July 2021 - Chimera-users - RBVI Mailing Lists

Minimization troubleshooting
by Nicole Ostrovsky 19 Jul '21

19 Jul '21

Hello, I am trying to perform minimizations on some structures I'm examining and each time the minimization is done and I open the reply log, the gradient norm says "-nan" and it tells me that no atoms were updated. I wasn't able to find anything online about how to fix this, so I'm emailing to ask if anyone would know how to troubleshoot this. Thank you. Nicole Ostrovsky

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Blast protein webservice error
by Stefan Dobrev 14 Jul '21

14 Jul '21

Hello! I'm trying to run a homology model on a protein sequence using BLAST, but my Blast: query window shows up empty. At first I got this error in the reply log: File "C:\Program Files\Chimera 1.15\share\blastpdb\pdbinfo.py", line 151, in fetch_pdb_info import replyobj ImportError: No module named replyobj I solved it by changing the code to "from python import replyobj". Now I can actually see what the error is. A few more functions are called until we get to this: File "C:\Program Files\Chimera 1.15\bin\lib\socket.py", line 480, in readline data = self._sock.recv(self._rbufsize) error: [Errno 10054] An existing connection was forcibly closed by the remote host I've allowed chimera through the firewall and I have a modeller license key, I believe I've entered it somewhere in Chimera at some point. Any ideas what might be causing this? Thanks for any advice, Stefan Dobrev

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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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