- Chimera-users - RBVI Mailing Lists

Met CH3 and NH3+ hydrogen optimization
by Visvaldas K. 09 Oct '12

09 Oct '12

Dear colleagues, Regarding H addition to protein structures, there are indications that hydrogens of NH3+ groups of lysine or N-termini, and side chain methyls of methionines need a rotational optimization (Richardson & Richardson, Chapter 15 in "Structural Bioinformatics", 2nd ed., 2009, p. 380) . I think this problem is not too common, but I did encounter it at least once when I had to rotate manually a Methionine methyl to remove a clash with the ligand. I think Chimera doesn't perform this optimization, or does it? If it doesn't, perhaps this could be put on a list of future improvements:) Best regards, Vis Kairys Institute of Biotechnology Vilnius University

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surface texture export
by Laura Lynn Gonzalez 09 Oct '12

09 Oct '12

Hi. Is there any way to export Coloumbic colored surfaces as JPG textures when you export geometry (obj, vrml, etc)? Or get the 3D texture data in some other format? I'm trying to import my Coulombic-colored protein into a 3D program. -Laura Lynn

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Re: [Chimera-users] APBS interface in Chimera
by Baker, Nathan 08 Oct '12

08 Oct '12

Hi Boaz -- That was news to me as well; thanks for making me aware of this! Best, -- Nathan Baker Pacific Northwest National Laboratory Tel: +1-509-375-3997 http://nabaker.me From: Boaz Shaanan <bshaanan(a)exchange.bgu.ac.il<mailto:bshaanan@exchange.bgu.ac.il>> Date: Monday, October 8, 2012 11:24 AM To: "chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Cc: Nathan Baker <nathan.baker(a)pnnl.gov<mailto:nathan.baker@pnnl.gov>> Subject: APBS interface in Chimera Hi, Totally due to my negligence I've only just discovered the long sought APBS interface in the daily build (the one I'm using is from 25/9). Well done Chimera and APBS teams! Practical question: I don't see on the APBS pull-down menu where I define the location of the executable (I'm talking about the Windows version right now, soon I'll try the linux version too). Is it clever enough to find it wherever APBS is installed or have I missed something? 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<mailto:bshaanan@bgu.ac.il> Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

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Re: [Chimera-users] using modeller through chimera
by Elaine Meng 08 Oct '12

08 Oct '12

On Oct 8, 2012, at 2:21 AM, Taufiq Rahman wrote: > Just wonder whether in using modeller through Chimera interface, we can use our own alignment file or not. Hi Taufiq, Yes, you can definitely use your own alignment file -- just open it in Chimera. To run Modeller using the Chimera interface, all you need is a sequence alignment of target and template (and if it has additional sequences, that is fine) plus the template structure, both opened in Chimera. There are several ways of obtaining these inputs, outlined here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mu…> See the third one, "using a pre-existing target-template sequence alignment" Regards, 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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НА: Chimera --send on MacOS
by Sp 07 Oct '12

07 Oct '12

Отправлено с моего коммуникатора HTC

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Re: [Chimera-users] Chimera-users Digest, Vol 114, Issue 2
by Pu Qian 05 Oct '12

05 Oct '12

Hi, I'm working on a big protein complex with MW ~500 kD. It contains a cave inside of the protein. Now I would like to high light this cave so that I can show the room that is big enough for a quinone molecule to move. Question is: is there a function in Chimera which allows users to produce such cave inside of the protein based on PDB file of the protein. If is, where can I find it and how to use it. It would be a great appreciated if anyone here could give me advices. Thanks. Best regards Dr. Pu Qian Department of Molecular Biology The University of Sheffield Sheffield, S10 2TN UK

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Chimera --send on MacOS
by François Stricher 04 Oct '12

04 Oct '12

Hi all, I want to be able to interact with Chimera from another program, sending commands and all. I tried the chimera --send my_file.com to test it under MacOS 10.7. Each time I do this, it opens a new instance (instead of reusing the previous one) and doesn't process my_file.com at all. When I open my_file.com from inside chimera, it operates the commands inside it without any problem. Any idea? Francois

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Global and per-user preference files?
by mike _ 03 Oct '12

03 Oct '12

I wish to deploy a Chimera installation across multiple machines for multiple users. For obvious reasons the users will not have write permission on the application directory. In this scenario Chimera's default behaviour of regularly checking for updates is unhelpful so I wish to disable it. Having read http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Preferences I assumed I could disable the update checking by putting a suitable preferences file in the application directory and then having users invoke Chimera in such a way that preferences file is found. That works, but generates a warning that the preferences file is read-only (which it is, it's in the application directory) and Chimera seems to only want to use the one preferences file. So the result is that users can't save any preferences. Is there any way to make Chimera read a global preferences file that contains some useful defaults and also allow each user to have their own preferences file? thanks, mike

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Re: [Chimera-users] using modeller through chimera
by Elaine Meng 03 Oct '12

03 Oct '12

Hi Taufiq, As you mentioned, the models will appear automatically in the Chimera main window, and there will be an additional dialog, Modeller results (a list of the homology models and other information). For example, the two bottom figures in the Comparative Modeling tutorial show this dialog: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html> I don't understand what you are clicking... it should not be necessary to click anything. More details about the Modeller results dialog: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modbase.html#modellist> Best, Elaine On Oct 3, 2012, at 6:16 AM, Taufiq Rahman wrote: > Dear Elaine, Many thanks for the reply. It was very helpful and I can now do it. The only fresh problem is: whenever Modeller seems to complete the job (I assume), I can't click on 'modeller results' - its there but clicking on it doesn't open up anything, whilst in the 3d space, I can see the modelled structure as well as the templates. > Any advice? > Regards, > taufiq > > On Oct 3 2012, Elaine Meng wrote: > >> Hi Taufiq, It is probably disabled because you are viewing a single sequence rather than an alignment of 2 or more sequences. In Chimera, there are several ways to get the needed inputs for Modeller, which include the sequence alignment and a structure to use as the template. Some ways are outlined here: >> >> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mu…> >> >> Once you have the inputs, you can run Modeller either via web service or via your local installation. If you haven't already, you would also need to obtain a Modeller license key before running (even if you are going to use the web service). >> >> I would also recommend that you get a newer version of Chimera (at least 1.6.2). The Modeller interface is improved in that version compared to older versions. The sequence window menu will then include both "Structure... Modeller (homology)" and "... Modeller (loops/refinement)" instead of a single "...Modeller Tools" entry. >> >> This documentation is for 1.6.2: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mo…> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> On Oct 2, 2012, at 7:49 AM, Taufiq Rahman wrote: >> >>> Hello, I want to use modeller through Chimera's interface. I have seen the video and read about the way to do it. My problem is my 'modeller tool' option in the structure menu remains disabled. I have installed modeller locally but don't know how to integrate it into chimera. >>> any suggestion? >>> taufiq >> >> > > -- > Taufiq Rahman > MSc(Manchester), PhD (Cantab) > Royal Society University Research Fellow > University of Cambridge > Cambridge > CB2 1PD > UK >

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using modeller through chimera
by Taufiq Rahman 03 Oct '12

03 Oct '12

Hello, I want to use modeller through Chimera's interface. I have seen the video and read about the way to do it. My problem is my 'modeller tool' option in the structure menu remains disabled. I have installed modeller locally but don't know how to integrate it into chimera. any suggestion? taufiq

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