June 2023 - Chimera-users - RBVI Mailing Lists

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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Saving Animations on Mac OS
by Natalie Walsh 25 Jul '23

25 Jul '23

Hello, I am having troubles saving my animations on my Mac OS. I get this error when I record and save my animation: An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: -1 Error message: Could not find ffmpeg executable —————————————— I googled some solutions regarding “ffmpeg” and I believe I successfully installed it to my terminal, but I am still receiving the same error. Thank you, Natalie Walsh

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Removing lonbond links from pipes-and-planks representation
by philip.robinson＠bbk.ac.uk 02 Jul '23

02 Jul '23

Hi, I'm trying to generate a pipes-and-planks representation of an atomic model that contains gaps. Before generating the pipes-and-planks representation I hid the long bonds to remove the links in the gap regions. However, the gaps are connected again in the pipes-and-planks representation and I cannot find the command to hide them. Any help would be appreciated. Phil

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ChimeraX Question
by Bani Kaur 01 Jul '23

01 Jul '23

Hi, I hope you are doing well! My name is Bani Kaur and I am an active user of ChimeraX for a research project concerning protein modeling, specifically with the CFTR protein. I have been running into issues with showing atoms on my residue, specifically after I change the romater. I am not sure what to do about this as I have downloaded the latest version of ChimeraX. Additionally, I am not able to see clashes for some very reason and am only able to see it when limit by selection is unchecked, but for my research project, we require that it is checked in the clashes settings. Thank you so much for your help! Best, Bani Kaur

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Questions regarding reply log
by Prathvi Singh 28 Jun '23

28 Jun '23

Hi Elaine, Is there a way to clear the Reply Log using the command line? Is there a way to write the contents of the Reply log to a text file? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Supoort for automating superimposition process of multiple pairs of structures using command line
by Vaibhav Anand 28 Jun '23

28 Jun '23

Hello Chimera team, I am seeking your assistance in automating the process of superimposing multiple pairs of structures using the command line. I've performed the MD simulation of the UBA domain (PDB ID - 1OQY), and for analyzing the structural changes, I've extracted the 11 structures from the trajectory at 500ns to 1000ns with steps of 50ns. In total, I've 12 structures [1 reference structure (em.gro - energy minimized structure) and 11 extracted structures]. Now I want to superimpose each extracted structure w.r.t. em.gro and save the image of superimposition with the image name to be (time + rmsd_value). For the RMSD value, I'll have to save the reply log file (or the last 10-15 lines of the reply log) and then copy the rmsd value and save my image file with it. Could you please give me an outline or references on how I can do this task? Thank you for your attention Regards, Vaibhav

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downloading and saving multiple PDB's
by Dmitry Semchonok 26 Jun '23

26 Jun '23

Dear colleagues, Is there a way to 1. download the multiple pdb/mmcif using Chimerax knowing their ID entry? 2. save multiple opened pdbs using their corresponding original names in Chimerax? Thank you in advance. Kind regards, Dmitry

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Regarding issue detected while running chimera
by Suman Dhungel 26 Jun '23

26 Jun '23

Dear concerned one, I have been using UCSF Chimera from another device for the past 10 years. Recently I tried to operate chimera-1.17.1 on my computer. I have been facing a repeated issue that has been reported below. I tried to reinstall however, the issue persisted. I even tried with the new version (Chimera alpha ), similar issue with that as well. [image: chimera error.JPG] [image: my device.JPG] Would you please help... Regards Suman...

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Error while startup
by Ramanakishore V.S 26 Jun '23

26 Jun '23

Respected sir I have downloaded the Chimera V 1.17.1 on my Laptop. But when I try to open it, I am getting an error code -1073741819. I tried multiple options and sources but couldn't fix it.So can you please look into it. I have attached a image of the error message Thank you

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Re: Seeking help with Chimera regarding superposition of multiple structures
by Elaine Meng 25 Jun '23

25 Jun '23

> On Jun 25, 2023, at 7:21 AM, Vaibhav Anand <dvaibhav(a)iitk.ac.in> wrote: > > Respected Mam, > I hope this email finds you well. I am seeking your assistance in resolving a problem I am currently facing. > > I have performed the Molecular dynamic simulation of the UBA domain (PDB ID - 1OQY), and for analysis, I've extracted the 11 PDB structures at [500ns - 1000ns with steps of 50ns], and I've one reference structure (em.gro - energy minimized structure). > > I want to superimpose 11 structures with respect to my reference structure and compute the RMSD corresponding to helical residues (162-172, 177-187, 192-197). > > I am aware that in Chimera, an in-built tool called Matchmaker can perform the superimposition for multiple structures, but it doesn't have an option for selecting required (helical) residues. > > I've tried using the command line but cannot select the C-alpha atoms of helical residues. I've used the following commands - > > >>mm #0:162-172, 177-187, 192-197@CA #1-11:162-172, 177-187, 192-197@CA (Error - "Invalid atom specifier syntax: '177-187,'") > > >> mm #0:162-172, 177-187@CA #1-11:162-172, 177-187@CA (Error - "Invalid atom specifier syntax: '177-187@CA'") > > However, the following command is running well - > > >>mm #0:162-172@CA #1-11:162-172@CA (Output - "RMSD between 11 pruned atom pairs is 0.607 angstroms; (across all 11 pairs: 0.607)") > > I've also checked the atom specifications from the documentation for further guidance. - Atoms specifications > > I kindly request your assistance in resolving this issue. > Thank you for your attention. > Regards, > Vaibhav Anand Dear Vaibhav Anand, Questions about using Chimera should be sent to chimera-users(a)cgl.ucsf.edu CC'd here. <https://www.rbvi.ucsf.edu/chimera/docs/feedback.html> If you want to specify the exact atoms to use yourself, then the command is "match" (not "matchmaker" or "mm"). See "match" and also the discussion of different superposition methods. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> You are also giving wrong atom specifications. They should not have spaces after the commas. I.e. should be something like the following. match #0:162-172,177-187,192-197@CA #1-11:162-172,177-187,192-197@CA Command-line specification: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic> 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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Chimera-users June 2023