- Chimera-users - RBVI Mailing Lists

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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electrostatic potential in active site at an interface
by Boaz Shaanan 26 Jan '11

26 Jan '11

Hi I need your advice on the following: I have an active site which is located at the interface between two subunits. The cofactor in the active site makes interactions with residues from the two subunits. I have a few mutants and would like to display their effect on the electrostatic potential around the cofactor in order to explain changes in the activity of the enzyme. I have a electrostatic potential calculated both in apbs (.px) and delphi (.phi) on the basis of whole dimer structure. My first question is whether those potential maps are relevant for displaying in chimera the potential in an inner part of the protein or should I calculate the potential over the interface region that I'd like to be displayed. If the latter is correct my second question how do I get a surface (molecular or accessible) depiction of this region. I tried several options in chimera (following some examples in the gallery) but none seems to be doing it right. I probably miss something. I would be grateful for any clues on how to go about this. Thanks for your help, 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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rotation centers
by Benoit Zuber 26 Jan '11

26 Jan '11

Hi, I have a set of density maps and PDB models. I have displayed the maps side by side. Each map has a pdb model docked in it. I would like to make a movie where each map rotates around its Z axis. Each pdb should rotate around the Z axis of its respective map. I tried: set independent roll z The problem is that the center of the pdb models is not the same as the center of their respective maps. Is there a way to group one pdb with one map so that they rotate around the same center? Or is it possible to set the center of rotation of a PDB to the same value as the center of rotation of the map? Thanks in advance Ben -- Benoît Zuber MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH United Kingdom +44 1223 402209 bzuber(a)mrc-lmb.cam.ac.uk

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registration
by Francesco Pietra 25 Jan '11

25 Jan '11

I have replaced previous installation of CHIMERA with chimera alpha version 1.6 (build 32272) 2011-01-06 08:36:33 GMT. I have attempted to register at the request but the answer is that no regular installation is seen. So, at any start I have to kill the request. francesco pietra

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Chimera Question
by graemeg＠rci.rutgers.edu 24 Jan '11

24 Jan '11

Hello Chimera Feedback Team, For clarity and conciseness, I will jump immediately to my issue. I wish to import a CIF file of an inorganic crystal structure into the Chimera Program so that I can selectively eliminate certain atoms, and potentially create a video similar to one of the examples given on the website with a rotation and zoom into the meat of the structure. The file I import (.CIF) should have the proper symmetry group listed in addition to the lattice parameters of a unit cell, but when I try to generate a unit cell, the space group, cell size, and cell angles sections are blank, and therefore no copies can be made. Also, the viewing options give a choice between part ball and stick, part full atom, and essentially nothing else even with selecting the different presets. I know I am not working with PDB files but if there is anything in there that you could help me with, I would greatly appreciate it. Sincere Thanks, Graeme Gardner Graduate Assistant Rutgers University Department of Chemistry and Chemical Biology

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selection (from distance) among PDB files after docking
by Damien Larivière 24 Jan '11

24 Jan '11

Dear all, I have numerous PDB files resulting from a docking run. From crosslinking experiments, we know here that one way to select among all the solutions is to identify the PDB files for which the distance between some residues of interest is lower than a specific value: distance between Res 246 in chain B and Res 131 chain C < 17 A distance between Res 162 in chain B and Res 135 chain C < 24 A The two constraints must be respected. So, is it possible to write a script which: - opens one by one the pdb files, -calculates the two distances for the current pdb file, - send in the reply log the name-number of this PDB file if it respects the two constraints? Then, I would just have a look to the reply log in order to know the pdb files to study in depth. Many thanks for your help Damien

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Re: [Chimera-users] font size in pull-down menus
by Greg Couch 24 Jan '11

24 Jan '11

The font size of the menus matches that of other applications on Windows. To change the size, bring up the Display Properties dialog (right-click on background, or via the Control Panel), switch to the Appearance tab, and change the font size, then Apply to see the change. If you only want to change the menu font size and leave the fonts alone (e.g., the window names and the names of icons), you can click on the Advanced button, select the Menu item, and change the font size. -- Greg On 01/24/2011 05:56 AM, Boaz Shaanan wrote: > Hi, > > Is there a way to change the font size of the pull-down menus? For > some reason on the Windows (XP) v.1.5.1 they seem smaller to me. > Nothing in terms of graphics (or my eyesight) has changed since I > upgraded to 1.5.1 recently. > > Thanks, > > Boaz > > Thanks, > > 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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rotate command
by Alexandra Deaconescu 24 Jan '11

24 Jan '11

Hi everyone: I am sure this can be done in Chimera, but I just could not find the proper command - I want to simply rotate a pdb file by let's say 90 degrees. Now, if I want to also rotate a map (so both map and pdb at the same time), what would I use? Can anyone help? Many thanks!!! Bests, Alex Alexandra Deaconescu, Ph.D. ----------------------------------- Research Associate, HHMI c/o Grigorieff Laboratory Brandeis University http://people.brandeis.edu/~deacona For mail: Brandeis University 415 South St., MS 029 Rosenstiel Center Waltham, MA 02454 For packages (FEDEX): Brandeis University 415 South St., Kalman Receiving Dock Waltham, MA 02454

