- Chimera-users - RBVI Mailing Lists

coloumbic coloring when surface can't be calculated?
by Oliver Clarke 29 Apr '17

29 Apr '17

Hi, I have a structure (well, lots of structures) for which surface calculation fails in Chimera. I can rescue surface calculation using the ‘grid’ option (e.g. surf #0 grid 1), but then I can’t figure out how to apply coulombic coloring to that surface. I could use APBS, but PDB2PQR seems to choke on especially large/complicated structures. Is there any way around this? Would it be possible to export the coloumbic potential as a .dx file and use that for electrostatic surface coloring? Cheers Oli

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Pipes and Planks
by chemocev marker 27 Apr '17

27 Apr '17

Hi Chimera users I am wondering if its possible to assign 2 different color to 2 different helix when use the pipes and planks option in depiction. best Jiri

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file opening problem
by Arthur Szabo 27 Apr '17

27 Apr '17

I had a major problem with my computer - too long a story - Needless to say a computer shop technician had to reinstall my operating system, Windows 7, install Microsoft Office 2016. Of course there were several other programs that had to be reinstalled. So recently I downloaded the latest version of Chimera and have been able to work with PDB files and do all the things that I am used to doing. However, I always save the sessions that I have worked on. They are saved to the desktop C:\users\user\desktop The session files are saved to the desktop. Now comes the problem. When I double click on the file I want [cid:image002.png@01D2A987.C67BFFE0] I get the following message [cid:image001.png@01D2A986.AAC7D360] If I right click on the file then in the menu window click on open with Another window opens with Chimera being the recommended program. Click on OK and the same window as above comes up. This happens even with a .py file that I worked on today. I am puzzled. Ideas will be appreciated. Arthur G. Szabo

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Hey I'm
by Lia Thompson 21 Apr '17

21 Apr '17

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cutting the structure
by Dmitry Semchonok 20 Apr '17

20 Apr '17

Dear colleagues, I did a fit using the predicted models. Now I would like to cut the those parts which don't ft in my EM map. How can I do that? (My EM model has C2 symmetry). Thank you! Sincerely, Dmitry

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[chimerax-users] Chimera bug report submission
by shumaila 19 Apr '17

19 Apr '17

Hi, I want to add oxygen molecule to iron atom in chimera . Kindly help me out how should I add O2 molecule? I tried by Addd bond option but the oxygen molecule is not attached at the desired place. Attached is the protein complex to which I want to attach O2 molecule.Kindly find the attachment. Thank You File attachment: pro time_15000ps.pdb _______________________________________________ ChimeraX-users mailing list ChimeraX-users(a)cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users

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Re: [Chimera-users] How to install package in chimera python?
by hy liao 19 Apr '17

19 Apr '17

Hi, this was posted here, but where exactly do I invoke the said chimera command? I open chimera with IDLE; a python shell opens with the following Python 2.7.10 (default, May 4 2016, 01:09:35) [GCC 4.6.2] on linux2Type "copyright", "credits" or "license()" for more information.==== No Subprocess ====>>> >>> import chimera>>> I tried what the posting said, but got an error>>> chimera --nogui --script get-pip.pyTraceback (most recent call last): File "<pyshell#3>", line 1, in <module> chimera --nogui --script get-pip.pyNameError: name 'nogui' is not defined Thanks,SL [Chimera-users] How to install package in chimera python? | | | [Chimera-users] How to install package in chimera python? | | |

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SAS exposure question
by Kyle Novakowski 17 Apr '17

17 Apr '17

Hi there, I'm hoping to get some clarification on how to calculate the SAS of a defined set of residues within a molecular structure. I currently have 3 molecular structures in a chimera file and was hoping to compare the SAS of a specific region within 2 mutant proteins relative to that same region of the wildtype protein. Thanks. Kyle -- *Kyle Novakowski, B.Sc.* *Ph.D. Candidate: Medical Science (Infection & Immunity) and Laboratory Manager* *Faculty of Health ScienceDepartment of Pathology and Molecular MedicineMcMaster UniversityE: novakoke(a)mcmaster.ca <novakoke(a)mcmaster.ca>P: 905-525-9140 ext. 21551 <905-525-9140%20ext.%2021551> (work/laboratory)*

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How to show local agreement between cryo-EM map and model
by #AHMED TOFAYEL# 17 Apr '17

17 Apr '17

Dear developers and users, Is it possible to generate/color a cryo-EM map to show local agreement between the map and the model generated using the same map? If I am not wrong, the following figure had accomplished the job but I don't understand how to generate a similar figure for my project: http://d2ni3bh4dzb2ig.cloudfront.net/content/embojnl/28/6/755/DC7/embed/inl… Best regards, Tofayel NTU Singapore

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How DMIN, DMAX, DMEAN is re-calculated if particular portion of MRC is chopped in Chimera
by SALIM SAZZED 13 Apr '17

13 Apr '17

Hello, I am a Ph.D. student of Computer Science department at Old Dominion University, USA. I am using Chimera for my research. Can you please tell me how Chimera calculates *DMIN, DMAX, DMEAN *value of MRC header after chopping a portion of original MRC/MAP*?* My understanding about that- *DMIN: T*he minimum density value of the voxels in the MRC/MAP Cube. *DMAX: T*he maximum density value of the voxels in the MRC/MAP Cube. *DMEAN: *The average density of voxels (add all the voxels density value and divide it by the number of voxels). It will be really helpful if you clarify. Thanks Salim Sazzed

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