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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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