- Chimera-users - RBVI Mailing Lists

Handling electrostatic potential in cube format
by Boaz Shaanan 06 May '19

06 May '19

Hi, It seems as if the new Delphi version (v8.4) only knows to produce potential phi files in cube format. Oh well. I'm beginning to play with this format via the volume viewer but so far the fit of the surface to the atomic model is bad, let alone that potential values on the surface (as reported by moving the mouse on the surface) make no sense. I'm wondering whether there is a chance to achieve as nice a fit of the cube surface to the protein model as is easily achieved with the good old .phi format and surface command. So far I'm lost. I'd appreciate any clues. Luckily, I still keep the older version but there might be some improvements in the potential calculations in the newer version. Thanks for your help. 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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Re: [Chimera-users] [chimera-dev] Loop refinement in chain A and Chain B
by Elaine Meng 06 May '19

06 May '19

Hi Aashish, The address for questions about using Chimera is chimera-users(a)cgl.ucsf.edu (CC’d here). Chimera-dev is for programming questions. It sounds like you did find the “model/refine loops” dialog for using the Modeller web service. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> In that dialog, you would need to choose either “non-terminal missing structure” (if the missing residues are in the middle) or “all missing structure” (if some of the missing residues are in the termini), and also enter a license key for running Modeller. However, I have no idea what you mean by “not running,” so I can’t give any more help than that. Also, be aware that in Chimera using this dialog, you can only model one chain at a time. I.e. when it is adding the residues to chain A it does not care if they are in a bad place relative to chain B, and vice versa. Our newer program ChimeraX has the advantage that you can sensibly model the dimer using the Modeller web service, with the two chains “seeing” each other. However, to use that you would have to download and learn a different program. <http://www.rbvi.ucsf.edu/chimerax/index.html> <http://www.rbvi.ucsf.edu/chimerax/download.html> <http://www.rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html#comparative> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 6, 2019, at 5:39 AM, Aashish Bhatt <aashish.ph16221(a)inst.ac.in> wrote: > > Dear Sir/ Ma'am > > I have dimer PDB structure in which 40 amino acid is missing in both chain A and B. > Is it possible to make a model with a chimera? I have tried the same with chain A and but it is not running. > > Can you please give me an idea of how to build the complete structure? > > Best regards > > Aashish > INST-Mohali > India

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How do I find the active site?
by Abryn Jeuness Luna 06 May '19

06 May '19

Good day! I am currently using UCSF Chimera for my protein structure analysis. However, I cannot find the active site of my protein structure. How do I find the active site, including the amino acids in it using UCSF Chimera? Thank you. Regards, Abryn

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regarding to minimization and preparation of sdf files for docking.
by prasad ssv 05 May '19

05 May '19

hi, i had a database which contains a set of molecules,all molecules in sdf format i would like to minimize all sdf files and dock preparation.can you please help me do that. i had performed dock prep for those sdf files but it showing some reply log and bugs.when i am adding hydrogens it is gvng reply log as attached in below files. can you please go through and suggest me a solution. thanking you,

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Re: [Chimera-users] Chimera-users Digest, Vol 193, Issue 5
by Boaz Shaanan 05 May '19

05 May '19

Hi Again, Following my complaint on the cube format I started to play with .dx format of APBS which so far seems more promising in how it projects on the protein surface. Cheers, 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 ________________________________________ From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: Sunday, May 5, 2019 8:18 AM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 193, Issue 5 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. save sequence alignment (Hernando J Sosa) 2. Re: save sequence alignment (Eric Pettersen) 3. Re: RR distance map, scale normalization (Arvind SHARMA) 4. Handling electrostatic potential in cube format (Boaz Shaanan) 5. How to select residues/atoms only those within my cryo-EM map region (Kim, Doo Nam) ---------------------------------------------------------------------- Message: 1 Date: Fri, 3 May 2019 21:03:33 +0000 From: Hernando J Sosa <hernando.sosa(a)einstein.yu.edu> To: Chimera <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] save sequence alignment Message-ID: <F0E461AAE34D0448B6EE7D31E433B7080154B87577(a)AEWEXCPM21.yuad.uds.yu.edu> Content-Type: text/plain; charset="utf-8" Dear Chimera, Is there a command option to save a sequence alignment (after executing matchmaker) or a way to do it in a python script? Thanks H. ------------------------------ Message: 2 Date: Fri, 3 May 2019 15:19:36 -0700 From: Eric Pettersen <pett(a)cgl.ucsf.edu> To: Hernando J Sosa <hernando.sosa(a)einstein.yu.edu> Cc: Chimera <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] save sequence alignment Message-ID: <EFACEFC8-FD06-4C10-AE7B-704CD8925BCF(a)cgl.ucsf.edu> Content-Type: text/plain; charset="utf-8" Hi Hernando, This old chimera-users message shows how to find the alignment in Python and save it: [Chimera-users] easy way to make alignments in chimera <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010017.html>. You can?t do it in nogui mode since the MAV window has the alignment data. You would be able to do it in nogui mode in ChimeraX, but the code would be significantly different of course. Anyway, if you are doing this in a loop you may want to call mav.Quit() after saving your alignment in order to quit MAV and conserve memory. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On May 3, 2019, at 2:03 PM, Hernando J Sosa <hernando.sosa(a)einstein.yu.edu> wrote: > > Dear Chimera, > > Is there a command option to save a sequence alignment (after executing matchmaker) or a way to do it in a python script? > > Thanks > > H. > > > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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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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