Hi Elaine, Thanks so much for your reply. Yeah, I just can't get this to work, since there is no dialogue box for this command (as far as I can tell), I can't adjust any of the parameters in any meaningful way. I've tried using different combinations of atom numbers and it always says it expects a certain number of destination atoms and somehow it ends up with more. Just trying to tug the end atom over to the other end atom (tug #16/A:356 toAtoms #18/A:355 ) gives this error message: Missing atoms or parameterization needed by force field. All heavy atoms and hydrogens with standard names are required. Error with ignoreExternalBonds=False was No template found for residue 1 (MET). The set of atoms is similar to MET, but it is missing 9 hydrogen atoms. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template Error with ignoreExternalBonds=True was No template found for residue 1 (MET). The set of atoms is similar to MET, but it is missing 9 hydrogen atoms. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template So I guess there is something wrong with this first structure (it came from AlphaFold)....So I thought I'd try chopping up the sequence and moving it around. As a test before doing this, I tried moving some structures individually and I can't seem to get this to work either, despite selecting them first, using left, middle and right mouse buttons and all combos of shift, cntrl and alt. If you could please help with this very elementary skill I would very much appreciate it. Thanks so much and best wishes, Maja -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, 5 March 2024 12:48 PM To: Maja Divjak <Maja.Divjak@petermac.org> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Trying to join two structures unsuccessfully ! EXTERNAL EMAIL: Think before you click. If suspicious send to CyberReport@petermac.org Hi Maja, The error message says that your first atomspec (#16/a:345-355) specified zero atoms, whereas the second one (#18/A:345-355) specified 84. So you need to figure out what is wrong with the first one, I guess. Also this means to put the first set of atoms on top of the second, did you really want to overlap those 11 residues, and do they really have the same numbers of atoms in the two models? Other than that seems like the correct syntax, but what exactly to specify depends on what's in your structure, and of course what you actually want. Also there are a bunch of other options for how long and how forcefully to jiggle the structure to get the two sets of atoms overlaid. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/tug.html> For how to join (subscribe to) the members list, see the "contact us" webpage and links therein: <https://www.rbvi.ucsf.edu/chimerax/docs/contact.html> I hope this helps, 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
On Mar 4, 2024, at 4:59 PM, Maja Divjak via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Alternatively, I guess I could just cut this disordered domain into fragments, move them around and the rejoin them....
-----Original Message----- From: Maja Divjak Sent: Tuesday, 5 March 2024 11:44 AM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: RE: [chimerax-users] Trying to join two structures unsuccessfully
Dear Elaine,
No worries at all, I have received multiple replies, so it is working!
Thank you for your response below. Basically, it seems what I'd like to do can't really be done in this way. In another conversation, someone mentioned the tug command. Could this yield what I'm hoping for please?
The two ends I'm trying to join are indeed in separate models, so I tried the following command: tug #16/a:345-355 toAtoms #18/A:345-355
which gave the following error: For 0 tugged atoms expected 0 destination atoms, got 84
Would this be the correct approach (I've clearly got the syntax wrong) or is there really no way to do this in Chimera X?
Thanks so much and best wishes,
Maja
PS. How do I join the member's list please?