July 2022 - ChimeraX-users - RBVI Mailing Lists

How to complete docking with ChimeraX
by 刘金鑫 11 Jul '22

11 Jul '22

Dears, I want to use ChimeraX to dock. The old version can combine with Vina. But I cann't to find the menu in the ChimeraX. Would it be possible? Best regards Jinxin

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Measuring distance between two atoms in a single protein
by McClean, Phillip 11 Jul '22

11 Jul '22

Hi Chimerax Group, I am trying to measure the distance between two atoms in a protein in Chimerax v1.4. The .pdb file I am working with was generated using Alphafold2 in the ColabFold application. I select the two atoms by using CTRL+SHIFT, go to the TOOL -> Structure Analysis -> Distances. The Structure Measurements panel appears in the lower right of the screen. When I click on the Create button, a Chimerax box appears on screen with the following message: Exactly two atoms must be selected! I was surprised to see this message since I thought I had properly selected two atoms. Any advice on how to calculate the distance would be greatly appreciated. Thanks in advance for any help you can provide. Phil McClean Professor North Dakota State University

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Unable to run the option region all
by Edoardo D Imprima 11 Jul '22

11 Jul '22

Dear all, I saved two sessions with different data to make a movie using the same command lines. However, I am not able to obtain the same result when I use the command volume region. In one instance Chimerax renders the whole 3D volumes I selected with “volume #x-y region all". In a second session, with different data but virtually the same commands, the rendering halts at the step before (~disp #1). I am puzzled because in both instances the logs show the command “volume #x-y region all” as executed. And, in the “faulty session" if I manually input the same command that I passed through the script it eventually shows the complete regions of the volumes. Could you please help me to understand what am I doing wrong? I am using ChimeraX 1.4 on Linux. I am pasting here the piece of the scripts that work and do not respectively, Many thanks in advance, Edoardo Working fly p2 p1 100; wait; volume #2 show style surface level 0.8 color #5555ff; volume #3 show style surface level 0.8 color #aa557f; volume #4 show style surface level 0.8 color #f514fd; volume #5 show style surface level 0.8 color #11ffcc; volume #6 show style surface level 0.8 color #ff9429; volume #2-6 transparency 0.8; wait 20; volume all planes z,1344,60; wait 1284; ~disp #1; volume #2-6 region all; Faulty fly p1 p2 100; wait; volume #2 show style surface level 0.8 color #5555ff; volume #3 show style surface level 0.8 color #aa557f; volume #4 show style surface level 0.8 color #f514fd; volume #5 show style surface level 0.8 color #11ffcc; volume #2-5 transparency 0.5; wait 20; volume all planes z,1604,1594; wait 10; ~disp #1; volume #2-5 region all; ------------------------------------------------------ Dr. Edoardo D'Imprima Postdoctoral fellow Structural and Computational Biology Unit EMBL Heidelberg - Mahamid Group Meyerhofstraße 1 69117 Heidelberg Germany Phone: +49 6221 387-8531

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color zone with markers
by HUI WANG 08 Jul '22

08 Jul '22

Dear Developers, I have a need to color a huge ring-like structure with markers, I used to know that we could color the density by the markers as well as the links between them, so It's not necessary to have too many markers. However, I cannot figure out how to color the density covered by the links now. I am using ChimeraX 1.3. Any comments or suggestions will be appreciated! Thanks! Best regards, Hui

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Re: [chimerax-users] [Chimera-users] Coloring model by b-factor
by Elaine Meng 08 Jul '22

