January 2018 - Chimera-users - RBVI Mailing Lists

Inactive atoms
by Nazahiyah Rodzli 22 Jan '18

22 Jan '18

Dear Chimera Users, My Chimera seems to display atoms and side chains in dimmed dark colour (picture below). I’ve tried to change the colour but they don’t work. I also can’t select any of the atoms/sidechains by mouse click+ctrl unless I pick select all from the select menu. I am using Chimera 1.10 version. Could you help me how I can change the settings perhaps? Best regards, Naza

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Rotate and transform command
by 大帅 22 Jan '18

22 Jan '18

Hi, Therefore, we used UCSF Chimera to have a map's smmetry axes (approximately) parallel to the XYZ axes. The procedure followed by the relion tutorial we used for that was to read in InitialModel/symC1/run_it003_class001.mrc; use the duplicate option under the File menu of the Volume viewer. Then to deactivate map #1 on the Model Panel; rotate map #0 to have it’s symmetry axis more or less parallel to the XYZ axes; and then to use in the Command Line entry field: run_it003_class001.mrc; and save this model in the InitialModel/symC1/ directory with the name inimodel.mrc I have done as the above tutorial in relion, but the saved inimodel.mrc file does not change its position or orientation at all. So, my question is what commend can save a map after rotating or transforming its x,y,z coordinate ? What is the procedures to do so ? Thanks Dashuai

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emails
by Aga Szydlik 20 Jan '18

20 Jan '18

May I please ask to be unsubscribe from all "chimera users questions" emails, thank you Aga Szydlik PhD Candidate, School of Pathology, University of the Witwatersrand National Institute for Communicable Diseases, a Division of the National Health Laboratory Service Centre for HIV & STI's: HIV Virology Section (Morris Laboratory) 1 Modderfontein Road Sandringham, 2131 South Africa email: agas(a)nicd.ac.za<mailto:agas@nicd.ac.za> | www.nicd.ac.za<http://www.nicd.ac.za/> [cid:image003.png@01D2F0EE.60CC2540] Practice Number: 5200296 The views expressed in this email are, unless otherwise stated, those of the author and not those of the National Health Laboratory Service or its management. The information in this e-mail is confidential and is intended solely for the addressee. Access to this e-mail by anyone else is unauthorized. If you are not the intended recipient, any disclosure, copying, distribution or any action taken or omitted in reliance on this, is prohibited and may be unlawful. Whilst all reasonable steps are taken to ensure the accuracy and integrity of information and data transmitted electronically and to preserve the confidentiality thereof, no liability or responsibility whatsoever is accepted if information or data is, for whatever reason, corrupted or does not reach its intended destination.

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Adding Menu items to Python Shell
by Batra, Vinod (NIH/NIEHS) [C] 16 Jan '18

16 Jan '18

Hi How to add menu items to IDLE-> Python Shell opened with Chimera 1:1x running on OS X. Vinod Batra NIEHS

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Command line selection in Chimera
by Jerry Honts 16 Jan '18

16 Jan '18

Is there any easy way to select *a range of chains* in complex models like the ribosome in Chimera at the command line? I haven't been able to work out the syntax for this type of complex selection at the command line. For example, what is the syntax of the command to select chains 1G through 1Z and chains 10 through 19 in PDB file 5DOY [without explicitly listing them one by one]? I may be missing something simple, and I have not been able to get it to work or find an example in documentation. I have been able to do this in Chimera X but not the current version of Chimera. Thanks, Jerry E. Honts -- Jerry E. Honts, Ph. D. Associate Professor of Biology Drake University 2507 University Avenue Des Moines, IA 50311-4505 Science Connector Building 210 (faculty office)

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Re: [Chimera-users] Pseudobonds in mmCIF
by Elaine Meng 16 Jan '18

16 Jan '18

Just for the benefit of the list, the problem with spurious bonds between residues in Chimera was solved by adding sequence information to the input mmCIF file. Elaine > > On Jan 11, 2018, at 1:35 PM, Henry Nguyen <nguyen.henry.c(a)gmail.com> wrote: > > > > Thanks everyone for all the help. My problem is fixed by running mmtbx.prepare_pdb_deposition with the sequence information. The new cif file is displaying pseudobonds correctly and can be toggled on/off. > > > > Thanks again! > > Henry > > > > On Thu, Jan 11, 2018 at 11:43 AM, Greg Couch <gregc(a)cgl.ucsf.edu> wrote: > > Hi Henry, > > > > Sorry about the problems with mmCIF in Chimera. Those problems are a major reason why we wrote ChimeraX. So please check out ChimeraX, http://www.rbvi.ucsf.edu/chimerax/. The mmCIF reader is several orders of magnitude faster than Chimera's and presents the author numbering to identify residues instead of the internal mmCIF numbering. The graphics in ChimeraX are better too. If there is some feature in Chimera that isn't in ChimeraX yet that you need, please let us know. ChimeraX also works with VR headsets. > > And while ChimeraX shows your structure "correctly". It could do a much better job if the missing sequence information were in the mmCIF file. In Phenix, that is done by running the mmtbx.prepare_pdb_deposition program, i.e, by preparing the mmCIF file so that is suitable for submission to the PDB. That would probably help Chimera too. > > > > HTH, > > Greg

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Does Chimera support stereo with a Nvidia Quadro M4000 graphics card?
by xzhang1999＠zju.edu.cn 13 Jan '18

13 Jan '18

Hi, Does Chimera support stereo on the Nvidia Quadro M4000 graphics card? I have a workstation with a Nvidia Quadro M4000 graphcs card (64bit, win10&ubantu), but cannot successfully have Chimera displaying sequential stereo? Any suggestion would be greatly appreciated. Thanks a lot. Best regards, Xing

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Output of distance measurements
by Marco Sette 13 Jan '18

13 Jan '18

Dear all, I have a very primitive script to measure distances, like distance :1.a@ha :5.b@ha distance :1.a@ha :4.b@ha distance .... etc. I run the script in File --> Open and get the distances in the Structure Measurements panel and then Save. The output file list all the distances but, for my analysis, it would be better to keep the lines separated by a blank line, or something like this. Maybe this is possible by some change in my primtive script but I have no idea... Thanks for your help, Marco

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Pseudobonds in mmCIF
by Henry Nguyen 10 Jan '18

10 Jan '18

Hi, I am trying to disable all pseudobonds between gaps in my structure in an mmCIF file. I've tried: In the Pseudobond Panel, there is only one group (distance monitor) and it has 0 pseudobonds in the group. Hiding that group doesn't change anything. I also tried disabling them using setattrr ("setattr p display false"/ "setattr p display false") but neither didn't change anything. If I select a psuedobond and examine it using the Selection Inspector, the Pseudobond tab is unselectable under Inspect. Only if I go to the Bond tab can I hide it. I have to use mmCIF format as I have too many chains for a pdb. Thanks, Henry

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Re: [Chimera-users] importing chimera module question
by Mysteray Rice 10 Jan '18

10 Jan '18

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