- Chimera-users - RBVI Mailing Lists

Measuring the distance between an atom and the protein surface
by Sergio Garay 18 Dec '18

18 Dec '18

Dear Chimera Users I want to measure the distance between an atom (or group of atoms) and the protein surface. I need a sort of residue depth, so the shortest distance between an atom and the molecular surface would be fine for me. I found that command "measure distance" could help, but it does not appear to be working, because every atom that I choose give aproximately the same value. For example (I have only one molecule loaded in Chimera) :. measure distance #0:1@ca #0 log info: minimum distance from #0:1.B@CA to 1752 atoms, 1 surfaces = 1.4814 measure distance #0:58@ca #0 minimum distance from #0:58.B@CA to 1752 atoms, 1 surfaces = 1.4484 The second selected atom is clearly deeper inside the protein Thank you in advance Sergio -- *Sergio GarayDr. en Ciencias BiológicasFacultad de Bioquimica y Cs. BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 - Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54 (342) 4575-221 *

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Re: [Chimera-users] Chimera
by Elaine Meng 16 Dec '18

16 Dec '18

> On Dec 16, 2018, at 6:05 AM, Xhoela Bame <xhoelabame(a)yahoo.com> wrote: > > Hello, > > I hope this message finds you well. > > I had posed a question in chimera website but maybe it did not come to you. > > I am studying ligand interaction with a protein and there are pi pi interaction. I am not sure on what is the principle I have to use to show that there is this type of interaction and illustrate that with chimera. > > Also, when showing H bonds, I want to show residue side chain as well in the picture as open structures. Any suggestion on that? > > I am quite new in using chimera and I would be extremely helpful if you would help me on these questions. > > Best, > Ann Hello, In the future, please send questions to chimera-users(a)cgl.ucsf.edu rather than to me directly, and put something useful about the topic in the Subject line like “showing side chains” or “pi-pi interactions.” I did reply to you already about the pi-pi question but perhaps you did not see the answer. I changed the subject line because “Chimera Usage” was not descriptive. Here is that previous answer: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018-December/015270.html> To show the side chains, turn on this option of FindHBond before running the H-bond calculation: "If endpoint atom hidden, show endpoint residue” <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbo…> If you click Help on the FindHBond dialog it would show you that page. Or if you are using the commands, command “help hbonds” would show you the “hbond” command help and its “reveal” option to do the same thing. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Question about Gaussion filtering
by CAO, Sheng 13 Dec '18

13 Dec '18

Dear Sir/Madam, I am a Ph.D student from The Chinese University of Hong Kong that have just begun to learn structural biology. I found that the Gaussion filtering in Chimera has a much better result than other programs. And I an quite interested in it. Could you please share the principle of the Gaussion filtering algorithm used in Chimera? Thank you. Best Regards, Cao Sheng Postgraduate of The Chinese University of Hong Kong Major: Chemistry E-mail: 904323223(a)qq.com<mailto:904323223@qq.com> Address: G55, Science Centre South Block, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong P.R.China

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Trajectory superposition question
by Samo Lešnik 13 Dec '18

13 Dec '18

Dear Madam/Sir, I have a long MD trajectory (dcd files), and before performing analysis on it I would like to superimpose every frame to the protein from the first frame or the protein from the average one. I am not sure how can this easily be performed. Thank you for your answer, Samo Lešnik

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An oddity in ribbon.
by Yehuda Halfon 13 Dec '18

13 Dec '18

Hi, I have an oddity when showing ribbon. When I show the loop (see figs) in ribbon I get the small thing in the middle and when I show it in atom the loop is longer. In coot the loop looks fine. Is it in the PDB? is in a chimera error? It only happens in this loop in this PDB. The same loop in other PDBs is fine. Thanks, Yehuda Halfon

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Color subunits for map density
by BuddySphinx 12 Dec '18

12 Dec '18

Dear Chimera developers, I have a quick question about coloring. I have a filament map with multiple monomers, how can I color each monomer density with different color? I have a built model, should I do it based on the atom number or should I segment the filament? Best, Yangqi Sent from Mail for Windows 10

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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 10 Dec '18

10 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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