08 Jul '22

Dear Yang, I guess you are using ChimeraX (not Chimera) -- the commands are somewhat different between the two programs. There is also different address for asking ChimeraX questions that you might want to use in the future: chimerax-users(a)cgl.ucsf.edu (CC'd here). As far as I can tell, your ChimeraX command is correct. I'm not sure why you said it was not working. Maybe it is because the Log will still tell you the whole range in the structure. However, the coloring range (different than the value range) will be what you specified in the command. For example, if I open 2gbp and use color by bfactor #4/A palette red:green:blue range 35,45 It works correctly. Although the Log says: 2575 atoms, 525 residues, atom bfactor range 2 to 63.9 ... that is just telling you the values in the structure are 2 to 63.9. The red-blue-green coloring, however, is spread from 35-45 and everything below 35 is red and everything above 45 is blue. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 7, 2022, at 1:48 PM, 师扬 via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear developer, > > I am trying to color a model by b-facor and used the command like : color by bfactor #4/A palette red:green:blue range 35,45. However, the range setting was not working. So my question is how to color with a user-defined palette and a user-defined range. > > Best wishes, > Yang

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Morphing animation
by Daniel VillanuevaAvalos 06 Jul '22

06 Jul '22

Hello, I am trying to export a sequence of objs for a morphing animation that I want to use in Houdini FX. The objs do export but they are apparently empty. This is what I am typing on the command line: perframe "save F:/Caltech/CALTECH/04_Growth/4_04_Enzyme_Filaments/objs/from_chimera/AdhE_dimers_morph_01/model$1.obj model #3.$1" ; coordset #3 1,51; wait 51; ~perframe Am I missing something? Thank you, Daniel.

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Obtaining the list of contacting residues for the command interface select
by svle＠tiscali.it 06 Jul '22

06 Jul '22

Hi, I have three chains in a pdb. With the command interfaces select /A contacting /B bothSides true in the Log I receive the following: 19 contacting residues. It is possible to obtain the list of these residues? Thanks. Saverio Voucher MISE per P.IVA e PMI: fino a 2500€ per la Banda Ultralarga. https://casa.tiscali.it/promo/?u=https://promozioni.tiscali.it/voucher_busi…..

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sphereFactor interpolation
by James Hodgkinson-Bean 05 Jul '22

05 Jul '22

Hi I have been playing around with developing some scripts that can measure sphericity directly from input icosahedron virus models. The scripts are working well, however my sphericity measurement is currently not represented as a relative scale between an icosahdron (sphericity = 0) and a sphere (sphericity = 1) as appears the case in chimeraX. I wondered if you could possibly tell me the equation used in ChimeraX to interpolate this scale when generating icosahedral shapes with variable sphericalFactor? Apologies if this question is to complex for a simple quick answer; I'm a first year PhD student and am new to making such calculations. If it's too complicated I'm sure I can figure it out myself. Cheers, James.

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ChimeraX Version 1.4 on CentOS/RHEL 7
by Long Gui 01 Jul '22

01 Jul '22

Dear Chimera community, We are interested in the new version of the ChimeraX/1.4 but we could not find the installation file of ChimeraX/1.4 on our CentOS/RHEL 7 system. Only ChimeraX/1.3 supports CentOS/RHEL 7. So we would like to ask if there is a way to install ChimeraX/1.4 on our CentOS/RHEL 7 system? In addition, our computational source would prefer to install the program using docker. Currently I only find this docker file supports ChimeraX/1.3 https://github.com/maduprey/chimerax-docker/ ? Have anyone tried it for ChimeraX/1.4 yet? Thanks! Long Long Gui, Ph.D. Postdoc Researcher, Nicastro Lab University of Texas Southwestern Medical Center Long.Gui(a)utsouthwestern.edu Tel: (214)-645-1561 ________________________________ UT Southwestern Medical Center The future of medicine, today.

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User/expert community of chimera/chimeraX
by Shivam Gupta 01 Jul '22

01 Jul '22

Hello chimera team, Greetings of the day! I was wondering if we have any official support, user or expert community of chimera and chimeraX where I can get my queries,problems and bugs solved. Looking forward to your reply. Thanks -- 株式会社ファーマフーズ Biomedical Department グプタシヴァム Gupta Shivam 〒615-8245 京都市西京区御陵大原1-49 TEL:075-748-9811 FAX:075-948-9818 E-mail: *shivam-gupta(a)pharmafoods.co.jp <a-higashiyama(a)pharmafoods.co.jp>* URL: http://www.pharmafoods.co.jp/

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