- Chimera-users - RBVI Mailing Lists

AutoDock Vina
by Hernando J Sosa 02 May '19

02 May '19

Is it possible to specify more than 10 'Number of Binding models' on the AtoDock Vina dialogue? Thanks Hernando

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get_view, set_view
by Pranav Shah 02 May '19

02 May '19

Dear Devs, Apologies for asking a naive question, but i was wondering if there exists a function similar to pymols' get_view and set_view in chimera/chimeraX? If yes, is there a way to do this? Cheers, Pranav -- Pranav Shah Postdoctoral Research Fellow. Hogle Lab Department of Biological Chemistry and Molecular Pharmacology, Building C2 - First Floor 240 Longwood Avenue Boston, MA 02115 (617) 432-4360 (fax) (617) 432-3839 (lab)

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Installing vina webserver?
by Antoine Daina 01 May '19

01 May '19

Dear, Is there any possibility to install a local AutoDock Vina webserver (not the executable, really the WS) through the scripts I can see in the Chimera install directories? Thanks a lot in advance fro your help. Best, Antoine. -- Antoine Daina, PhD SIB | Swiss Institute of Bioinformatics | Molecular Modeling Group Quartier Sorge | Bâtiment Amphipôle | CH-1015 Lausanne | Switzerland

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Re: [Chimera-users] Reading electrostatic potential map in cube format into Chimera
by Boaz Shaanan 30 Apr '19

30 Apr '19

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Reading electrostatic potential map in cube format into Chimera
by Boaz Shaanan 30 Apr '19

30 Apr '19

Hi, Does Chimera accept electrostatic potential in cube format (apparently that's what the new Delphi version 8.4 produces). I noticed a cube input under gaussian cube grid, is that the one I should use? Apparently the source of my recent problem with reading an electrostatic potential map had to do with this change of format. I'd appreciate your input. Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710

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Deleting data contained in a session
by David Sáez 30 Apr '19

30 Apr '19

Dear Chimera experts: I have saved multiple sessions of molecular dynamics trajectories. Each session is about 5MB. Nevertheless, one of those files is huge, about 120MB. Checking the differences, I noticed that one of the files contained in the session, which normally is a one-frame .pdb, in the large case corresponds to a .nc file, a whole trajectory containing a large number of frames. I did not notice this before because when I opened the .py file, the MD movie box is not shown. As I am only interested in the currently displayed frame of this .nc file, is there a way to delete the additional frames? Some command line trick that would allow me to get rid of the uninteresting frames, and decrease the file size, without having to re-make the whole session again? My most immediate concern is that the file size is too large to be uploaded to a journal online platform. Any help is appreciated, Regards.

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How to join two modelled chain of protein using chimera
by Bhanu Sharma 29 Apr '19

29 Apr '19

I have modelled two chains of protein(A,B) sepratrely. now i want to join these two chains as like of original protein and want to save it as a pdb file format . Can anyone please help me? Best regards, Bhanu sharma

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A query
by Bhanu Sharma 27 Apr '19

27 Apr '19

Dear sir/mam I have done homology modelling for a protein having two chains (A,B). I have modelled them seprately one after another. Now i want to join these two chains to make complete protein. And i want to do it using chimera. Can you please help me how to do this. Best regards, Bhanu sharma

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Changing the default temp folder for chimera
by Yehuda Halfon 25 Apr '19

25 Apr '19

Hi all, I try to make a movie in chimera and it fills my C drive. Can I change the temp folder, in which the pics are stored, to another empty drive? Thanks, Yehuda Halfon

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Surface representation
by MARIA CLARA BLANES MIRA 25 Apr '19

25 Apr '19

Hello, I would like to know if Chimera could show the surfaces like VMD does with the command QuickSurf (I attach the image with the protein in yellow and the lipids in green). I have been trying with a lot of different variations of the surface command but I can not find the way to make the surface ’softer'…. I have also been trying with spheres representation but the image shows too much information. I need a simplest view, similar to the image because this way it is easier see them move in the .dcd file. It not so important for the protein, just for the lipids. Could you help me with this, please? Thank you very much, clara

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