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how to delete saved state in the "savepos list"
by jinghua 21 Jan '11

21 Jan '11

The savepos is a very useful command to save the state of the graphics. But after a while, the "savepos list" contains a long list. Is there a way to delete some of the states in the list? Thank you in advance, Jinghua

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Display only selection
by Damien Larivière 20 Jan '11

20 Jan '11

Dear Chimera team, I'm identifying a complex between two proteins thanks to crosslink data. I have the following questions: 1/ I would like to select two residues that belong to two different chains and highlight them in the viewport. By using the sequence tool and then ctrl/shift+drag, I can select two residues (ex: 45 and 246 of chain A), they are highlighted in the view. But when I operate this way with res 45 of chain A and res 246 of chain B, only one remains highlighted in the view port. One way to sort this out would have been to rename all the chains with the letter A. But once the residues are highlighted, I have to measure the distance between them, then to make one chain active and then to move it and try to fit crosslink data (I hope I'm clear:-\ ). Is it possible to directly select and highlight in the viewport residues of interest belonging to different chains? 2/ Supposing that I can select and highlight in the viewport residues of interest belonging to different chains: How can I display only them in the viewport (and hide all the others)? The technical goal behind these questions is to better appreciate visually the distance between residues of interest and, thanks to the distance tool, to move one protein with respect to the other and fit crosslink data. Many thanks for your help. Damien

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Chimera 1.5.1 on CentOS 5.5
by Yohei Norimatsu 18 Jan '11

18 Jan '11

Hi all, I just installed the latest version of Chimera (1.5.1 x86_64) on CentOS 5.5. I'm having a problem with MSMS surface representation. It doesn't show the surface for all the atoms and it just looks messed up. I installed the same version of Chimera on RedHat Linux 5 and it works without any problem. I don't know what the problem is. Does anyone use Chimera on CentOS? Any comment is appreciated. Thank you! Yohei

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TZD Tautomer Distributions
by Nancy 17 Jan '11

17 Jan '11

Hi All, For pioglitazone, are the two tautomers depicted in the attached figure the major forms at pH 7.0? Also, are there any published articles, or other evidence that would confirm that this is indeed the correct tautomeric distribution at pH 7? Thank you, Nancy

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Fwd: distance between 2 residues
by Damien Larivière 17 Jan '11

17 Jan '11

Hi everyone, As explain in the Chimera user guide, I used the command such like distance #0.2:246@N#0.5:131@N to measure the distance between two atoms of interest. To be more explicit regarding my first email, it was necessary to re-edit the pdb file and to assign a model number to each chain. In the example above, the chain B is named model 2 (then model 0.2 in Chimera) and the chain D is named model 5 (then model 0.5 in Chimera). It works fine but I suppose that there is a simpler and more direct way to specify the chain in the command? Many thanks Damien -------- Message original -------- Sujet: distance between 2 residues Date : Mon, 17 Jan 2011 18:09:11 +0100 De : Damien Larivière <damien.lariviere(a)fourmentinguilbert.org> Pour : chimera-users(a)cgl.ucsf.edu Dear all, I would like to know the (mean or approximative) distance between two residues within a protein (let's say Res 5 of chain A and Res 246 of chain C). I suppose that I have to select one atom in each of the residues and use the Distance tool. I confess I have trouble to do so, either by picking in the viewport or by using the atom identifier. May you tell me a simple way to achieve such a distance? Many thanks for your help Damien

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distance between 2 residues
by Damien Larivière 17 Jan '11

17 Jan '11

Dear all, I would like to know the (mean or approximative) distance between two residues within a protein (let's say Res 5 of chain A and Res 246 of chain C). I suppose that I have to select one atom in each of the residues and use the Distance tool. I confess I have trouble to do so, either by picking in the viewport or by using the atom identifier. May you tell me a simple way to achieve such a distance? Many thanks for your help Damien

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Cavities
by Beale, John 12 Jan '11

12 Jan '11

Is it possible to find cavities in a protein structure using Chimera? Thanks in advance! John 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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Tautomer Prediction
by Nancy 11 Jan '11

11 Jan '11

Hi All, Using MarvinSketch v5.3.3 (ChemAxon software), the predicted pKa value of the acidic hydrogen on the thiazolidinedione ring of pioglitazone is 4.57 (see attached "Figure_1.gif"). Therefore, the predominant species at pH 7.0 predicted by MarvinSketch is the one depicted in "Figure_2.gif". The different tautomeric forms predicted by MarvinSketch are shown in "Figure_3.gif". Can anyone explain where these predictions come from, and if they are correct? Also, are there other programs that can accurately predict tautomeric forms? Thanks, Nancy

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