- Chimera-users - RBVI Mailing Lists

job opening for ChimeraX developer
by Elaine Meng 06 May '21

06 May '21

Hello everybody, We're looking for somebody to join the ChimeraX development team! Please see this posting for details: <https://sjobs.brassring.com/TGnewUI/Search/Home/Home?partnerid=6495&siteid=…> On behalf of the team, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Contact in angstrom
by Arthur Pereira da Fonseca 06 May '21

06 May '21

Hello, I’m trying to measure contacts between a protein and a peptide using Chimera. I have to do this with different angstroms distances, 2, 3 and 4 Å. I'm using the command line: findclash :.A test :. B overlap -0.4 hbond 0.0 namingStyle simple save However I don’t know exactly how to modify the overlap to the desired distances. Which values can I use to measure contacts within 2, 3 and 4 Å. Thanks in advance, Arthur Pereira

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python code to loop over molecules
by Julian Tirado-Rives 04 May '21

04 May '21

Dear Chimera (and ChimeraX) team: I need to find some python example or code snippet capable of looping over all the molecules in a particular model and do some actions separately in each one. In our research we use several different docking programs and other ways of generating poses of protein-ligand complexes, and using several different programs to analyze them gets quite complicated. Instead, we've found that the easiest way is to generate from each code, or using conversion utilities such as babel, a pdb file of the host and a sdf or mol2 file containing all the ligand poses and read them into chimera. An excellent program, by the way. We use it all the time. I would love to automate the process even further by doing all the coloring, rendering, Hydrogen Bond and contact analysis, etc. in Python rather than manually. I have been trying to do this, but have not found a way to do the following: If we have, for instance, the host in model #0, and the ligand poses in model #1 (#1.1, #1.2, ..., #1.N): - Get from chimera the number of molecules in model #1 (e.g what is N) - loop from the first #1.1 to the last #1.N molecule - do some cations there (e.g select, color, find HB's, etc) I think this should be a problem other people have encountered and solved before, but I have not been able to find an example in your depository, the mailing lists, or even the book ... I would appreciate your input. Thanks for your help, and for an excellent program! - Julian - -- ----------------------------------------------------------------- | Julian Tirado-Rives | | | Department of Chemistry | Phone: (203)432-3356 | | Yale University | Fax: (203)432-6144 | | P. O. Box 208107 | email: Julian.Tirado-Rives(a)yale.edu | | New Haven, CT 06520-8107 | | -----------------------------------------------------------------

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Rotate model
by C.J. 03 May '21

03 May '21

Hi all, I tried "turn y 180 #1" ( https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html) but it doesn't work. It said "turn frame arguement must be an integer". While I tried "turn y 180 0 #1" or "turn y 180 1 #1", it said "wait_frames arguement not implemented". Even "turn y 180 0 0 #1" doesn't work. Did I miss something? Thank you! Jianhao

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Combine focuse refined maps in Chimera
by Zheng, Fengwei 03 May '21

03 May '21

Dear Chimera developers: Thank you so much for developing this powerful and elegant software for our community! I am a newbie in cryoEM, and recently I got a consensus map, and split it into two parts to do the further focused refinement, after that I want to combine them together, and then to build my model. I learned that the command "vop maximum #0 #1" can achieve this, what I did is that, firstly, I used this command to merge my consensus map with one focused map, and then merged the resulted map with my second focused map, but it seems that the order of those two maps in my executable command (e.g. #0 #1 or #1 #0) will lead to slightly different resulting map~ I just wondering if this is the correct way to combine my focused maps, or there are other commands can achieve this better? Appreciate! Best, Fengwei

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Fwd: Hydrogen bond
by Eric Pettersen 03 May '21

