- Chimera-users - RBVI Mailing Lists

How to show certain hydrogen bonds and hide others
by Karjalainen, Mikael 29 Aug '23

29 Aug '23

Hi! I am having problems to show certain hydrogen bonds and hide others. For example, I would like to hide some completely. Then others should be shown always. Even when atoms are not shown and only ribbon is. I couldn't find how to do this by googling or for example reading how to use hbonds command. I am using Chimera 1.16. I know that there is ChimeraX, but now I need to modify old project. Regards, Mikael

2 1

Atlocs
by Hernando J Sosa 28 Aug '23

28 Aug '23

Dear ChimeraX, I have an atomic model with several chains that have residues with alternate locations A and B. I noticed that while Chimera by default displays alternate locations A. ChimeraX for some chains display alternate locations A and for other chains alternate locations B. Why is this behavior different in Chimera and ChimeraX? Is this a novel feature of ChimeraX? I this is the case how ChimeraX decides which of the two alternate locations A or B to display? Thanks Hernando ___________________________________ Hernando Sosa, PhD. Dept. of Biochemistry Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 emai: hernando.sosa@einsteinmed.<mailto:hernando.sosa@einsteinmed.org>edu ___________________________________

2 1

Saving the resolution of structure to a file
by Prathvi Singh 22 Aug '23

22 Aug '23

Hi Elaine, Is there a way to save the resolution of a protein structure to a file using command line, either in chimeraX or chimera? Thanks -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 1

dms from command line
by Guido Leoni 21 Aug '23

21 Aug '23

Dear list Is there an option to write dms from command line? I' m able to launch the command line interface with a pdb loaded within . Then I estimate the surface with this command surface #0 now I would write a dms ... Please do you have any tips that can help me? Thank you Guido

2 1

non-integral charge warning
by Chris Ellis 21 Aug '23

21 Aug '23

Hi, After running the dock prep, I get the following warning in the reply log. Charges for residue MHS determined Total charge for #0: -79.622 The following residues had non-integral charges: VAL 124.A -0.2719 LYS 38.F 0.66 1 model(s) had non-integral total charge Details in reply log How can I fix this warning? Do I need to fix this? Thank you for any help you can provide. I truly appreciate it. Chris

2 6

San Jacinto College Software Intake Form Chimera
by Yates, Michael 18 Aug '23

18 Aug '23

Greetings. I am the Supervisor of Desktop Support Services for San Jacinto College. Information Technology Services (ITS) has been asked to evaluate Chimera to ensure that the San Jacinto College computing environment meets the requirements for the service as well as to ensure that the service offering complies with our requirements. As part of our standard process we reach out to software vendors to request the completion of the attached form after the requestor has completed section 1. At this time we request that you complete section 2 or 3 of the attached form and return it to us by August 21st so that we may complete our evaluations and grant purchase eligibility if the service qualifies. Additional questions may follow. In addition to what is in the form, please include (if applicable) any information / documentation that you have available regarding the options below and please indicate if there are any additional charges for the implementation of such: * Azure AD Single Sign On capability * Office 365 Integration features * Ellucian Banner Integration features [Description: Description: cid:image001.png@01CEC8EF.F2E97C50] Michael Yates San Jacinto College Supervisor of Desktop Support Services 4624 Fairmont Pkwy, Pasadena, TX 77504 Direct: (281) 998-6150 X7325 | Technical Support: (281) 998-6137 Web<http://blogs.sanjac.edu/its> | Facebook<http://www.facebook.com/sanjacits> | ITS Twitter<http://www.twitter.com/sanjacits>

2 3

Moving atoms of a protein
by Abril Gijsbers 18 Aug '23

18 Aug '23

Hi Elaine, I have this alphafold structure (see picture) that is basically a huge string/thread and then a folded domain. I wanted to stretch the string to make its length more obvious. Is it possible to pull the residues without messing with the connections (peptide bond)? I am using chimeraX and I saw that you can "move atoms" but when you pull one you don't pull the others. If chimera cannot do this, do you know if another program will allow me to do it? Thank you in advance for your help, Best regards, Abril Gijsbers [image: image.png]

2 2

Re: ChimeraX license and download
by Elaine Meng 17 Aug '23

17 Aug '23

Please disregard and delete the previous message. I messed up and accidentally CC'd the chimera users list instead of the licensing address. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 17, 2023, at 12:56 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > [...] > Thank you for licensing the commercial version of ChimeraX, the next-generation molecular visualization and analysis program from our research lab. ChimeraX is under active development, with version 1.6.1 released in May 2023. As new features are added, daily development builds are also available for download. Daily builds are not tested as thoroughly as production releases, but in practice are highly usable. > [...]

1 0

Requesting protocol to find protein configuration units
by Panapakam, Jyotheeswaran 17 Aug '23

17 Aug '23

Dear Officail, This is Jyo writing from UNT biological sciences at Denton, TX, USA. I have been using your software for my research project for about an year. I was looking for a help/instructions about how to find out the configuration change in the protein after docking with a ligand. I have heard about RMSD docking value, that will be given in Amstrong units, could you kindly instruct me the process to perform it. It would be more glad if you are able to answer me withing a week from now : ) Sincerely, Jyotheeswaran Panapakam, PhD Candidate &Teaching Assistant, Department of Biological Sciences, University of North Texas. Jyotheeswaran Panapakam, PhD Candidate &Teaching Assistant, Department of Biological Sciences, University of North Texas.

2 1

Re: [chimerax-users] re error with Movie recorder utility
by Elaine Meng 17 Aug '23

17 Aug '23

Hi Anna, This chimerax-users email address is for questions about ChimeraX, but it sounds like you are using the Chimera program instead, since only Chimera has a Movie Recorder tool. So I am CC-ing the chimera-users email address on this reply, and you do not need to re-send your question. There is no separate "freeware version" -- Chimera is free for academic use and the download is the same for academically or commercially licensed users. (This is also the case for ChimeraX). The Command Line is always for entering one command at a time, i.e. that is the normal situation, not a problem or bug. If you have just a few commands you can enter them as one line with semicolons between them. However, if you mean that you have a script that contains many Chimera commands, you do not enter them one at a time into the command line. Instead you use some text-editing program (outside of Chimera) to create a plain text command file containing those commands, then you open that file using either the Chimera menu File... Open, or the Chimera "open" command. Normally command files are named with the filename extension ".com" or ".cmd" so that Chimera knows what kind of file you are trying to open. See Chimera help pages and tutorials on making movies, namely: Making movies: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html> Movie Recorder help page (you can just click the Help button on the tool, or see the copy of the same thing at our website here): <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/recorder/recorde…> Chimera movie-making tutorials: <https://www.rbvi.ucsf.edu/chimera/data/tutorials/movies09/moviemaking.html> <https://www.rbvi.ucsf.edu/chimera/data/tutorials/movies08/moviemaking.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 16, 2023, at 6:31 PM, Anna Lohning via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi > I have the freeware version installed and trying to make a movie using the Tools/Utilities/Movie recorder window. > At this stage, I seem to only have the command line available for commands one at a time. > Anyway, under the Tools/Utilities, the only options there currently are > Register > Updates > > Be grateful for some clarification as I cant seem to find anyone having this issue. > Many thanks > Kind regards > > Anna > Dr Anna Elizabeth Lohning > Associate Professor - Biochemistry > Faculty of Health Science & Medicine > Bond University > ROBINA 4229 > (07) 5595 4779 > alohning(a)bond.edu.au >

2 1