March 2018 - Chimera-users - RBVI Mailing Lists

defining attribute from python
by Wood Ortiz, Francisca (NIH/NEI) [F] 27 Mar '18

27 Mar '18

Hello, I am a post-bac fellow at the NEI/NIH working with protein modeling. We are hoping to automate a procedure which requires the protein structure to be colored using an attribute file and exported as an .html and .py session. We would like this to be completed from the command line without the need to open the Chimera graphics window. Could this be done? Thank you for your help. Best, Francisca Wood Ortiz Postbaccalaureate Fellow, Ophthalmic Genetics and Visual Function Branch, NIH/NEI

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Chimera Help Desk: Missing Output file
by Arturo Estolano Cobián 26 Mar '18

26 Mar '18

Dear Chimera Help Desk, I have a problem while running molecular docking on Chimera. After running Tools --> Surface/Binding Analysis --> AutoDock Vina, I do not get the results from the docking analysis. I get the regular *name*.receptor.pdb , *name*.receptor.pdbqt , *name*.ligand.pdb , *name*.ligand.pdbqt and *name*.conf files, but the *name* file (the docking results) does not generate. In the Reply Log I found this, which I assume is involved in the problem: standard error ----- Unable to initialize environment because of error: cannot register event client. Only 99 event clients are allowed in the system Exiting. ----- Traceback (most recent call last): File "C:\Program Files (x86)\Chimera 1.11.2\share\chimera\tasks.py", line 179, in runStatusCB task.statusCBList[0]() File "C:\Program Files (x86)\Chimera 1.11.2\share\WebServices\appWebService.py", line 171, in statusCB self.finishCB(self.backend, fileMap) File "C:\Program Files (x86)\Chimera 1.11.2\share\vina\ws.py", line 179, in _wsFinish raise NonChimeraError("No data file returned from " NonChimeraError: No data file returned from AutoDock Vina web service And I can't find how to solve this and get the results from the docking experiments I'm doing. Can you please help me solve this problem? Thank you in advance for your attention. Arturo Estolano Cobián <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Libre de virus. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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vina error
by Sofia Vasilakaki 25 Mar '18

25 Mar '18

Dear Chimera developers, I am trying to run vina 1.1.2 on opal server and I am getting the following error: Unable to initialize environment because of error: cannot register event client. Only 99 event clients are allowed in the system Exiting Any suggestions? Thank you, Sofia

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Custom Preset Folder not detecting any scripts
by Eiros Zamora, Juan 22 Mar '18

22 Mar '18

Hello everyone, >From what I’ve gathered, I can save custom presets in a text file with Chimera commands, directly as I would type them in the Command console. So for example my custom preset file is simple, for testing purposes: ribbon protein color white protein repr sphere :CAL disp :CAL I’ve saved the file with a .com extension (as specified here http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Presets), and then indicated the directory it’s in by Clicking on Presets > Add Custom Presets … (after selecting it, I press the Save button). >From here, I’m a bit lost. I think the file is not detected as I get no new options under the Presets tab, nor does the command `preset list c` give any output in the Reply log. Also closing and opening Chimera again does not help (although the custom preset folder is remembered if I try the previous steps). What am I doing wrong? Best regards, Juan

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FW: Question about 3D visualization by chimera
by Williams, Joanne 21 Mar '18

21 Mar '18

From: "Ahmet Cenk ANDAC, ISU" <acandac(a)istinye.edu.tr> Date: Monday, March 19, 2018 at 5:28 PM To: "chimera(a)cgl.ucsf.edu" <chimera(a)cgl.ucsf.edu> Subject: Question about 3D visualization by chimera Hi! I was wondering if it would be possible to view 3D projections of molecules in chimera using polarized glasses? If not, would the Chimera team consider adding such feature in the next release of chimera? Thanks,, Cenk Andac, M.S., M.S., Ph.D., Head, Chair Asst. Professor of Medicinal Chemistry Head of Pharmaceutical Sciences Division Chair of Medicinal Chemistry Department School of Pharmacy, Istinye University, Zeytinburnu-Istanbul, TURKIYE http://eczacilik.istinye.edu.tr/akademik-kadro/ahmet-cenk-andac.shtml Cell: +90-(536)-4813012 E-Mail: cenk_andac(a)yahoo.com

