October 2023 - Chimera-users - RBVI Mailing Lists

Selecting chain via command line
by Ellen Shrock 19 Sep '24

19 Sep '24

Hello, I am trying to write a script that will iterate through lists of PDB IDs, the relevant antibody chain labels within those PDBs, and antigen chain labels, and annotate the contacts between the antibody and antigen using the command findclash. After opening each PDB file, I am struggling to find a way to select the antibody chains as "sel1" and the antigen chain(s) as "sel2" since the command "select" does not seem to recognize chain labels. Could you please help me find a way to accomplish my goal? Thank you, Ellen

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Chimera interface to Modeller
by Vonderviszt Ferenc 03 Sep '24

03 Sep '24

Hello, I have been using the Chimera interface to Modeller via a web service. This service has been down for a few days. It always stops with the following error message: Service 'opal:Modeller9v8Service' is unavailable What should I do? Please help me. Thanks, Feri

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Finding SASA for individual residues
by Prathvi Singh 29 Aug '24

29 Aug '24

Hi Elaine, Can I use chimera or chimeraX to know the solvent accessible surface area (SASA) for selected residues? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Question about save images
by Chang, Jufang 29 Apr '24

29 Apr '24

Hi, there, I used Chimera for a very short period of time. When I just started using Chimera I was able to save image by going to "file" and "save image" to save the image on the display window. For some reason, this stopped working. Now, after I did the same thing, the image I saved has complete blackness (attached). I wonder whether I might get be able to get help from you. I also tried using command line to save image. The result is the same. The exact procedure I used are: Go to "Presets", choose "publication 1" , then go to "File" and "save image" I used window system. Thank you J ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Unable run Modeller: [Errno 13] Permission denied
by naghmehn85＠gmail.com 27 Oct '23

27 Oct '23

Hello, I was trying to use the Modeller (run it locally) on Chimera UCSF but I encountered this error: Unable run Modeller: [Errno 13] Permission denied. I, as well, received this error when I wanted to load PDB files from my local MacOs. Would you mind please telling me what the issue is? Thank you so much.

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Chimera(X) website and web services down Oct 30-31
by Elaine Meng 26 Oct '23

26 Oct '23

Dear users, Due to system upgrades, the Chimera and ChimeraX websites, associated web services hosted by the UCSF RBVI (Modeller, Blast Protein, etc.), and the ChimeraX Toolshed will be unavailable -- the estimated downtime is from Monday, Oct 30 8:00 am PDT through Tuesday, Oct 31 11:59 pm PDT. Please pardon the inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Error on Chimera
by Giovanni Stelitano 23 Oct '23

23 Oct '23

Dear developers, first of all thank you for your work, the program is quite useful and interesting. I'm using it to perform molecular dynamics for small organic molecules but I have quite a few troubles. I was able to perform a MD in void, but I got this error when I try to analyze the energies, for both kinetic and potential. File "C:\Program Files\Chimera 1.17.3\share\md\mdMovie.py", line 22, in <lambda> name, lambda i, values=values: values[i-1]) Moreover, when I try to run a MD in water (I followed a tutorial on youtube to set up the system and balancing), it stops at the first step of minimization (after 2 days of running it didn't go further according to the log file). I used the Amber preparation (since Gestgeiger seems to not work for my molecules) integrated with AmberFF18SB or 99 that are the one that mostly worked out. I don't think the problem is the calculation power of my machine since I've an Intel i5 processor with a GeForce MX230 and in the options I set up 4 processors. Probably the troubles are just related to the fact that I'm working with small organic molecules instead of proteins? Hoping to find some help/hint in your kind reply, whish a good day and good work, Giovanni. -- *Giovanni Stelitano, PhD in Biomedical Science - Biochemistry* *Department of Biology and Biotechnology "L. Spallanzani"* *University of Pavia* *via Ferrata 9, Pavia, Italy*

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How to obtain transformation matrix between protein structures
by 夏前程 22 Oct '23

22 Oct '23

Hi, I want to use chimera to obtain the transformation matrix between two protein structures. I know that matchmaker can superimpose them together, but I still want to obtain the transformation matrix. I've noticed that matchmaker in chimerax (https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html) offer a keyword "reportMatrix" to do that. But when I use that keyword in chimerax, "Expected a keyword" will be returned without match or a matrix. With Regards, Qiancheng Xia National Institute of Biological Sciences Beijing, China 2023/10/20

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Questions about phosphorylating residues on proteins
by Hoang-Long Bui 16 Oct '23

16 Oct '23

Hello, My name is Andy and I am a student researcher at San Jose State University with the Grazioli Research Group. I am trying to research a section of a protein using your software and was wondering if I could phosphorylate certain residues of the protein, and how. Thank you! Andy Bui

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ChimeraX Redistribution Policy Question
by Patrick Rynkiewicz (RIT Student) 09 Oct '23

09 Oct '23

Hello! I am a co-developer on a molecular dynamics software package that relies on UCSF ChimeraX, and am looking to package this software in a docker container. It's unclear to me from the licensing process what the policy is for ChimeraX redistribution, such as including the .deb package in a docker build. Can you please clarify if I would be able to cite and redistribute ChimeraX 1.6, Ubuntu 22.04 to* non-commercial users* in my software package, or does each individual user need to accept the non-commercial license agreement separately? Thanks! Pat Rynkiewicz

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