- Chimera-users - RBVI Mailing Lists

My anti-virus software detected a trojan in chimera
by Morais, Marc C. 15 Feb '11

15 Feb '11

Hi, I recently installed chimera 1.5.2 on my laptop (runs windows 7). It installed fine, but when my anti-virus software (Kaspersky) ran a scheduled scan, it claims to have found a trojan in the chimera installation. Specifically, it reports: Virus: HEUR:Trojan.Win32.Generic Location: C:\Program Files\Chimera 1.5.2\bin\ffmpeg.exe Is there a chance the program is actually infected, or is this just a false positive? Thanks, Marc

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dome/image seams
by Dougherty, Matthew T 14 Feb '11

14 Feb '11

I am getting image seams on some camera positions, attached. Any suggestions on how to minimize them? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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movie spatial sizes
by Dougherty, Matthew T 14 Feb '11

14 Feb '11

Normally I am generating movies at 640x480 or 1280x960. My graphics display is 2000x1500. I need to generate movies at 4000x4000 & 2000x2000. When I set the window size to 4000x4000 it limits it to the graphics display. How do I generate movies at the larger size? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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How to assign a unique chain ID to a receptor with two chains
by Qin Shao, Mr. 12 Feb '11

12 Feb '11

Hello I am currently using Chimera 1.5 to analysis docking simulation results from HadDock, because one of my receptor has two chains, it cannot be accepted directly. Through a communication to HadDock, I was advised that I should avoid overlapping numbering between the two chains and use a unique chain ID. Could you tell me whether I can do it on Chimera based on Windows platform, how to do it. Thank you very much. Best regards Dr. Qin Shao Montreal Neurological Institute McGill University Montreal, Canada

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Choose a specific rotamer
by Elisabeth Ortega 11 Feb '11

11 Feb '11

Hi all, I'm trying to do a script to display the "best" rotamer of all the rotamers that the funcion getRotamers give to me. I use the function useRotamers to display them but now I only want to display the rotamer with the less number of clashes and the highest number of h-bonds. I know that getRotamers return to us a list with all the rotamers of an aminoacid sorted by probability but I don't have any idea about how display only one of the rotamers. Anyone know how I can do it? Thanks in advance. Elisabeth Universitat Autònoma de Barcelona (Spain)

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zone
by Jean-Paul Armache 10 Feb '11

10 Feb '11

hello, there is a zone function for density maps+pdbs, which zones the map around the pdb in a certain radius. is it somehow feasible in chimera to do such thing with two pdbs ? what i mean is to zone a molecular model around another molecular model? (the reason for that is the speed, in which elaborate models are shown, sometimes zoning would be very useful for fast-checking). would be grateful for your help, best regards, jean-paul

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Showing actual electrostatic potential on surface
by Boaz Shaanan 10 Feb '11

10 Feb '11

Hi, Is there a way to show the actual potential value of a point on the electrostatic surface, say by pointing at it with the cursor, in an analogous way to the atom names that show up that way? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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3D with Nvideo
by Larry Simpson 09 Feb '11

09 Feb '11

I have a problem getting 3D with Chimera using a Quadro 600 video board on a Win7 64 computer. I am not sure what settings are required. Screen grabs are attached which show my current settings. Any assistance would be greatly appreciated. Larry

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Molecular weight of an EM map
by Tom Goddard 08 Feb '11

08 Feb '11

Hi Pu, Use the "Measure Volume and Area" dialog under menu Tools / Volume Data to show the volume in cubic Angstroms enclosed by your map contour surface. It will update automatically as the threshold changes. Make sure the voxel size of your map is set correctly in Angstroms because the reported enclosed volume uses that. That is set in the Volume Viewer dialog under the Coordinates panel. To estimate molecular weight from the volume you could use an approximate value for globular proteins from the literature of 1.21 cubic Angstroms per Dalton (Harpaz 1994). http://www.cgl.ucsf.edu/chimera/tutorials/eman07/chimera-eman-2007.html#par… Tom > Hi Tom, > > I have a question to ask you. > > I'm working on a 3D EM map from single particle reconstuction using Chimera. I > would like to know the total volumn of this 3D model or its molecular weight > when I change thresholds. How can I do it or where can I find this value? > > Best regards > > > Pu Qian

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Unrecognized command: "source"
by Pam Wang 08 Feb '11

08 Feb '11

Hi, I've just downloaded your program and was trying to run some alignments between two peptides. However, whenever I type in the command "source", I keep seeing the following error message: unrecognized command: "source" Could you please help me? I am able to run all the other commands, I just don't know why "source" is not recognized. Thank you, Pam Wang

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Script for positioning particles according the coordinates.
by Alexander MYASNIKOV 08 Feb '11

08 Feb '11

Dear colleagues, I would like to fit about 300 particles inside of the map according to it coordinates (X,Y,Z) what I have found before. Is it possible to make this procedure automatically, such that program would load one particle, shift it according to its coordinates (change pixel size if necessary) and so on? Thank you in advance, Alexander

