February 2022 - ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] Bundle dependency
by Anthony James Schaefer 21 Feb '22

21 Feb '22

Katie, I'm not sure. I tried adding pdb-objects to one of my bundle's dependencies, and it was installed. I'm testing this on a ChimeraX 1.4 daily build. My bundle_info.xml has this: <Dependencies> <Dependency name="ChimeraX-Core" version=">=1.2.dev"/> <Dependency name="pdb-objects"/> </Dependencies> and my log has this after installing (along with a bunch of other stuff): Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\normn\documents\github\chimerax_themes\dist\chimerax_themes-0.3.1-py3-none-any.whl Requirement already satisfied: ChimeraX-Core>=1.2.dev in e:\chimerax 1.4.dev202202010639\bin\lib\site-packages (from ChimeraX-themes==0.3.1) (1.4.dev202202010639) Collecting pdb-objects Using cached pdb_objects-0.1.3-py3-none-any.whl (6.6 kB) Installing collected packages: pdb-objects, ChimeraX-themes Successfully installed ChimeraX-themes-0.3.1 pdb-objects-0.1.3 --- Successfully installed ChimeraX-themes-0.3.1 pdb-objects-0.1.3 Installed ChimeraX-themes (0.3.1) Towards the bottom, it says it installed pdb-objects and my bundle. I can then go into the shell and import pdb_objects without error. Best, Tony ________________________________ From: Zeng, Katie <jingrou.zeng18(a)imperial.ac.uk> Sent: Monday, February 21, 2022 2:59 PM To: Anthony James Schaefer <tony.schaefer(a)uga.edu> Subject: Re: Bundle dependency [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Hi Tony, Thanks for pointing that out. I've now changed the dependency to pdb-objects, but I still get the same error when I try to use the bundle in ChimeraX. Have you got any idea why it's giving this error? Best Regards, Katie ________________________________ From: Anthony James Schaefer <tony.schaefer(a)uga.edu> Sent: 21 February 2022 17:57 To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu>; Zeng, Katie <jingrou.zeng18(a)imperial.ac.uk> Subject: Re: Bundle dependency This email from tony.schaefer(a)uga.edu originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address. Katie, It looks like PDB objects on PyPI is called pdb-objects, not pdb_objects. For dependencies, ChimeraX looks for the package name and not the import name. Best, Tony ________________________________ From: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu> on behalf of Zeng, Katie via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> Sent: Monday, February 21, 2022 11:50 AM To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Subject: [chimerax-users] Bundle dependency [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Hi, I'm currently working on building a membrane builder bundle and it requires the use of a python library called 'pdb_objects'. Following the tutorial on the website, I'm adding the following line to my bundle_info.xml file under the dependencies tag: <Dependency name="pdb_objects"/> It still gives me an error of <No module named 'pdb_objects'> when I load my bundle in ChimeraX. How can I allow the use of this library in my bundle? Thanks for your help! Best Regards, Katie

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Bundle dependency
by Zeng, Katie 21 Feb '22

21 Feb '22

Hi, I'm currently working on building a membrane builder bundle and it requires the use of a python library called 'pdb_objects'. Following the tutorial on the website, I'm adding the following line to my bundle_info.xml file under the dependencies tag: <Dependency name="pdb_objects"/> It still gives me an error of <No module named 'pdb_objects'> when I load my bundle in ChimeraX. How can I allow the use of this library in my bundle? Thanks for your help! Best Regards, Katie

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Re: [chimerax-users] No suitable models found for viewDockX
by Rangarajan, Amith 21 Feb '22

21 Feb '22

hello chimeraX, I am trying to open a glide docking result using viewdockx and i am getting this error message ('no suitable models found"). I tried opening the file as .mae file ( protein and ligand are both in same model )and a pv.mae file ( protein and ligand are in diff models). I am still getting the same error. I am using chimerax ver 1.3 please help me see what i am missing. thanks amith

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Question about Coulombic electrostatic potential
by Sunisa Yoodee 21 Feb '22

21 Feb '22

Dear UCSF ChimeraX We used the ChimeraX program to calculate electrostatic potential. By using the coulombic command, a molecular surface was generated and colored. However, we also need the electrostatic potential value (kcal/(mol*e))of the protein. Could you please give some advices how to get this value? Best Regards, Sunisa Yoodee -- *Sunisa Yoodee*, Ph.D Medical Proteomics Unit, Faculty of Medicine Siriraj Hospital, Mahidol University, 6th Floor SiMR Building, 2 Wanglang Road, Bangkoknoi, Bangkok 10700, THAILAND Tel: 66-8-06691102 e-mail: yd.sunisa(a)gmail.com

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Define axis tool missing?
by James Hodgkinson-Bean 20 Feb '22

20 Feb '22

Hi I am currently doing some geometric analysis of a protein complex, and was wanting to define certain axis normal to planes I have defined; on the online chimerax documentation there seems to be an option “define axis”, however in my actual chimeraX program, this command doesn’t work, and is not listed under the “help define” command which shows how to define planes and centroids. I am running ChimeraX version 1.3 (2021-12-08), which I downloaded recently. Any assistant would be much appreciated 😊 P.S I absolutely love chimeraX!! It is one of the best pieces of software I’ve ever used. Cheers, James.

