- Chimera-users - RBVI Mailing Lists

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

2 1

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...

2 1

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

2 1

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

1 0

regarding movie making
by lumbini yadav 22 Jun '23

22 Jun '23

2 1

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

2 3

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

2 2

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

2 1

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:

1 0

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

3 2

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

2 4

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

2 2

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

07 Jun '23

2 1

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

3 3

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

1 0

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

1 0

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".

1 0

question regarding relative rotation
by Jannick Cornelius Snel-Prentø 21 May '23

21 May '23

Dear Chimera team, I would like to rotate a protein chain with respect to an axis that I define, but I cannot seem to find any way to do that. I have defined the axis, but the turn command will not allow me to use this as the center of rotation. I have also tried constrained motion, but this does not seem to have the parameters needed to do this. Is there a command or a menu that permits rotating a chain or structure around an axis you define yourself? Kr, Jannick

2 4

Making a rotation matrix file by UCSF Chimera or indexing the position
by Dmitry A. Semchonok 19 May '23

19 May '23

2 1

3D_printing
by Francois-Hugues Poree 18 May '23

18 May '23

Dear Chimera Team, first of all, I would like to thank you for providing a sotfware solution to molecular visualization and by the way 3D- printing. I send you this message concerning the UCSF Chimera X version. We usually are preparing our 3D-printing files from data collected from the pdb and to ensure the rigidity of the system, we thick the ribbon size and also add some H-bonds (mainly for helices). However, we are not able to find the way to do it in this version. In the previous version (1.17), the command line was : Tools-depiction-ribbon style editor Could you explain us the new procedure to make this ? We also noticed that the opportunity to save the file in a stl extension was not allowed in the 1.17 version. This option is running in the X version. Thank you very much for your reply Best regards. fhporee François-Hugues Porée Professeur de Chimie Thérapeutique Institut des Sciences Chimiques de Rennes UMR CNRS 6226 Faculté de Pharmacie - Université de Rennes 2 Avenue du Pr Léon Bernard F-35043 Rennes France Tel.02 23 23 41 87

4 4

error
by Athithi Prakash 16 May '23

16 May '23

Hello, I have been trying for a while to build the structure using the SMILES ID, and every time, this error pops up and I am not sure what to do.

2 2

UCSF Chimera Molecular Dynamics: CPU vs GPU
by Alan Carbajo 07 May '23

07 May '23

Good morning, I'm running a molecular dynamics simulation in Chimera, and it seems that the program is only using my cpu for the calculations. Why is this? Is it possible to switch it to use my GPU? Thank you, Alan

3 3

Web site downtime
by Eric Pettersen 04 May '23

04 May '23

Hi all, Due to a scheduled power outage at UCSF followed by server upgrades, the Chimera website and web services will be unavailable from Tuesday May 16 through most of Wednesday May 17. 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. --Eric Eric Pettersen UCSF Computer Graphics Lab

1 0

Re: [Chimera-users] use with iPads
by Levy,Hazel C 04 May '23

04 May '23

Hello. I'm looking to use chimera on iPads to introduce High School and Middle School students to structural biology. Do you offer a discount for education licenses? Can Chimera be used on an ipad, even if not to its full capacity? Kind regards, Hazel C. Levy, M.Sc., Ph.D. Associate Director – UF Center for Precollegiate Education and Training (CPET) Adjunct Assistant Instructional Professor – Department of Biology | College of Liberal Arts and Sciences Doctoral Student – Higher Education Administration and Policy | College of Education ______________________________________________ Office: 339 Yon Hall | Box 112010 | Gainesville, FL 32611-2010 Phone: (352) 392-7683 Fax: (352) 392-2344 www.cpet.ufl.edu<http://www.cpet.ufl.edu/> [Image result for uf logo] ________________________________ From: Levy,Hazel C <hclevy(a)ufl.edu> Sent: Thursday, May 4, 2023 10:08 AM To: chimera(a)cgl.ucsf.edu <chimera(a)cgl.ucsf.edu> Cc: Desai,Ayan D <ayan.desai(a)ufl.edu>; Anthony, Michael S. <anthonym(a)cpet.ufl.edu> Subject: use with iPads Hello. I'm looking to use chimeraX on iPads to introduce High School and Middle School students to structural biology. Do you offer a discount for education licenses? Can Chimera be used on an ipad, even if not to its full capacity? Kind regards, Hazel C. Levy, M.Sc., Ph.D. Associate Director – UF Center for Precollegiate Education and Training (CPET) Adjunct Assistant Instructional Professor – Department of Biology | College of Liberal Arts and Sciences Doctoral Student – Higher Education Administration and Policy | College of Education ______________________________________________ Office: 339 Yon Hall | Box 112010 | Gainesville, FL 32611-2010 Phone: (352) 392-7683 Fax: (352) 392-2344 www.cpet.ufl.edu<http://www.cpet.ufl.edu/> [Image result for uf logo]

2 1

Midas Error- reg
by Johnson Paul 03 May '23

03 May '23

Dear Sir, I am J Johnson Paul, I have recently used your software for my study and research purposes after usage of your software in the area of peptide build structure area I have got an error like MidasError: Dunbrack rotamer library does not support ASX File "C:\Program Files\Chimera 1.17.1\share\Rotamers\__init__.py", line 680, in useBestRotamers raise MidasError("%s rotamer library does not support %s" %(lib, rType)) This type of error is soon to me,So please kindly reply to my mail to solve the problem as soon as possible *With Regards,* *J Johnson Paul.*

2 2