Hi Elaine, Thank you so much for this, I finally got the tug command to work. First, as you mentioned, I had to add all the hydrogens. I did this with 'consider each model in isolation' and 'also consider H bonds' selected. I was then able to use the tug command by selecting two residues with the same number of atoms eg. tug #16/A:350 toAtoms #15/B:351 (they both have 14 atoms). I didn't adjust any other parameters. It was quite entertaining watching the end swim over to join the other! Thanks so much and best wishes, Maja -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, 5 March 2024 2:21 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 As mentioned in the "tug" documentation and links therein, you have to add all the hydrogens first and you can't have nonstandard molecules like ligands in the structures. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html#openmm> You might also try just using alpha-carbons or just backbone, maybe that would be easier for getting you the same numbers of atoms in the two specified sets, e.g. 4 backbone atoms from each residue tug #16/A:356@N,CA,C,O toAtoms #18/A:355@N,CA,C,O You have to get the numbers of atoms right (same as each other) before it will even run, so figure that out before even trying to adjust any parameters. The parameters are adjusted with option keywords in the tug command, see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/tug.html> Elaine
On Mar 4, 2024, at 6:29 PM, Maja Divjak via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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://smex-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3 a%2f%2fgithub.com%2fopenmm%2fopenmm%2fwiki%2fFrequently%2dAsked%2dQues tions%23template&umid=bb0d9413-5218-414b-8d46-e860eae09a1c&auth=2af547 3c4b03509246eb08bd803a6cf835f69953-4006b24c990b653a542119f8ee993ec7f9c 55c3a 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://smex-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3 a%2f%2fgithub.com%2fopenmm%2fopenmm%2fwiki%2fFrequently%2dAsked%2dQues tions%23template&umid=bb0d9413-5218-414b-8d46-e860eae09a1c&auth=2af547 3c4b03509246eb08bd803a6cf835f69953-4006b24c990b653a542119f8ee993ec7f9c 55c3a
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