Dear ChimeraX, Please unsubscribe me from the mail list. Thanks. Travis ________________________________ From: chimerax-users-request@cgl.ucsf.edu <chimerax-users-request@cgl.ucsf.edu> Sent: Tuesday, July 4, 2023 3:00 PM To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: ChimeraX-users Digest, Vol 79, Issue 2 Send ChimeraX-users mailing list submissions to chimerax-users@cgl.ucsf.edu To subscribe or unsubscribe via email, send a message with subject or body 'help' to chimerax-users-request@cgl.ucsf.edu You can reach the person managing the list at chimerax-users-owner@cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of ChimeraX-users digest..." Today's Topics: 1. Re: [Chimera-users] Opening MTZ files on Mac OS (Elaine Meng) 2. Coloring proteins by Ca rmsd when they have different sequences (Vorländer) 3. Re: Coloring proteins by Ca rmsd when they have different sequences (Elaine Meng) 4. Re: Coloring proteins by Ca rmsd when they have different sequences (Elaine Meng) 5. Extract settings/parameters from a chimerax cxs session file (alan.cheung@bristol.ac.uk) ---------------------------------------------------------------------- Message: 1 Date: Mon, 3 Jul 2023 19:24:07 -0700 From: Elaine Meng <meng@cgl.ucsf.edu> Subject: [chimerax-users] Re: [Chimera-users] Opening MTZ files on Mac OS To: Natalie Walsh <natalie.walsh@slu.edu> Cc: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu>, ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Message-ID: <56AC7019-083A-43B6-97DE-B674733A0561@cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii Hi Natalie, This is a ChimeraX question, although sent to the chimera-users list -- although unnecessary this time, for future reference please send chimeraX questions to the chimerax-users@cgl.ucsf.edu list CC'd here (we try not to confuse Chimera users with ChimeraX answers and vice versa). The instructions of how to open MTZ files with ChimeraX are here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#clipper> "Opening an MTZ file requires specifying an already-open atomic structure with the structureModel option..." with example command, etc. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 3, 2023, at 8:52 AM, Natalie Walsh via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
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
------------------------------ Message: 2 Date: Tue, 4 Jul 2023 14:02:10 +0000 From: Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at> Subject: [chimerax-users] Coloring proteins by Ca rmsd when they have different sequences To: "chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu> Message-ID: <3944043A-628C-43CD-8A65-67B361695EDB@imp.ac.at> Content-Type: multipart/alternative; boundary="_000_3944043A628C43CD8A6567B361695EDBimpacat_" Hi all, I would like to color proteins by the Ca-RMSD after aligning them, and found the Youtube tutorial on how to do this for proteins with identical sequence. However, I would like to compare structures from different species, as for example done in Figure 2 in this paper https://www.sciencedirect.com/science/article/pii/S0959440X16302408?via%3Dih... . Is this possible in ChimeraX? Many thanks, Matthias