03 May '21

> Begin forwarded message: > > From: shakira shukoor <shakirashukoor1993(a)gmail.com> > Subject: Hydrogen bond > Date: May 2, 2021 at 3:09:46 PM PDT > To: chimera-bugs(a)cgl.ucsf.edu > > Dear sir > Does chimera software have any option to set the distance and angle criteria to view the hydrogen bond. I was not able to see any hydrogen bond in my system although hydrogen bonds do exist which I have confirmed from vmd. Why is it not visible in chimera then? > > -- > Best Regards > > Shakkira E > PhD student INSPIRE Scholar > Department of Chemistry > sdmdlab <http://sdmdlab.xyz/>-iitp.com <http://iitp.com/> > IIT Patna > Bihta > Patna 801106 >

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Problem downloading Chimera
by Mahmoud Soliman 02 May '21

02 May '21

Hello there, We are trying to download Chimera, however, the link below never works, not sure if the server is down, but we have been trying for a few days with no luck. Can you please guide us on how to download chimera perhaps you send us a working link. <%0b%0dhttps:/www.cgl.ucsf.edu%20›%20chimera%0d> https://www.cgl.ucsf.edu › chimera<%0b%0dhttps:/www.cgl.ucsf.edu%20›%20chimera%0d> Thanks & Best Regards -------------------------------------------------------- Prof. M Soliman Professor of Pharmaceutical Chemistry M.Pharm, B.Pharm, MPhil/PhD (Bath, UK) Discipline of Pharmaceutical Sciences School of Health Sciences University of Kwazulu-Natal Westville Campus, Durban 4000 Email: soliman(a)ukzn.ac.za<mailto:soliman@ukzn.ac.za> Webpage: http://soliman.ukzn.ac.za/ ---------------------------------------------------------

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2D panorama view of a 3D model
by Kandolf,Susanne 30 Apr '21

30 Apr '21

Hello, I was wondering if it is possible to display a 3D model as a 2D panorama view? I would like to show all sides of a holoenzyme and instead of taking several pictures of each view, I thought it would be more convenient to have one picture displayed as panorama showing all sides at the same time. Thank you for your help, Susanne …………………………………………………………………….. Susanne Kandolf Research Technician at Haselbach Lab Mobile: +43 699 17250493 susanne.kandolf(a)imp.ac.at<mailto:susanne.kandolf@imp.ac.at> www.imp.ac.at<http://www.imp.ac.at> IMP Research Institute of Molecular Pathology Campus-Vienna-BioCenter 1 1030 Vienna, Austria Part of Vienna BioCenter www.viennabiocenter.org<http://www.viennabiocenter.org>

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Problem Saava9ng merged PDB Files
by Stephen P. Molnar 30 Apr '21

30 Apr '21

I am using Chimera v-1.14 (build 42094) on my Debian Buster Linux computer and have run into a problem saving a pdb file containing two pdb files. The files are attached to this email.This is a portion of the combined flies: The structure of the D21.pdb file isthe ball image. I followed the instructions in the Building Structures, Modifying and Saving Data in the Help pages. However, when I open DD21Mod1 in LigPlot to identify the docked ligand I get: Clearly, this is not the ligand docked int the active site. I have used LigPlot on a number of pdb files with good results and am forced to conclude that there is a problem with D21Mod1.pdb. I would appreciate help in solving this problem. Thanks in advance. -- Stephen P. Molnar, Ph.D. www.molecular-modeling.net 614.312.7528 (c) Skype: smolnar1

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problem (exit code -1073741819)
by Ichrak Benamri 23 Apr '21

23 Apr '21

Hello, I hope you are doing well. I have problem launching the chimera tool (error code: -1073741819), I don't know exactly where the problem is. Please, can you help me? Thank you [image: image.png] -- *Ichrak BENAMRI* PhD Student in Bioinfomatics *+212648548583* ichrakbenamri(a)gmail.com Systems and Data Engineering Team, National School of Applied Sciences, Abdelmalek Essaâdi University, BP1818 Route Ziaten, 90 000, Tangier, Morocco Chlamydiae and Mycoplasma Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco

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