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Autodock Vina outputs
by Elaine Meng 20 Mar '18

20 Mar '18

Hi Simon, The various output files are described in Chimera’s Autodock Vina documentation. As also mentioned in that page, when the docking results are returned they get opened up automatically: i.e. you do not have to explicitly open any files. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> That link is the copy on our website, but you should see basically the same page if you just click the Help button on the Autodock Vina dialog. If no results appeared automatically, the possibilities include: - job is still running - job failed for some reason, check Reply Log - job finished but zero results possible given the input structures/parameters I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco >> >> From: simon chapman <rowanlodge19(a)gmail.com> >> Subject: Re: [Chimera-users] substituting atoms >> Date: March 20, 2018 at 4:31:04 AM PDT >> To: Eric Pettersen <pett(a)cgl.ucsf.edu> >> >> Many thanks Elaine and Eric, much obliged. Sorry if I got the protocol wrong! >> >> 5 files appear on my desktop after a docking run. One is the conf fie, the others are PDB or PDBQT files for ligand and receptor. >> >> I'll keep battling, but perhaps cc.ing your colleagues will help. I'llet you know if the puzzle is resolved. >> >> Simon >> >> On 19 March 2018 at 17:26, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: >> Hi Simon, >> You should initially send these types of questions to the chimera-users list. I’m one member of a programming team and therefore not the expert on all aspects of Chimera — AutoDock Vina being one of the ones I’m not an expert on. I have cc’ed the team members who are the AutoDock Vina experts on this mail and one of them should be able to help out… >> >> —Eric >> >>> On Mar 19, 2018, at 8:17 AM, simon chapman <rowanlodge19(a)gmail.com> wrote: >>> >>> OK, me again....the Irish troublemaker. >>> >>> I've been tinkering with the AutoDock Vina facility in Chimera Tools. All goes well until a pop-up asks me to specify a file type to open the resulting configuration file. >>> >>> I have no idea what those abbreviations mean. I tried a few, but error messages appear every time. >>> >>> Any thoughts? More beers if you can help. >>> >>> Best wishes Simon >> >> <vina 1.PNG> >> <vina 2.PNG> >> >

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Save Image problem
by James Boyd 19 Mar '18

19 Mar '18

Hi, I am a new Chimera user although I have used other molecular graphics programs from time to time. I like the CHimera feel and the menus are pretty easy to navigate. I am trying to save on screen images as .jpg files. I keep getting an error message that says that the file doesn't exist ( e.g. C:\Users\james\desktop\protein\protein.jpg does not exist.) When I look in the folder an image file by that name has been created but it has no image in it. (see NADPH2 for an example). I was able to get an image saved correctly one time (NADPH.jpg) but not again so things appear to be working, it's just that I am doing something wrong. Any suggestions? Thanks, Jim James G Boyd, PhD HealthTell, Inc. 145 S 79th St Chandler, AZ 85226 james.boyd(a)healthtell.com (cell) 860-941-9566 (off) 925-215-5615 (x1001)

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Metal Geometry
by Pascal Auffinger 16 Mar '18

16 Mar '18

Dear All, Metal Geometry is a great tool. However, it can be tedious to use it when the list of metals is long like in some ribosomes where sometimes over 200 of them are found. Is there a quick way to move from a given metal to the next one without using the pulldown menu ? Thanks a lot, Pascal ----- Pascal Auffinger IBMC/CNRS 15 rue René Descartes 67084 Strasbourg Cedex p.auffinger(a)ibmc-cnrs.unistra.fr <mailto:p.auffinger@ibmc-cnrs.unistra.fr> -----

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Topology file creation
by Sankaran SV . 16 Mar '18

16 Mar '18

Hi users, Currently Iam working on protein glycosylation. Can anyone could give me a reference for topology file creation for running the simulation of glycosylated protein. -- Sankaran.s.v bbin

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Permission to use Chimera for non-academic purposes
by Helander, Jon 16 Mar '18

16 Mar '18

Hello, I'm a computational biologist at Wash U. in Saint Louis and have been using Chimera for some years now. I also do some stock market research in biotech and write informative articles about some companies that do small-molecule research. To aid in this, I would like to include some Chimera-generated images. Would this be alright and can I obtain some written confirmation if so? Thanks Jon Helander

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Chimera-users March 2018