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The ChimeraX-Modeller interface
by Ralph Loring 18 Feb '22

18 Feb '22

Hi, The intracellular domain (ICD) of Alpha7 nicotinic receptors, like almost all eukaryotic Cys-loop receptors, is not resolved using X-ray crystallography or cryo-EM. Last week the PDB for an ensemble of NMR ICD structures for the receptor was released (PDB 7RPM). I've been unsuccessfully trying to use ChimeraX and Modeller to make a model of a subunit that includes the ICD. The 7RPM models include all 4 transmembrane domains and the ICD (but lacks the extracellular domain), so there is considerable overlap with the 7KOO PDB fo a7. I started by deleting all but one of the identical subunits in the 7KOO pdb and loaded one of the 7RPM models and tried to use Modeller to make a construct that includes both the extracellular domain and the ICD. Unfortunately, even though both 7KOO and the single 7RPM are in the sequence alignments window, the ChimeraX-Modeller combination ignores the structure that is not chosen as the target (e.g. if 7RPM is the target, there is no extracellular domain, but if 7KOO is the target, there is either no ICD or the ICD that is shown bears no relevance to the structure in 7RPM). I can align the two structures well with a low RMSD using Matchmaker because of the TMDs overlapping. I just want to fill in the missing parts. Is there a special trick to get Modeller to fill in the missing parts using ChimeraX as the interface? I'm not that experienced using Modeller. Thanks, Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring(a)northeastern.edu

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surfvalues.py
by 始夏谨柘 18 Feb '22

18 Feb '22

      Hello,          This python script was downloaded on UCSF CHIMERA page (https://www.rbvi.ucsf.edu/trac/chimera/attachment/wiki/Scripts/surfvalues.p…) and running it on UCSF CHIMERA X will cause an error. UCSF CHIMERA X (https://rbvi.github.io/chimerax-recipes/) has not found the corresponding script. If I still want to achieve the function of this script (surfvalues.py) , what should I do? I tried that at UCSF CHIMERA, but the volume of the protein is too large for it. Best Wishes,                                                                                                  FAYE

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System Requirements
by Niver, Terry 17 Feb '22

17 Feb '22

Hello, I am attempting to assist a researcher here at the University of Rochester configure a new laptop on which he wants to run ChimeraX. I was trying to locate the system requirements on the website but didn’t have any luck. Would someone be able to send me a list? Thanks, Terry Terry Niver Manager, Research and Academic Information Technology Technical Support University of Rochester School of Medicine and Dentistry E-mail: terry_niver(a)urmc.rochester.edu<mailto:terry_niver@urmc.rochester.edu> Phone: 585-276-5538

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fine tuning depthcue
by vincent Chaptal 17 Feb '22

17 Feb '22

Hi, I've been playing around a lot with depthcue-ing but I can't get it to do quite what I would like. I want to display a protein structure, with a focus on one zone and a "heavy" depthcue to have a strong "fog" hiding much of the background (without deleting the residues in the back). my script includes: lighting full #(sometimes I use soft too) lighting shadows true intensity 0.3 lighting qualityOfShadows finer lighting depthcue true depthCueStart 0.1 depthCueEnd 1.0 First, I have selected one residue and setting the rotation around it by using "cofr sel" My max depthcue is with "depthCueStart 0.1 depthCueEnd 1.0". I've tried to change these numbers in many different ways, including negative or very large numbers) but I can't get it to be thicker. Could you help me please. I missed the meaning of these values, so I'm blind on their use. Thank you Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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Re: [chimerax-users] VR Support
by Jessie Lopez 16 Feb '22

16 Feb '22

I am writing an article promoting the use of VR for modelling. I use an HTC Vive to access ChimeraX VR, but I have heard rumours it will be discontinued soon. The Samsung Odyssey is already discontinued. With Meta dominating the VR headset market, many companies are bailing out. Do you have any recommendations about which headsets should scientists invest in if they want to use ChimeraX? Thank you! -. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. . ||*\*|||*\* /|||*\*|||*\* /|||*\*|||*\* /|||*\*|||*\* /|||*\*|||*\* /|||*\*|||*\* /| |/ *\*|||*\*|||/ *\*|||*\*|||/ *\*|||*\*|||/ *\*|||*\*|||/ *\*|||*\*|||/ *\*|||*\*|| ~ `-~ `-` `-~ `-` `-~ `-~ `-~ `-` `-~ `-` `-~ `- *Jessie MNG Lopez Suzuki* PhD Candidate, Molecular, Cell and Developmental Biology *Zahler Laboratory* The Center for Molecular Biology of RNA University of California, Santa Cruz Sinsheimer 419 (831) 459-5127 *jlopez99(a)ucsc.edu <jlopez99(a)ucsc.edu>* (they, she or he pronouns)

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