June 2016 - Chimera-users - RBVI Mailing Lists

vector from atom
by Fabian gmail 29 Jun '16

29 Jun '16

Hi, I have an ion in a membrane transporter which I am simulating in MD, now, I need in order to pull the ion outside the transporter to use a vector to identify a water molecule which is exactly in the direction of the exit tunnel. For that purpose I need to draw such a vector or to at least identify a water molecule in the right direction. Can Chimera help me with that? I mean is there a way to identify which water is on the exact pathway of the ion exit? How can I do it? Thanks a lot in advance, Fabian Fabian Glaser Head of the Structural Bioinformatics section Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa 32000, ISRAEL fglaser at technion dot ac dot il Tel: +972 4 8293701 http://bku.technion.ac.il

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Transfer of the selection from reference to the ensemble
by James Starlight 29 Jun '16

29 Jun '16

Dear Pymol Users! Within the Pymol session I have 2 loaded superimposed objects: 1) one experimental pdb consisted of protein with co-factors (ligand and metals); 2) ensemble of 20 MD snapshots of the same protein (superimposed on each others) without any cofactors; For my particular task I need 1) to copy the selection (which include metals and ligand atoms) from the reference structure to each model of the MD ensemble (via Pymol), 2) make quick geometrical optimization of side-chains (I guess it better to do it using Chimera) within the active side of each model from MD ensemble 3) perform post-processing - analysis of the distances between cofactors and optimized side-chains of each MD conformers to obtain statistical distribution of averaged distances (I guess it better to do it via some MD software like Gromacs). I will be very thankful for any suggestions for practical realization of those steps! James

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Highlighting the H bonds during simulation
by Natesh Singh 28 Jun '16

28 Jun '16

Dear Sir, How could I highlight the formation and breakdown of Hbonds with the ligand to that of residues during the md simulation. I tried using the script (per-frame commands) chain @ca ~disp solvent hb line 2 color yellow reveal true Using this command, highlights all Hbonds in the system during the simulation, but I would like to see only Hbond interactions with ligand to that of nearby residues. How could I do this? what would be the appropriate per-frame script? Looking forward for the guidance. Best regards, Natesh Uni.Wien

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tmp files for MAC OS
by James Starlight 27 Jun '16

27 Jun '16

Dear Chimera Users! I am interesting where actually Chimera saves various tmp files produced by various analysis and post-processing tools on my MAC X OS? For instance I made calculations of residue contacts using network method from MD ensemble tool and would like to obtain txt files of residue pair contacts (on Linux it usually saved in tmp folder). Thanks for help! Gleb

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opening large xyz file
by Michał Kadlof 27 Jun '16

27 Jun '16

Hello, I'm trying to open a xyz file that contain ~66000 entries (1.7 MB). Chimera hangs and rapidly allocates huge amounts of RAM (more than 60 GB) which is close to limits of my PC, is it normal? Is there any "rescue mode opening" that wouldn't search for bonds to render and/or would show particles as dots or 2D disks instead of ball? My system is spatially small and probably Chimera is trying to search all-to-all particles to render bonds between them, but I do not need this. Is there any way to prevent this behaviour? -- best Michał

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(no subject)
by Nicole Mckinney 27 Jun '16

27 Jun '16

Hi I was wondering if you can tell me why my cell phone has chimera modules installed into the internal storage if I did not download and put them there

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Chimera question
by Smart Biology 24 Jun '16

24 Jun '16

Hello, I understand Chimera is for non-commercial use only. We would like to use this program simply to open a .map file and export as .obj for use in another 3D modelling program, for commercial use. Would this be allowed, or do we need to obtain a licence for commercial use? We have been looking throughout the web for the past few days and your program is the only way we have come across to convert .map to .obj. Thank you, Andrew -- Andrew Catalano, PhD Science and Animations Director Smart Biology www.smart-biology.com <https://www.smart-biology.com/> email: info(a)smart-biology.com <https://www.linkedin.com/company/smart-biology?trk=top_nav_home> Linkedin-Email-Signature

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Solvent Accessibility of Amino Acids
by Eric Berg 24 Jun '16

24 Jun '16

Hello, I've been spending some time trying to determine solvent accessibility for certain regions of protein complexes. I need something that is precise enough to determine the solvent accessibility of individual amino acids within a selected region (or the entire complex). There are a few tools online, but so far I haven't found something that does this. Does Chimera currently have a tool for measuring solvent accessibility of individual amino acids? Eric Berg

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default directory for opening files
by Dougherty, Matthew T 24 Jun '16

24 Jun '16

Starting chimera without a session file, I would like to use the open pulldown menu. The default directory is at root "/". If I use a 'cd somedirectory' command and open with the gui, it still defaults to the root. Is there a command that will set the open/save directory for the gui? If not, a way in python? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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Module import error
by Subha Kalyaanamoorthy 24 Jun '16

24 Jun '16

Hi There, I am trying to call a script with Chimera commands(saved as sample.py file) in another python program using os.system("chimera --nogui --nostats sample.py") and I get an module load error as below, import chimera ImportError: No module named chimera However, if I call the script with chimera it works, for eg., chimera --nogui --nostats sample.py typed directly in terminal is working. Can anybody help fix this error? Thanks in advance, Best Regards, Subha

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Chimera-users June 2016