- Chimera-users - RBVI Mailing Lists

Need instructions how to do MD simulations of Protein-ligand complex using Chimera
by P Srivastava 01 Jun '20

01 Jun '20

Dear Chimera Team I Need instructions on how to do MD simulations of Protein-ligand complex using Chimera. Please give me in details. With regards, Pratibha Srivastava प्रतिभा श्रीवास्तव Scientist वैज्ञानिक Bioprospecting Group जैव पूर्वेक्षण समूह Agharkar Research Institute आघारकर अनुसंधान संस्थान Pune, India पुणे, भारत

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(no subject)
by Preantha Poonan 01 Jun '20

01 Jun '20

Good afternoon, I am writing to you regarding an error I am experiencing with working with Chimera. When I begin the docking process the following appears: Service 'opal:vina_1.1.2 is unavailable . See Reply Log for more details. Kindly assist. Preantha Poonan Sent from Mail for Windows 10

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Conversion of Chimera session .py file to Pymol .pse file
by Joanna Smietanska 01 Jun '20

01 Jun '20

Dear UMSF Chimera Users, I would like to ask how to convert Chimera session .py file into .pse Pymol format? I have a few saved Chimera sessions, my approach was to save protein coordinates in .pdb format and subsequently read them in Pymol 2.0 to save as Pymol session, but during this procedure all informations about specific colouring of chains and other settings are lost. May I ask about possibilities for direct import Chimera .py files into Pymol without losing saved settings? I would be very grateful for any help and advice. Best regards, Joanna Smietanska

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Molecular dynamics
by Сергей Владимиров 01 Jun '20

01 Jun '20

Good day! My name is Sergei Vladimirov, I'm a student at Moscow State University. As far as I know, when running a molecular dynamics of ligand-protein interaction one must use different force fields to the ligand and the protein. There is a mm14ff to calculate interactions within a protein but there are only two different force fields to calculate interactions within a ligand. I've been led into believing that the best ff for small organic ligands is GAFF. So my question is, is there any way to implement the GAFF force field into the production of molecular dynamics? Is there anything I'm missing? I will be awaiting your reply. Best regards, Sergei Vladimirov.

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CHIMERA code in R
by Farzaneh Amanpour 27 May '20

27 May '20

Dear CHIMERA users, I am a PhD student in biostatistics and I want to run this algorithm in R. Can I have access to R code for CHIMERA? Thank you in advance

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Molecular docking
by Schaf, Judith (2017) 27 May '20

27 May '20

Hi everybody, I have a quick question: when I analyse the results of a molecular docking assay (performed with SwissDock) on Chimera I sometimes see a green line between the protein and the ligand. Does someone know what this line represents? [cid:fc8bd8ab-4117-464a-b2fb-0f512e867f88] Thank you, Judith

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Re: [Chimera-users] Adding New Covalent Bond?
by Elaine Meng 26 May '20

26 May '20

> On May 26, 2020, at 9:52 AM, Ammar Jastaniah <ajasta2(a)uic.edu> wrote: > > Hi Elaine, > Is there any way to connect/make new bonds between adjacent, somewhat distant carbon atoms within a ligand structure (perhaps still using the 'Build Structure' feature)? > Thank you. > Ammar Hi Ammar, Assuming this is a Chimera question (we are now developing ChimeraX) the answer is yes, in the Adjust Bonds section of Build Structure, you can choose to add a bond between any two selected atoms regardless of the distance between them. Just choose the "all possible" option. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h…> Or, you could use the "bond" command: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html> The chimera-users(a)cgl.ucsf.edu address (CC'd here) is recommended for Chimera questions, unless private data are included. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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save images/scene - independent of chimera window
by Dominique Gutierrez 26 May '20

26 May '20

Good Morning, Is there a way to save an image independent of the chimera window size. When I reopened a saved session and saved an image from a scene it was not the same and it seems to be due to change in the chimera window. Best Regards. Dominique Gutierrez

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Color by electrostatic potential
by Francesco Pietra 22 May '20

22 May '20

I was able to open with chimera 1.1.3.1 (linux) electrostatic-potential cube files generated from ORCA package and view them in colors (red lowest, blue highest potential). I can't remember how I succeeded and now, from chimera help, I am no more able. Only a single color. Thanks for putting me on the right way. chiendarret

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Load AMBER trajectory from command line?
by Rodrigo Galindo-Murillo 20 May '20

20 May '20

Hello! I wonder if there is a way to load an AMBER topology/trajectory directly from the command line without having to go to tools->Md/ensemble-> MD movie, etc... For example, in VMD you can use: vmd -parm7 topology.parm7 -netcdf trajectory.nc I am NOT implying VMD is better than Chimera :) It will be just faster to be able to quickly load trajectories from the command line to save some time. Thanks! Rodrigo.

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