and can be referenced Many thanks for a reply. Cheers Joern

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