- Chimera-users - RBVI Mailing Lists

morphs
by Moses Adenaike 17 Apr '14

17 Apr '14

Hello Chimera users, Is there a way to make a morph between two PDBs that don't have the same amount of atoms or chains. For example, I want to morph between an enzyme bound to DNA and one without DNA. Moses

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call file-> open gui popup from script ?
by Katrina Lexa 17 Apr '14

17 Apr '14

Hello All, I’m wondering if there is a way to call the file->open popup within chimera when running a python script? I know that it’s possible to run the script on the command line and read the desired arguments in that way, and obviously the files I want could be coded in and then changed every time I want to look at something new, but I’m not seeing an obvious option from the mailing list or in the runCommand list for writing in a mid-script call for the user to select a file. Is such a thing possible? Thanks for your help, -- Katrina

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Doubts regarding building a structure using Build Structure option
by Garg, Ayush A. 16 Apr '14

16 Apr '14

Dear Developer I was working with with UCSF Chimera. I was trying to reproduce structure 1V4S - Glucokinase structure using the Build Structure option under the tab Structure Editing in Tools. I have the sequence of the 455 amino acids and also know the sequence which is alpha helix, beta helix but the sequence of connectors between these structures is not a secondary structure. I was wondering how to reproduce those using your structure builder option. I have attached a word file with the sequence and the image of 1V4S in UCSF Chimera. I hope that will help you understand my doubt better. Thank and Regards Ayush Arpit Garg Graduate Student Ohio State University

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Working with several proteins
by Navya Shilpa Josyula 16 Apr '14

16 Apr '14

Hi, I am working on a set of 400 proteins and for all these proteins I have specific list of amino acid residues. I wanted to know if there is any available script or a command to get the following 1. atomic areaSAS 2. atomic B-factor values 3. CASTp identified pocket residues and 4. CASTp identified pocket volumes for all the residues of these 400 proteins to be written in a single file. Kindly help me at your earliest. Thank you in advance for your help. Regards, Navya

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Relevant interacting amino acids between molecules
by Ogunniyan, Abisola 15 Apr '14

15 Apr '14

Hi, My name is Abisola Abisoye-Ogunniyan, a first year Biology Graduate student in Tuskegee University. I got to learn about the use of Chimera in my Biochemistry Class. I have been having difficulty in trying to determine the relevant interacting amino acids between molecules. Please, I will really appreciate it if this is made clearer to me. Thank You. Best Regards, Abisola Abisoye-Ogunniyan.

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Structure editing: addH
by George Tzotzos 10 Apr '14

10 Apr '14

Hi everybody, I’ve been trying to add hydrogens to a ligand (7-octenoic acid) obtained from docking. Hydrogens are added but not on the carboxyl group. I’m attaching the ligand.pdb for easy reference. I’d appreciate any suggestions regarding this behavior Best regards George

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Request for guidance
by MUHAMMAD RAMZAN MANWAR 08 Apr '14

08 Apr '14

Dear Dr. Ferrin, Hope this email finds you the best of your health. First of all, I did appreciate the effort that You and Your team did in the form of UCSF Chimera. Being the part of academic/government university, I have used Chimera tool for protein modeling and cited in my two articles: one published in JCB-Wiley and other in Hundawi in 2014. Current email I am sending to request for guidance about how can I substitute an amino acid (wild type to mutant residue) within protein 3D model by using Chimera. I will be thankful for your guidance, if possible. With regards Hussain MR PACER-HD, KAU, KSA

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Surprising "measure symmetry" result
by ingvar 08 Apr '14

08 Apr '14

Hello, I fetched entry EMD-2463 from EMDB and issued: measure symmetry #0 nMax 24 and got the result "Symmetry emd_2463.map: C13, center 64 64 37" Increasing the number of sampling points does not change the result, but if I increase the correlation criteria a little, to say 0.992, I get the expected C12 symmetry. Also if I change the contour level to 0.05, the author recommended level, I get C12 again. Looking at the volume at several different contour levels, it is difficult to see how it could be considered C13, and also how it would go from C13 to C12. Kind Regards, Ingvar Lagerstedt -- Ingvar Lagerstedt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD Tel: +44 (0)1223 492533

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Docking ligands and protein using Chimera
by Sook Wong 08 Apr '14

08 Apr '14

Good morning, I am currently doing research with a professor for protein-ligand structure and would like to dock the receptor molecule (pdb file of the protein) and ligands (pdb file of the sugars). Since I have both the structure files from Chimera, how would I predict and assume which orientation bound to each other forming a stable complex? Looking forward to hear from you. Thank you so much! Sincerely, Sook Y Wong Chemical and Biomolecular Engineering '14 A. James Clark School of Engineering University of Maryland, College Park, MD 20742 swong18(a)terpmail.umd.edu

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Calculating SAS and SES with Chimera-MSMS wrap
by Jaime Rodríguez-Guerra 07 Apr '14

07 Apr '14

Dear Chimera dev team, I am trying to use your MSMS wrapper to compute some SAS/SES values for a given set of atoms. As suggested in a previous post in this list, I've taken a look into Measure.measure.buried_area() and I think I've got it, but just wanted to make sure. Here is my current procedure: ``` import chimera, Measure, MoleculeSurface atoms = chimera.selection.currentAtoms() xyzr_data = Measure.measure.atom_xyzr(atoms) surfaces = MoleculeSurface.xyzr_surface_geometry(xyzr_data) for i, a in enumerate(atoms): print "Atom: {0}, SAS: {1}, SES: {2}".format(a.name, surfaces[3][i,0], surfaces[3][i,1]) ``` Is this OK? I don't know how to handle all that output that MSMS is giving back! Thanks in advance, Jaime.

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