- Chimera-users - RBVI Mailing Lists

Remove me from mailing list
by Saima Sam 10 Jul '23

10 Jul '23

Hi, I am no longer a user of Chimera so please opt me out of these emails. I would truly appreciate it.

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Placing of a hame-ion centre into an AlfaFold structure
by George Tzotzos 10 Jul '23

10 Jul '23

I’d be grateful for any suggestions regarding the following problem/question. Problem Placing of the haem-iron centre in mosquito P450 structure(s) obtained by means of AlfaFold. This is required for follow up docking simulations. There no insect P450 structures deposited in PDB. However, there are numerous mammalian P450 crystal structures some of which are homologous to the mosquito structures I’m dealing with. A distinctive feature of these structures is a haem-iron centre tethered to the protein via a cysteine thiolate ligand. Six regions have been designated as substrate recognition sites (SRS 1-6) based on comparative sequence analysis methods. These SRS are conserved and are thought to participate in the formation of the substrate access channel, and form part of the catalytic site surrounding the haem iron center. My initial approach would be to use Chimera to align the AlfaFold structure against its mammalian homologue PDB structure and assume that the haem-iron centre would be located in the same place. Is there a better way to achieve the same objective?. Your help will be greatly appreciated. Best regards George

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Chimera?
by Emma 05 Jul '23

05 Jul '23

Chimera, this is me again

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Opening MTZ files on Mac OS
by Natalie Walsh 03 Jul '23

03 Jul '23

Hello, I am having troubles opening MTZ maps from PDB on ChimeraX 17.1. on Mac OS. I read somewhere that you need to download the Clipper plug-in. I went ahead and installed that (although I am not sure that I was successful) and am still struggling to open these files. 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 30 Jun '23

30 Jun '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 27 Jun '23

27 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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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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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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chimera-users mailing list will be down temporarily
by Greg Couch 23 May '23

23 May '23

We're upgrading the mailing software. Should be back "soon".

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