Re: Trying to join two structures unsuccessfully
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? -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, 5 March 2024 11:33 AM 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 Dear Maja, Apologies if you are getting multiple copies of this answer from me. I keep getting error messages that my reply could not be sent to the list! So, here is my third try. If you've been getting my previous messages (even though I don't think the rest of the list is), please ignore and pardon me for the spam! Adding a bond only works when the atoms are in the same model as each other (typically a structure opened from one PDB file is one model). Also simply adding a bond won't move anything. It will just make a long bond between the atoms in their current positions, or if you choose "reasonable" only, it won't add any bond because the bond would be too long to be reasonable. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds> You can see what model(s) you have by looking in the Model Panel: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelpanel.html> If the two atoms are in two different models (typically opened from two different input files), the "join models" Peptide Bond option should work if you really have exactly two atoms selected, the peptide terminal "N" in one model and the peptide terminal "C" in the other model. As far as I can tell these two are selected in your image, so I couldn't say why you get an error message. If the atoms are in the same model as each other, however, it will not work. You would need to split the model so that they are in separate models first. You can try command "info atoms sel" to list in the Log what you have selected. In my "join peptide" test case I get the following, which confirms I have the correct atoms from two different models selected: info atoms sel atom id #1/A:29@C idatm_type Cac atom id #2/A:1@N idatm_type N3+ However, join models is not going to change the conformation of the peptide, it will just move one model (e.g. the entire green one if it has more atoms than the purple one) as a rigid body to form the specified bond with the other model. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#join> 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
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?
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?
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://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
Oops didn't answer this part of your question in my previous reply.
On Mar 4, 2024, at 6:29 PM, Maja Divjak via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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.
In ChimeraX, you have to use a selective-motion mouse mode. Selecting does not automatically mean to move only that part, because that would be very annoying when you're using selection to specify some other action like coloring or joining. See the link below for how to move different models separately from each other (see the "selective manipulation" section at the bottom): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#selective> 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
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
Thanks Elaine, this works well! Best wishes, Maja -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, March 5, 2024 2:48 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 Oops didn't answer this part of your question in my previous reply.
On Mar 4, 2024, at 6:29 PM, Maja Divjak via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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.
In ChimeraX, you have to use a selective-motion mouse mode. Selecting does not automatically mean to move only that part, because that would be very annoying when you're using selection to specify some other action like coloring or joining. See the link below for how to move different models separately from each other (see the "selective manipulation" section at the bottom): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#selective> 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
participants (2)
-
Elaine Meng -
Maja Divjak