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findclash "batch" calculations
by Elaine Meng 07 Feb '11

07 Feb '11

On Feb 4, 2011, at 2:51 AM, Julien wrote: > Hi Elaine, > I would like to find clashes between a ligand and a protein. I have around 100 000 poses of this ligands. > The information to get the poses are at the moment saved in a pdb file. Indeed three pseudo atoms are used to place the ligand in the correct position using the command match. > > The workflow would be the followin: > open ligand > open protein > open pseudo.pdb > > match ligand position1 > findclash > match ligand position2 > ... > > First, this is very slow, even in batch mode. Maybe you know a better way to do that. > Second chimera does not open more than 9999 residues, the pseudo pdb have nearly 100 000 residues. Is there a way to get around that. > > I guess the routine findclash calculates all distances brutally and compare them to a threshold. > many greetings > Julien Hi Julien, Findclash does calculate distances between atom centers, but the cutoff parameter is compared to "overlap" between the VDW spheres -- in other words, smaller atoms must be closer together than larger atoms to be considered overlapping or clashing. The output information (optional) includes both the center-center distances and the overlaps, however. You can limit the calculation to only certain atoms. There are also options to control cutoff and other settings. Details are here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> If you are really just using "findclash" without arguments, that would look at the whole structure and take more time than necessary. For example, if your ligand is model #0 and the protein model #1, one way to limit the calculation to only clashes between them and send info to the Reply Log is: findclash #0 test #1 log true Otherwise, I'm not an expert on any large-scale calculations or how you might optimize the procedure for large sets of atoms, so I'm CC-ing this question to the chimera-users list. (It is generally better to send Chimera questions to this list rather than to me personally.) The other users or developers may have good ideas. Best, Elaine ----- 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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Fixing registration for older versions of Chimera
by Eric Pettersen 07 Feb '11

07 Feb '11

Hi everyone, About 10 days ago I sent mail about upgrading to 1.5.2 to fix Chimera registration problems and promised a fix for older versions soon. That fix is now available from this page: http://www.cgl.ucsf.edu/chimera/fixreg/ It involves running a script on that page or, for the slightly paranoid cautious among us, downloading two files and putting them in your Chimera distribution manually. Thanks for your patience. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Rotamers
by Angelica Nakagawa Lima 03 Feb '11

03 Feb '11

Hi I can get the rotamers if I use the graphical version (when I click in tools -> Structure Editing -> rotamers). But I would like to do same thing with the comands. I used the comand swapaa (swapaa ile :10.a) and I write the pdb with the ile's rotamer (the most probable), however I would like to write the pdb file with the second most probable rotamer too. How do I do this? Thanks Angelica

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rotamers
by Ricardo Silva 03 Feb '11

03 Feb '11

I am using chimera program to view the rotamers list of pdb archive. I have proceeded from the following form: first I open an archive for chimera, later go to tools menu and alow: Structute Editing > Rotamer, after that i chose* rotamer type* and* rotamer library* then select aply and chimera display rotamers values and its respective probabilities. My objective is to save the rotamers list in an archive. Would like know how as can I make these procedures using the chimera commands. Thanks Ricardo

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surface hydrophobicity display
by Elaine Meng 03 Feb '11

03 Feb '11

Hi Sumitro, I did a little more digging for related information and thought I would share -- however, none of these methods are available in Chimera currently. Miguel Ortiz Lombardia has pointed out that the GRID program calculates a hydrophobic potential, and sent us the following links: <http://biop.ox.ac.uk/www/lj2000/noble/noble_02.html> <http://www.moldiscovery.com/docs/vsplus/grid.html> -- the following web server sounded promising, but apparently no longer exists: PLATINUM: a web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes. Pyrkov TV, Chugunov AO, Krylov NA, Nolde DE, Efremov RG. Bioinformatics. 2009 May 1;25(9):1201-2. <http://www.ncbi.nlm.nih.gov/pubmed/19244385> -- the following paper discusses what surface properties of the receptor correlate well with the types of nearby ligand atoms. If I understood it correctly, they looked at how successfully Coulombic electrostatic potential and the gradient in that potential can be used to identify hydrophobic areas of surface (areas that bind hydrophobic atoms in the ligand). Both were somewhat successful, but even better was a simple definition of hydrophobic surface as the part of the surface that is not close to hydrogen-bonding groups. This paper is fairly old and the data set of ligand/receptor structures small. Definition and display of steric, hydrophobic, and hydrogen-bonding properties of ligand binding sites in proteins using Lee and Richards accessible surface: validation of a high-resolution graphical tool for drug design. Bohacek RS, McMartin C. J Med Chem. 1992 May 15;35(10):1671-84. <http://www.ncbi.nlm.nih.gov/pubmed/1588550> -- then there are some other complicated functions based on molecular fragments and distances among them and to the molecular surface: A new approach to analysis and display of local lipophilicity/hydrophilicity mapped on molecular surfaces. Heiden W, Moeckel G, Brickmann J. J Comput Aided Mol Des. 1993 Oct;7(5):503-14. Estimating and representing hydrophobicity potential Fauchere et al. Journal of Molecular Graphics Volume 6, Issue 4, December 1988, Pages 203-206 If I understood correctly, these have many parameters and the functional form is not simple. It would not be straightforward to put them into Chimera. Finally, I also saw that the program MDL Chime has something called hydrophobic potential display, but I couldn't find a description of how it really works -- it might just be coloring whole amino acids by hydrophobicity value like Chimera does now, or atoms based on element. Elaine ---------- 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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rotamers
by Ricardo Silva 02 Feb '11

