August 2024 - Chimera-users - RBVI Mailing Lists

Selecting chain via command line
by Ellen Shrock 19 Sep '24

19 Sep '24

Hello, I am trying to write a script that will iterate through lists of PDB IDs, the relevant antibody chain labels within those PDBs, and antigen chain labels, and annotate the contacts between the antibody and antigen using the command findclash. After opening each PDB file, I am struggling to find a way to select the antibody chains as "sel1" and the antigen chain(s) as "sel2" since the command "select" does not seem to recognize chain labels. Could you please help me find a way to accomplish my goal? Thank you, Ellen

3 8

Chimera interface to Modeller
by Vonderviszt Ferenc 03 Sep '24

03 Sep '24

Hello, I have been using the Chimera interface to Modeller via a web service. This service has been down for a few days. It always stops with the following error message: Service 'opal:Modeller9v8Service' is unavailable What should I do? Please help me. Thanks, Feri

4 4

Finding SASA for individual residues
by Prathvi Singh 29 Aug '24

29 Aug '24

Hi Elaine, Can I use chimera or chimeraX to know the solvent accessible surface area (SASA) for selected residues? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

3 6

display cartoon and H-bonds
by Bryan Sutton 27 Aug '24

27 Aug '24

I can't for the life of me figure out how to display ONLY a cartoon representation of my protein and backbone H-bonds. ChimeraX keeps forcing side-chain:backbone bonds.. I don't want that. I can do it if I show the backbone atoms, but I don't want to do that either. I only want it to show ONLY backbone H-bonds.

2 1

Problem of starting Chimera
by 郭家瑞 24 Aug '24

24 Aug '24

Hello, This is the first time I am stalling Chimera, but I meet the problem of starting the software. According to the Debug command, I have tried update my graphic driver, installed Gzip and tried different Chimera releases including 1.18, 1.17 and 1.14. However, the software still cannot be started. The content of debug log is copied as following: D:\Chimera 1.14\share\chimeraInit.py:99: UnicodeWarning: Unicode equal comparison failed to convert both arguments to Unicode - interpreting them as being unequal if chimera_env.get(e) == _original_environ.get(e): initializing general preferences loading Tix initializing graphics Return code: -1073741819 I am looking forward to any guidance or help for solving the problem. My graphic is NVIDIA Geforce 3050Ti and the opperation system is Windows 10. If necessary, more details can be supplied. Sincerely Appreciated, Jiarui Guo from China

2 1

Mac Version
by Gonzalo de Prat Gay 22 Aug '24

22 Aug '24

Hello I have downloaded Chimaera 1.18 for Mac I am running Ventura 13.4.1, and it tells me the file is corrupted when I try to open de dmg Is there any compatibility issue or should it run on this OS X? Thanks Gonzalo

3 5

chimera
by 2719354821＠qq.com 13 Aug '24

13 Aug '24

After installing and opening the UCSF Chimera software, pythonw.exe keeps popping up new windows, causing the software to malfunction. I have tried downloading various versions of the UCSF Chimera software, but after installation, when I double-click to open it, various interfaces keep popping up. At the same time, Microsoft Edge also continuously opens web pages, rendering both the software and the computer unusable. I found that a few years ago, someone in the community had the same experience. How can this be resolved? Most concerning is that, like them, I am also using a Honor laptop.

2 1

Chimera
by Kotin, Robert 13 Aug '24

13 Aug '24

Good afternoon – I’d appreciate advise for virus capsid viewing. Adeno-associated viruse structures, e.g., 1lp3, consist of the asymmetric unit repeated 60x to form the icosahedral capsid (T=1). I’d like to highlight the equivalent residue in each of the 60 subunits but haven’t figured out how to do that (except by manually going through each of the 60 chains). Please let me know if there are commands that can specify the residue in chains 1, 2, 3,…60. Thank you Robert Kotin

2 2

.crd file not opening
by safi ch 05 Aug '24

05 Aug '24

Greetings, hope you are doing well. I want your guidance on how can I open a .crd file on UCSF Chimera. I am working on a protein and its mutants and performed their docking via Swiss Dock, it gave results in form of .crd file that I cannot open. My supervisor also has no idea how to open it, so please help me in this regard, I need to open it to work further on my research. Waiting for your kind response please.

2 7

August 1 Chimera(X) website downtime
by Elaine Meng 01 Aug '24

01 Aug '24

Planned downtime for server maintenance: The Chimera and ChimeraX websites, Toolshed, web services (Blast Protein, Modeller, ...) and cgl.ucsf.edu e-mail will be unavailable August 1, 3-6 pm PDT. Apologies for any inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

1 1