- 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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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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Per-atom RMSD
by Ibrahim Moustafa 08 Oct '10

08 Oct '10

Dear Chimera, I have a question regarding RMSD: I have two structures to superimpose using certain residues; and I am interested to get the RMSD value for each CA-atom in the structure. I wonder if there is a way to do that in Chimera? I think there is no direct way; but I wonder if there is a script that can be used for that. For the developer: It might be useful to have a tool that can directly do that in Chimera Many thanks for help, Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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Compatibility Question
by ayassin＠wadsworth.org 07 Oct '10

07 Oct '10

Hello, I have had some problems using chimera on a PC/Vista laptop with Intel graphis card. Any advice/experience on using chimera with PC/Windows7 laptop and NVIDEA graphics card? Is it better/more compatible/same type of problems? is it the PC or the graphics card? Thank you very much, any feedback will help... Aymen Yassin IMPORTANT NOTICE: This e-mail and any attachments may contain confidential or sensitive information which is, or may be, legally privileged or otherwise protected by law from further disclosure. It is intended only for the addressee. If you received this in error or from someone who was not authorized to send it to you, please do not distribute, copy or use it or any attachments. Please notify the sender immediately by reply e-mail and delete this from your system. Thank you for your cooperation.

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colour residue by value
by Sumitro Harjanto 07 Oct '10

07 Oct '10

Hi Elaine, I am looking into using CHIMERA to create a diagram. Each residue will be coloured according to an assigned value; say if the value is high, the residue will assume a bright red colour; if the value is low, the residue will be coloured light yellow; residue with a medium value will appear somewhat orange. So my question will be: is there a way to specify the colour of a residue by its RGB value? And how does the command look like (as I will be scripting to do it in large scale)? Thanks! =] Cheers, Sumitro Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."

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thousands of black rectangles?
by Brandt, Gabriel S. 06 Oct '10

06 Oct '10

Colleagues - Yesterday, I seem to have acquired a case of the Chimera measles. My proteins are being rendered with spots all over them. When I select any atom, all the spots are selected as well. I initially thought it was a problem with that particular PDB file, but formerly fine files all seem to have this problem. The issue seems like it arose spontaneously - I haven't recently updated any software that I'm aware of. I was running 1.2470 under X Windows (Mac OS 10.4.11). I downloaded a new version (1.4.1, Aqua) but the problem persists. Am I being foolish here? Is it simply a setting that I can change? G Malaria Research Institute Johns Hopkins School of Public Health 615 N. Wolfe St. W8704 Baltimore, MD 21205

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Re: [Chimera-users] [chimera-dev] some questions
by Elaine Meng 04 Oct '10

04 Oct '10

On Oct 4, 2010, at 7:44 AM, Gentile, Maria Antonietta wrote: > Hi, > I would have some information about CHIMERA. Is it possible to obtain the topology of a protein structure by using CHIMERA? How? And the second question is about the secondary structure representation of a protein, in my case wiht CHIMERA I am not able to visualize all secondary structure elements, how can I modify the settings for this problem? > Thank you > Hi Maria, I don't understand what you are asking, but I will try to answer. If by topology you mean give you some classification of what fold the protein has, no, Chimera does not do that. You might try using the "Dali server" or "Cathedral server" (google those) or something similar to compare your structure to a set of other proteins and report back which ones are the most similar. For the secondary structure, Chimera just uses the information in the input PDB file on which parts are the alpha-helices and beta-strands, and these are shown in the ribbon representation. If your structure doesn't have HELIX/SHEET information in the input PDB file, Chimera will run the "ksdssp" program to try to identify them. If you are not seeing helix and strand where you expect helix and strand, it might be that they HELIX/SHEET information in the PDB file is that way, or that the geometry is irregular/distorted so that "ksdssp" does not identify what you expect. EIther way, you could either (A) try re-running the secondary structure identification with different parameters (see the "compute SS" function in the Model Panel, which is itself in the Favorites menu, or the command "ksdssp") <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#functions> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html> (B) just manually change secondary structure assignments. Several ways are described in this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2007-April/001514.html> Elaine P.S. for Chimera questions the better address is chimera-users(a)cgl.ucsf.edu (chimera-dev is for chimera-related python programming questions). ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Minimization and dielectric choices
by r charbel maroun 04 Oct '10

