April 2013 - Chimera-users - RBVI Mailing Lists

Generating trajectory of a user-defined plane
by Lili Peng 18 Apr '13

18 Apr '13

Hi, I am interested in measuring the deviation of an helical segment with respect to the initial structure in a GROMACS trajectory. I have already uploaded my *.tpr and *.trr files into MD Movie and have defined a plane through the helical segment within the initial structure. Is it possible to define another plane through the same helix and track the intersection angle throughout the trajectory? Thank you, Lili

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python script running OUTSIDE chimera possible?
by frederick lee 18 Apr '13

18 Apr '13

hello chimera experts, as far as i know, python scripting for chimera is done within the context of chimera like chimera --nogui myscript.py parameters ... is it possible to run myscript.py without the need of the chimera executable and use import statements of some sort to access the chimera module(s) like python myscript.py parameters best regards, fred

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selecting amino acids and labeling
by Gonzalez, Mireya 18 Apr '13

18 Apr '13

To whom it should concern I am working on some docking structures. Previously I used to have Quimera version 1.7 installed in my computer. Recently I downloaded the version 1.8 but I am having problems identifying the amino acids that are in contact with my compound using the cursor. This function is inactivated. Furthermore if I hold the key Ctrl for selecting them and labeling it is also not doing it at all. Any help with this issue will be greatly appreciated. Mireya Gonzalez

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question
by sunwei_223 18 Apr '13

18 Apr '13

Dear sir I have some question in using your excellent Chimera. How can i set 5 symmetry to a 3 symmetry map? thank you

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AutoDock Vina and hydrogens
by Elaine Meng 16 Apr '13

16 Apr '13

Hello, Users of the AutoDock Vina interface in Chimera 1.7 should be aware of a potential "gotcha": the structures should include hydrogens, at least the "polar" (potentially H-bonding) ones. For the receptor, this is generally taken care of because the "add hydrogens in Chimera" option in the AutoDock Vina interface is turned on by default. However, there is no corresponding option for the ligand in that interface: instead, you need to add hydrogens to the ligand beforehand, for example with Chimera AddH. Polar hydrogens are needed for Vina to correctly recognize the atom types, to correctly calculate docking scores. In the current daily build (and for future releases) we have built in more protections so that if there are no hydrogens and you haven't added them with Chimera, they will still be added by the AutoDock prep scripts before the docking calculation. Recent fixes: <http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html#bug_fixes> Download the daily build: <http://www.cgl.ucsf.edu/chimera/download.html#daily> 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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Tube representation of the motion projections along the eigen vectors
by Prasanna Venkatesh 16 Apr '13

16 Apr '13

Dear all, I request you to give me the steps for "Tube representation of the motion projections along the eigen vectors" in Gromacs. Please give me step wise details with the input file types required. Thank you in advance. Prasanna.

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docking with flexible side-chains
by Thomas Evangelidis 16 Apr '13

16 Apr '13

Dear Chimera developers, Isn't docking with flexible side-chains supported in the AutoDock Vina GUI? I am surprised I didn't find any pertinent information about it in the documentation or the mailing list archives. thanks, Thomas -- ====================================================================== Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tevang(a)pharm.uoa.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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Technical problem!
by Narges Mortezaei 16 Apr '13

16 Apr '13

Dear Sir/Madam We have confronted with kind of problem using chimera. We have constructed an structure of P-pili containing subunits and epitopes. A few cylinders that are representing arms of antibody have also been added to the model. The problem comes when we want to copy the cylinders to make more out of them. I do select corresponding cylinder, but when it comes to copy in Model Panel a copy option is not activated. I also tried "mcopy" command, but it did not work as well. Would you please give me some hints how to copy these kind of objects. Sincerely, Narges Mortezaei

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(no subject)
by Muhammad ALi 16 Apr '13

16 Apr '13

hi can we make a DNA model with chimera???

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pdb
by Muhammad ALi 16 Apr '13

16 Apr '13

when I download a ligand from PDB site it contains may ligand molecules ..and kindly tell me how to get a single ligand????

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