- Chimera-users - RBVI Mailing Lists

Flipping the map - resolution question
by Dmitry Semchonok 14 Jul '21

14 Jul '21

Dear colleagues, I heard that flipping the map in Chimera with the command vop zflip # will decrease the resolution of the map https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#notes <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#notes> Did I understand that statement correctly? If yes, how to flip the map without losing the quality (resolution)? Thank you Sincerely, Dmitry

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Running/opening issue of chimera on HPC login node
by Rajiv Ranjan Singh 13 Jul '21

13 Jul '21

I am trying to open/run chimer; installed on a cluster login node without root privilege. Installed in Home//.local/UCSF-Chimera64-1.15rc/ Getting the following error. *login1:*~/.local/UCSF-Chimera64-1.15rc/bin $ ./chimera libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 152 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 716 Current serial number in output stream: 717 Kindly advise me to rectify this issue. Best, Rajiv Ranjan Singh

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unable to open more than one map in Chimera
by Merk, Alan (NIH/NCI) [C] 12 Jul '21

12 Jul '21

Hello, I recently updated to Catalina on my Mac and I am now not able to open more than one file at a time in Chimera. Uninstalling the program and then installing the latest version from scratch did not fix the problem. Is there any way to resolve this issue? Alan

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Users group
by Zachary Morton 09 Jul '21

09 Jul '21

Hi, My name is zach morton, I am from UC Santa Cruz and I would like to be added to the user group please. Best, Zach

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WebGL file
by Avnam Ohri 06 Jul '21

06 Jul '21

Hello Chimera Team i have been trying to make a script for looping through a set of pdb files and get WebGL (.html) file as the output import os import chimera import Midas from chimera import exports from chimera import runCommand as rc # use 'rc' as shorthand for runCommand # change to folder with data files os.chdir("E:/files to work/") # gather the names of .pdb files in the folder file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] # loop through the files, opening, processing, and closing each in turn for fn in file_names: rc("open " + fn) rc("ac wb") rc("ac c2") htmlname = fn[:-3] +'.html' exports.doExportCommand("WebGL",htmlname) rc("close") This is the code I have been using in the script , but the output i get is not working , i have been getting 26kb files instead of 3-5 mb files and it doesn't show anything when I open it. can you please help me with the same as i am new to python code

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Volume subtraction of surface area between homology model and template
by Kovacs, Nicholas (CDC/DDID/NCIRD/ID) 06 Jul '21

06 Jul '21

Hello, I have a homology model that I have made and I would like to create a visual that portrays small surfaces where there is change in the solvent accessible surface area of the homology model compared to the template structure. I am trying to use the "subtract" map from map calculation which requires volume data for the 2 structures. I have tried the following to generate volume data and then subtract the volumes, but I am getting hundreds of small surfaces all throughout the area of the molecule: molmap #1 3 molmap #2 3 volume subtract #3 #4 I know molmap is likely not the command I want to be using since I am interested in the solvent accessible surface area but I have yet to find a command that will generate a volume corresponding to the volume enclosed by the solvent accessible surface area. I would greatly appreciate it if someone could help me find a way to create 2 volumes enclosed by the solvent accessible surface area of the 2 structures in addition to correctly configuring the "volume subtract" command to get my desired output. Thank you, Nick

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Webgl, python script for multiple pdbs
by Avnam Ohri 06 Jul '21

06 Jul '21

Hello Chimera Team i have been trying to make a script for looping through a set of pdb files and get WebGL (.html) file as the output. import os import chimera import Midas from chimera import exports from chimera import runCommand as rc # use 'rc' as shorthand for runCommand # change to folder with data files os.chdir("E:/files to work/") # gather the names of .pdb files in the folder file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] # loop through the files, opening, processing, and closing each in turn for fn in file_names: rc("open " + fn) rc("ac wb") rc("ac c2") htmlname = fn[:-3] +'.html' exports.doExportCommand("WebGL",htmlname) rc("close") This is the code I have been using in the script , but the output i get is not working , i have been getting 26kb files instead of 3-5 mb files and it doesn't show anything when I open it. can you please help me with the same as i am new to python code

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Error in using chimera with structureviz2 and cytoscape
by SRUTHI NAMBIAR 30 Jun '21

30 Jun '21

Dear all, I have been using chimera for the past 1 year and recently wanted to club it along with the cytoscape software. But whenever I try to launch chimera through the structureviz app, I get the following message: Error message: Cannot run program "/home/students/chimera/": error=13, Permission denied I have changed the settings of structureviz to give the path of chimera which is /home/students/chimera. Still this error is occurring. Could someone help regarding the same? Thank you. Regards, Sruthi

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how to calculate RMSD
by Elaine Meng 30 Jun '21

30 Jun '21

> On Jun 30, 2021, at 7:19 AM, lufeiyu(a)jlu.edu.cn wrote: > > Dear Sir/Madam: > > I have a question about the analysing of the docking. I docked a peptide to the receptor using GALAXYpepDOCK. The results uncontained the scores of RMSD. Some literatures reorted the UCSF could calculate the RMSD. But I didn't get the way after reading the tutorials. Please help me to figure out how to obtain the RMSD of a docking structure .Thanks vwry much. Best wishes for you. > > sincerely yours > Feiyu Lu Dear Feiyu Lu, The chimera-users(a)cgl.ucsf.edu address is recommended for asking questions about how to use Chimera. I CC'd it here, so you do not need to send your question again. (Or if you are using ChimeraX, you should use chimerax-users(a)cgl.ucsf.edu in the future for asking questions.) An RMSD measures the difference between two different locations of a set of atoms. So in Chimera you would need to open not only the docking results, but also the position of that peptide that you want to use as reference to calculate their RMSD. Then, you can use the "rmsd" command to compare them. I cannot give an exact command since I don't know the model numbers you will have, but an example if you had the comparison peptide open as model #3 and the docking result models are #1.1, #1.2, #1.3 ... then your commands could be: rmsd #3 #1.1 rmsd #3 #1.2 [...] See rmsd command help: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> The results would be shown in the Reply Log (open from Favorites menu). Also if you don't know what model numbers you have, look in the Model Panel (also can be opened from the Favorites menu). Model Panel help: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.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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Join models function on Chimera
by Azad, Roksana 29 Jun '21

29 Jun '21

Hi There, I hope you are doing very well. My name is Roksana Azad, I am a Ph.D. Student at the CUNY ASRC. I have been working on building a full length model of my protein into a cryoEM map, I have models for individual domain but not for the full lenght structure. I am trying to join the domain models using chimera "join models" function, but unfortunately it's not working for me. I tried everything I could find online about the issue, I used the addh command and kssdssp commands and also tried joining them using other bond instead of C-N, however my button for "apply" always grey and I can't click on it (please see the screenshot attached). I also tried this command "#0:127.A@C #1:1.A@N" according to my model # and atom, but its not selecting anything for me. I tried "combine" it also didn't work.? Please let me know if there is something else I am missing or what else I can do to create this bond or connection between two models. Thank you so much for your time and help in advance - very much appreciated. Sincerely, Roksana ________________________________ Roksana Azad<https://asrc.gc.cuny.edu/people/roksana-azad/> Ph.D. Candidate in Biochemistry & Biophysics Advisor: Kevin H. Gardner<https://kglab.ws.gc.cuny.edu/> Structural Biology Initiative; CUNY Advanced Science Research Center 85 St Nicholas Terrace * New York * NY * 10031 Phone: 212-413-3233 Email: razad(a)gc.cuny.edu

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