June 2023 - Chimera-users - RBVI Mailing Lists

regarding movie making
by lumbini yadav 22 Jun '23

22 Jun '23

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Support for saving pdb files with 2 models in the same file using command line
by Raquel Cossío Ramírez 20 Jun '23

20 Jun '23

Hello Chimera team, I have been working with docking files obtained from cluspro and I'm working on a set of commands to open the files in chimera, perform a ksdssp and save them in a single individual file. The problem that I have found while doing it was that secondary structure was not well calculated for the second model, so when I run the save (write) command, I only obtain a file with 1 molecule and it does not include the MODEL 1 nor MODEL 2 header, which I need it so I can analyze it later. Here I send the code that I have been running (save_all.py) with the command and a log of the problems it present while running, as well as an example input (model.000.00.pdb) and output file (ch_model.000.00.pdb) that this code produces. Also, an example of the files that I would like to generate is included in ch_model.000.00_manually.pdb The save_all.py runs in the Ubuntu terminal as follows: chimera --nogui save_all.py I believe that the code could be improved by adding an option to "save multiple files in a single file" as the GUI can allow, but using the command line, I could not find that option. I would really appreciate if you had some insight about how it could be solved. Thank you for your attention and I wait for your prompt response. Raquel Cossío Ramírez Corelab Genomics at Tecnológico de Monterrey

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Solvent Accessible Surface Area results
by Abril Gijsbers 15 Jun '23

15 Jun '23

Hi, I calculated the SASA from an AlphaFold model and a homology model with Chimera. Some of the residues got a value of zero and I just wanted to know if that means that those residues are not accessed to the solvent at all or could be a problem in the calculation? Best regards, Abril

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How to tile different models without tiling submodels
by 夏前程 13 Jun '23

13 Jun '23

Hi, I want to use chimera to depict two conformation ensembles. Each conformation ensemble is a model, and each conformation in that ensemble is the submodel within that One of the possible way I've found to do that is to use tile command (tile #1-2.*). However, that command will consider each submodel (each molecule) instead of each model (each cluster) as a whole. So I am wondering if there is any solution or suggestion? With Regards, Qiancheng Xia National Institute of Biological Sciences Beijing, China 2023/6/13

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Re: Server problem ??
by Eric Pettersen 12 Jun '23

12 Jun '23

It seems you are in fact using Chimera 1.16. Web services only work with 1.17.1 on Windows. --Eric > > I just got the following error trying to run a python script that includes sequence alignments: within Chimera (1.17) > > TransportError: HTTP Error 404: Not Found > > Typically, if you get a TypeError, it's a problem on the remote server > and it should be fixed shortly. If you get a different error or > get TypeError consistently for more than a day, please report the > problem using the Report a Bug... entry in the Help menu. Please > include the traceback printed above as part of the problem description. > Traceback from web application request: > Traceback (most recent call last): > File "C:\Program Files\Chimera 1.16\share\WebServices\appWebService.py", line 48, in _initApp > self.backend = Backend(service, url) > File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 21, in __init__ > raise NonChimeraError("Web service appears " > NonChimeraError: Web service appears to be down. See Reply Log for more details. > > Ix this a problem with the server used to run the alignment ?? > > > Thanks > > Hernando > > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>: To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu <mailto:chimera-users-leave@cgl.ucsf.edu> > Manage subscription:

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REMINDER: Chimera website downtime
by Elaine Meng 12 Jun '23

12 Jun '23

REMINDER: Due to a scheduled power outage at UCSF followed by server upgrades, the Chimera website and web services will be unavailable -- the estimated downtime is from Tuesday May 16 8pm PDT through Wednesday May 17 8pm PDT. This upgrade will remove the Opal web services used by older versions of Chimera. Therefore, to continue using the Chimera tools running BLAST protein, Modeller comparative and loop modeling, and multiple sequence alignment with Clustal Omega and MUSCLE web services, you will need to upgrade to Chimera 1.17 (Mac) and 1.17.1 (Windows/Linux). Please pardon any inconvenience. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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getcrd command
by Yanhe Zhao 09 Jun '23

09 Jun '23

Greeting there, I am trying to get coordinate for fulcrum selection in cryoSPARC. I use volume tracer place a marker on the position of map density I wanted, with the maker selected, I use getcrd command report the coordinate in xyz in Angstroms, when I divide the values by the pixel size, the xyz in voxels are make no sense, as they are larger than my volume size. Like my volume size is 1024^3, got coordinates in Angstroms 2100,2100,2000, my pixel size is 1.475. Could you please anyone help me out? Do I did something wrong? Thanks and best, Yanhe

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Loading Trajectory Files from Command Line
by Shubham Devesh Ramgoolam 09 Jun '23

09 Jun '23

Hi all, Is it possible to load trajectory files directly from the command line in Chimera? In ChimeraX, it would be done as follows: open myfile.psf coords myfile.dcd I was wondering if there was a chimera version for this command. Regards, Shubham

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symmetrisation of the monomer - statistics issue
by Dmitry A. Semchonok 07 Jun '23

07 Jun '23

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missing bonds when visualizing in Chimera
by Aditi Laddha 01 Jun '23

01 Jun '23

Hello Elaine, I am facing some difficulties visualizing my structure in Chimera; whenever I open the .pdb file containing the sucrose molecule, the bond between glucose and fructose is missing (glycosidic bond). But all bonds are visible when I open the same file in other programs. I want to know about its hydrogen bond interaction with my protein and visualize them in Chimera. Please help me with this issue. -- Regards, Aditi Laddha PhD Scholar Indian Institute of Technology, Kanpur, Uttar Pradesh 208016

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Chimera-users June 2023