02 Feb '11

Chimera can be used to get rotamers from a selected residue of a given structure of protein and show such rotamers in a specific archive. I would like to know how to do it using a script(line commands) Thanks Ricardo

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rotamers
by Ricardo Silva 02 Feb '11

02 Feb '11

I am working in the development of a program that I need the possible rotameros (of one the 5 possible rotamers) for a set of amino acids and I would like to know as chimera can make this using the command line. Debtor, Ricardo

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rotamers_library
by Ricardo Silva 01 Feb '11

01 Feb '11

I have a archive .pdb and I woul like to obtain rotamers library using command Thanks Ricardo

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exporting the 2drms values
by Bala subramanian 31 Jan '11

31 Jan '11

Friends, I used Ensemble match command to calculate the 2rmsd of multiple pdb files concatenated in a single pdb file. I would like to know if there is any way to save the values (as a matrix). Precisely how to output the ensemble match values. Thanks, Bala

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Surface electrostatic and hydrophobicity.
by Sumitro Harjanto 28 Jan '11

28 Jan '11

Hi elaine, I've a few questions to ask about colouring surface by electrostatic potential and hydrophobicity: 1. I understand that I can use render by attribute to show surface hydrophobicity. But because it's a residue attribute, any surface of the same residue will be getting the same colour. Is there a way to calculate the surface hydrophobicity based on atoms in the vicinity instead of simply using the residue hydrophobicity values? 2. Because I have problem installing delphi, I have resorted to using the coulomb surface colouring tool. How different is this from the procedure of adding hydrogen, adding charge, then render by attribute ? Will I expect to see the same result ? Thanks elaine! 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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Error in SASA calculation
by Aditya Padhi 28 Jan '11

28 Jan '11

Hi Elaine, Hope you are fine. If you remember I was calculating per residue SASA using Chimera for my MD simulated protein. At that time it was working fine. But I did some more simulation run and now I want to calculate SASA for the entire trajectory but unfortunately Its showing the following error. *Error* Problem in per-frame script: IOError: [Errno 13] Permission denied: 'sas111.txt' File "<string>", line 3, in <module> See reply log for Python traceback. For your reference, I am giving the script also. It was working fine previously but with the same procedure which I followed this script is not working and showing the above mentioned error. * Script * from chimera import openModels, Molecule out = open("sas111.txt", "a") x='---------------------------------------------------------------------------------' for m in openModels.list(modelTypes=[Molecule]): for r in m.residues: try: sas = r.areaSAS except AttributeError: continue print>>out, r, sas print>>out,x out.close() Kindly help me. Thank you. Aditya.

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Chirality inversion ?
by R. Charbel Maroun 28 Jan '11

28 Jan '11

Hi everybody, Is there an easy and quick way to invert the chirality of an atom, say a Ca ? Greetings, ----------------------------------------- R. Charbel MAROUN, Ph.D., H.D.R. Neurobiologie et Pharmacologie Moléculaire Centre de Psychiatrie et de Neurosciences (INSERM U894/U. Paris Descartes) 2ter rue d'Alésia 75014 Paris FRANCE Tél. +33 1 40 78 92 77 Fax +33 1 45 80 72 93 e-mail charbel.maroun(a)inserm.fr ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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error message upon registration
by Boaz Shaanan 26 Jan '11

26 Jan '11

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1.5.2 release [fix for registration problem]
by Eric Pettersen 26 Jan '11

26 Jan '11

Hi everyone, As of a few days ago, the registration-verification certificate that has shipped with every version of Chimera for the last ten years expired. Consequently, any Chimera use after that would bring up the registration-request dialog regardless of how recently that version of Chimera had been registered. On top of that, the expired certificate caused new registrations to fail, so all you good people who were trying to help us out by registering your versions after this bug appeared were stymied. We have just released Chimera 1.5.2, which has a permanent fix for this problem. You can download it from: http://www.cgl.ucsf.edu/chimera For users who prefer not to upgrade immediately, we expect to have a solution for existing older versions in a week or less. We will send another email with details when that solution becomes available. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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