December 2018 - Chimera-users - RBVI Mailing Lists

Chimera Usage
by Xhoela Bame 12 Dec '18

12 Dec '18

Hello, I am new in using chimeraand new in this group. I was wondering if I can ask questions related to thetechniques here. I want to study the pi-pi interactions between a protein andits ligand. Any suggestions on how to do that using chimera? Thanks! Ann

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Programmatic selection and minimisation
by Miro Moman 11 Dec '18

11 Dec '18

Hello, I am trying to use Chimera programmatically in order to automatise a number of tasks. I have tree questions: 1) When I select a zone around the ligand (for instance "runCommand(select #0:501.A zr<5)" the selection level is either atoms or, in this case, residues. Is there a way to select molecules? Because the problem I am finding is that if I run "runCommand(select up)", depending on the PDB file, sometimes I need to do it twice and sometimes three times in order to select the entire molecules (be them proteins or not). I would like to have more control over this function. The purpose being deleting molecules that are far away from the ligand. 2) Right now I am running "DockPrep" followed by "minimize" (without further "prep"). The reason is that "DockPrep" enables me to set options, whereas for "minimize" with "prep" this possibility, if it exists, does not seem to be documented. Is that the case? 3) Finally, in "DockPrep", is there a way to select the charge model explicitly? For instance, to choose Gasteiger charges in order to save time. Kind regards, Miro -- Edelmiro Moman, PhD South Ural State University - SUSU Южно-Уральский государственный университет - ЮУрГУ Phone: +7 902 614 73 77 E-mail: miromoman(a)gmail.com https://www.linkedin.com/in/edelmiro-moman-3a9979a/ <https://www.linkedin.com/in/edelmiro-moman-3a9979a/> <edelmiromoman(a)rcsi.ie>

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Questions about the electric fieldline
by xmgign＠126.com 07 Dec '18

07 Dec '18

Hi I want to make the electric fieldline but there are always some problems. I did this as follows, 1. run add charge to the system 2. run APBS, the I get the electrostatic surface and a file named 1.dx 3. open 1.dx 4.measure fieldLines #0 lines 500 startAbove 10 color pink linewidth 2 then I get the problem : no volume specified I have check the userguide of measure fieldlines, but there is nothing about the volume. measure fieldLines map-model(s) [ lines N ] [ startAbove cutoff ] [ step s ] [ modelId model-number ] [ color line-color ] [ lineWidth width ] [ tubeRadius radius ] [ circleSubdivisions M ] [ markers true|false ] what should I do next? Thanks. Qiao Xue xmgign(a)126.com

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changing atomic radii in Chimera
by Elaine Meng 07 Dec '18

07 Dec '18

Hi Yu Guo, (including chimera-users in the message since it is a general question that other people might be interested in) You can change atomic radii as shown in sphere style with command “vdwdefine,” for example <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html> vdwdef -0.2 Ca (subtract from current size) vdwdef 1.0 Ca (set size to specific value) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html> Maybe the single O atoms (those without bonds) are in stick style, however, so you would also need to change them to sphere style to see a difference. Since the molecule also has O you wouldn’t want to use “O” in the commands or you would change them all. Instead you could select them (Ctrl-click on atom) and then use “sel” in the command, e.g. repr sphere sel vdwdef 0.8 sel Actually, if you select the atom(s) another way is to use Selection Inspector (open by clicking green magnifying glass icon near the bottom right of the Chimera window) to change their display style and radius. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 7, 2018, at 11:05 AM, Yu Guo <yg2(a)kth.se> wrote: > > The movie is fine now! I am now wondering how can I change the atomic radii in Chimera? I find Ca is much too big, and O is too small. See the attached movie.

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mmcif, auth_xx information versus label_xx information
by moocow＠mindless.com 07 Dec '18

07 Dec '18

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Re: [Chimera-users] Breaking down symmetry in Chimera
by Elaine Meng 06 Dec '18

06 Dec '18

Hi Anne, It is recommended to send Chimera questions to chimera-users(a)cgl.ucsf.edu (CC’d here) since others may be able to provide better answers or benefit from the exchange. My guess is that you might instead want to use symmetrical fitting, in which multiple copies of the atomic structure automatically maintain the specified symmetry. Symmetrical fitting is available in the “fitmap” command (not the GUI). See documentation <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#symmetric> and video tutorial <http://www.cgl.ucsf.edu/chimera/videodoc/SymFitDNAb/> The video is >6 minutes but worth watching, because like in that video you may need to first just fit one copy (not using symmetry), then use command “measure symmetry” to annotate the map with its symmetry, and then use command “sym” with “update true” to generate the symmetry copies of the atomic model. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 6, 2018, at 10:32 AM, Jecrois, Anne <Anne.Jecrois(a)umassmed.edu> wrote: > > Dear Dr Meng, > I have a 5A cryoEM map with D3 symmetry, howeve I am having some problem with rigid body fitting since I don't know where one assymmetric unit starts or ends . I was wondering if there is way to break down the symmetry in chimera and extract 1/6 of the map and use that for fitting? > Thanks, > Anne Jecrois > PhD Candidate > UMass Medical School > Schiffer Lab/Royer Lab > 364 Plantation St, LRB 970L > Worcester MA 01605

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Saving mrc EM-map
by Ibrahim M. Moustafa 06 Dec '18

06 Dec '18

Hi All, I'm trying to do the fitting of a model into EM (mrc map) for real-space-refine in phenix.First I read the map and clicked "center" in the Volume viewer. Then I saved the centered map, assuming that the header info will be updated in the saved map.I did the fitting and saved the model relative to the map. Reading the saved map and fitted model back looks OK. However, when I do the real-space-refine in Phenix, the CC-value during the run is really low (0.01) suggesting something is not properly done. I checked the header (using mrcfile) of the saved "centered" map and compared it to the original map and it is the same "0,0,0". Which means chimera did not update the header after centering. I'm not if there is a more proper way to do this! Any advice? Thank you for your help. Ibrahim Ibrahim M.Moustafa, Ph.D. Pennsylvania State University Biochemistry & Molecular Biology Dept. Millennium Science Complex University Park, PA16802 Tel (814)863 5940 Fax (814)865 7927

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join models
by Stewart Morley 05 Dec '18

05 Dec '18

I cannot for the life of me get join models to work. 1. I have two structures. 2. The structures overlap. 3. I align them using matchmaker. 4. I delete the overlapped residue from one chain. 5. I select the appropriate C and N terminal residues 6. I try to use join models under Build structure 7. The apply box remains gray, no matter what residue or atom I select. What are common problems that cause join models to not work? Stewart Morley Brigham Young University

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