- ChimeraX-users - RBVI Mailing Lists

Displaying methyl groups on DNA?
by Maja Divjak 18 Sep '24

18 Sep '24

Hi there, Hope you're well. I'm sure this is a rookie question, but I'm having trouble displaying the methyl groups on a methylated DNA sequence, as shown in PDB 6C1Y. [A colorful structure with multiple colors Description automatically generated with medium confidence] I've tried selecting the DNA and then showing the methyl functional group, but this selects all the methyl groups including those in the protein sequence. I also tried selecting the individual bases I know are methylated using eg select #2/C:6, but not sure of the command to show the methyl group following this ie select #2/C:6 show methyl does not work, whereas show methyl as a solo command shows all methyl groups in the whole structure. Couldn't find anything in the help files, unfortunately. Thanks so much and best wishes, Maja

2 2

(no subject)
by Kasia Ojar 18 Sep '24

18 Sep '24

Hello, I hope this email finds you well. I am writing because I have a couple of questions regarding opening up the ChimeraX program. I am a student and I have downloaded the ChimeraX and cannot seem to open the program despite it being on my desktop. I have Microsoft and the software is Windows 11. Thank you for your help.

2 1

Missing libraries from package install ChimeraX?
by Mike King 17 Sep '24

17 Sep '24

Hi I have just installed ChimeraX 1.8 from the RedHat 8 rpm package. In our previous Chimera installs there were some libraries that don't appear to be in the 1.8 rpm distribution. For example, _multiscale.so and _chimera.so which our developers have been using, are these available via a different route for ChimeraX 1.8? Many thanks Mike Mike King Director, Scientific Computing Astex Pharmaceuticals 436 Cambridge Science Park Milton Road, Cambridge CB4 0QA, UK Tel: +44(0)1223 435095 Email: mike.king(a)astx.com Website: http://www.astx.com<http://www.astx.com/> This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please delete the original and any copies of this email and any attachments thereto and notify the sender immediately.

2 1

MD
by SAWABE Tomoo 17 Sep '24

17 Sep '24

To whom it may be concerned, Thank you so much for developing excellent program for analyzing protein structures. I found Chimera could do molecular dynamics simulations. If I do MD to predict proton paths described in https://www.pnas.org/doi/epdf/10.1073/pnas.1706278114, please teach me which tool we can use. Best Tomoo Sawabe Hokkaido Univ.

2 2

Error when opening session file cross-platform
by Alexander Lee 17 Sep '24

17 Sep '24

I created a python session file on ubuntu and tried to open it on windows. Ubuntu was using Chimera 1.18 build 42535 but windows was using 1.18 build 42531. I've tried updating chimera on windows, but it said I was on the latest version already. When I open it on ubuntu, it works. My session file is ~ 1.5 GB including smoothed trajectory. What should I do? Here are the outputs after running debug on windows: Cannot execute 'gzip': no automatic decompression of .Z files initializing general preferences loading Tix initializing graphics create application loading Pmw creating main window creating menus creating toolbar creating viewer initializing OpenGL initializing preferences initializing dialogs initializing COM initializing extensions Return code: -1073741819 Press return or enter to to exit [cid:0c988132-7bb8-429c-a6c7-f91f6db3b590] [cid:55bba9bf-1168-4782-b772-4d2e36e05e97]

1 0

Change fetch download location
by Walker Orr 13 Sep '24

13 Sep '24

Hi, I was wondering how to change the fetch download location from downloads to a custom-assigned folder. I saw how to do this on chimera, but couldn't find guidance for ChimeraX in the documentation. Is there a way to do this? Thanks, Walker

2 1

Molmap default to cubic box?
by Oliver Clarke 13 Sep '24

13 Sep '24

Hi, Currently, molmap defaults to creating the new map in a minimal bounding box - a minimal rectangular prism. Most cryoEM software doesn't like rectangular prisms, and rather prefers cubes (ideally with sides that are an even number of voxels). Would it be possible to either (a) alter molmap so it defaults to a minimal cubic box or (b) add an option to automatically resample to a cubic box of specified dimensions? Often this doesn't really matter as we have a map already loaded that we can resample on the grid of, but it would be convenient to be able to do this in a single command. Cheers Oli

3 5

Save Session
by F.Xavier Gomis-Rüth 12 Sep '24

12 Sep '24

Dear Elaine, I am trying to save the session under ChimeraX v. 1.8 but the program refuses to do so with the message below. Any suggestion is welcomed. Best, Xavier --

2 2

Chimerax's download link is no longer working
by 卢健之 11 Sep '24

11 Sep '24

Hello, I tried to dowonload the chimerax from the link https://www.rbvi.ucsf.edu/chimerax/download.html. But it seems the server is down. I wonder if you could provide me with a new download link. I would really appreciate it.

2 1

no template at MD forcefield
by Dmitry Semchonok 11 Sep '24

11 Sep '24

Dear Tristan and colleagues, I hope you are doing well. I have a question about the cofactors and residues that ISOLDE cannot see immediately. [cid:17de3c4d-4ac6-471b-b5b9-ecaa4e534d18] What is the proper way to treat them? The program proposes that I do a search and then give the options. Shall I select the most probable one out of the list? And how do we deal with Chlorophylls (Chl a; Chl b) and carotenoids (car)? And sometimes, even with regular ones like ARG [cid:8ff9222b-feb1-47b3-9b5e-a52e714e2355] Thank you in advance. Kind regards, Dmitry

2 1