04 Oct '10

Hi Conrad, Thanks for your answer. Don't worry, you needn't make a disclaim though. In my opinion, it's not a question of knowing which non-default option is more suitable for use in Chimera, but rather giving the user the choice to use the options that suit him, such as letting him choose the value of the dielectric constant, instead of forcing the value of 1, which would make minimization results useless, i.e. non realistic. It's not either a question of a full-blown MM/MD interface in Chimera, but I feel that the any decent program that does energy minimization should give the user access to steepest-descent *and* conjugate-gradient (CG) methods. Why? Because the 2nd is usually used after the 1st, given that the 1st, as the manual says, is very inefficient if the goal is to find a local minimum of the potential energy. And our purpose is to find energy minima and the conformations that are associated with. To the best of my knowledge, there is no server or free academic program doing energy minimization with these options. Introduction of the choice of dielectric constant and of CG would thus make Chimera rather complete and unique in this sense leading to an increased usage by the community of biocomputational people. Given that MMTK contains CG, what would it take to include the algorithm in Chimera ? Cheers, CM On Wed, Sep 29, 2010 at 8:54 PM, Conrad Huang <conrad(a)cgl.ucsf.edu> wrote: > Before I provide any answers, I have a disclaimer. I only have a > rudimentary familiarity with energy minimization and molecular dynamics. I > understand what force fields are and some of the algorithms used for > minimization and integration, but not much about the details of force field > options. My experience with MMTK is mainly playing with example scripts for > the excellent documentation. So, with that in mind, here are some answers > to your questions. > > The code in MMTKinter uses the Amber 99 forcefield with all default > arguments. THere is an "es_options" parameter that let's you control > electrostatic options, but I'll be the first one to admit that I do not know > which non-default option is more suitable for use in Chimera. The MMTK > documentation ( > http://dirac.cnrs-orleans.fr/Manuals/MMTK_reference/MMTK.ForceFields.Amber.…) > does not explicitly mention dielectric value or functional form for any of > the options. The code that creates the MMTK forcefield instance is in the > MMTKinter_makeUniverse method. (The MMTKinter class is actually designed so > that programmers can pass force field parameters through to MMTK, but > Chimera does not use this capability.) > > As for why only SteepestDescentMinimizer was used, it was mainly for > simplicity. The minimization options that Chimera provides is not very > extensive. Our intent is to provide a tool for simple clean up of small > (regions of) systems. That's why we chose to use default MMTK parameters, > infinite (non-periodic) universe, steepest descent minimizer, etc. The > scope of providing a full-blown MM/MD interface in Chimera is too large for > us to undertake. There are just too many degrees of freedom and we > currently do not have enough resources to do a proper job of it. > > If you are familiar with programming MMTK, there is another way of using > MMTK with Chimera. > http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts/MMTK describes an > approach where you can program mostly in MMTK, but display results in > Chimera. Obviously, this is mainly for programmers, but it does let you get > to the full power of MMTK along with visualization from Chimera. > > Conrad > > > On 9/29/2010 8:55 AM, r charbel maroun wrote: > >> Hi everybody, >> >> The value of the dielectric constant used by Chimera is 1, corresponding >> to calculations in vacuo. Is there not an easy way to change this value >> to, say 78 or to include a sigmoid function or the Generalized Born >> approach so as to mime the presence of the solvent ? I looked for it but >> couldn't find it : where in the >> {chimera_install_location}/share/MMMD/MMTKinter.py file can the value of >> the dielectric be changed ? Otherwise, how to mime implicitly the solvent >> ? >> >> Also, it seems that only the Steepest descent, and not the Conjugate >> gradients method, for energy minimization has been implemented in >> Chimera. Why is this so? >> >> It'd be so nice to have these two functionalities added as I don't know >> of any free academic program allowing us to do energy minimization with >> these options without having to parametrize every new ligand (Charmm, >> Namd), a painful task. >> >> Cheers, >> >> Charbel >> >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > -- R. Charbel MAROUN, PhD, HDR Neurobiologie et Pharmacologie Moléculaire Centre de Psychiatrie et de Neurosciences Broca-Sainte Anne (INSERM U894) 2ter rue d'Alésia 75014 Paris FRANCE Tél. +33 1 40 78 92 77 Fax +33 1 45 80 72 93 e-mail rmaroun(a)gmail.com charbel.maroun(a)inserm.fr

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pseudo bonds in mol2 files
by Francesco Pietra 01 Oct '10

01 Oct '10

I am confused about the meaning of pseudobonds for the aromatic portion of mol2 files. Typical example sustiva.mol2 in the antechamber-sustiva tutorial b4 of amber. I have the same representation for aromatic bonds in modified amino acids. In contrast, normal bonds from pdb files of the same molecules. Thanks for clarifying. francesco pietra

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multiple frames 1topology
by Francesco Oteri 30 Sep '10

30 Sep '10

Dear AMBER users, I've one file with the AMBER topology of my system, but I saved some rappresentative structures as pdb. Since my system is made of a set of circular DNA, I'd manipulate pdb to obtain the correct connectivity. There is a way to load a correct pdb ( or topology file) and exporting this connectivity on the other pdb? For example, should be useful if I load at the beginning the correct pdb and than I'will load the remaining structure whit the same number of atoms of the first but without CONECT and/or TER tag.

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Finding the angle between two aromatic rings
by Miriam Gochin 30 Sep '10

30 Sep '10

Chimera has an Axes / Planes function where you can define the plane through three atoms. If you define two planes, is there a way to get the angle between the planes? Thanks! Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

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