- Chimera-users - RBVI Mailing Lists

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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Re: permission denied (Chimera file saving)
by Elaine Meng 01 Jun '23

01 Jun '23

Hello Dr. Sarkar, For questions about Chimera, please use the chimera-users(a)cgl.ucsf.edu address CC'd here. The problem is most likely that you are trying to save the file in a location (folder) where you do not have permission to write files. You need to choose a location on your computer in which you have permission to write files. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > From: Dr Sankar P <sankarp1(a)gmail.com> > Sent: Thursday, June 1, 2023 12:53 AM > Subject: permission denied > > Dear sir I am faculty in the dept of ECE. and I was curious and downloaded your software and tried to use it. But i faced a problem that I cannot save any ligand file as mol2IT says permission denied how do I solve this problem? Please clarify. Awaiting your reply > regards > -- > Dr SANKAR . P

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chimera-users mailing should be working
by Greg Couch 24 May '23

24 May '23

But the web interface to look at old messages will take some time to get to work. -- Greg

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