Re: [Chimera-users] Analysis of the protein-protein binding interphaces in MARTINI models
Thank you so much for the suggestions, Elaine! Indeed, I have turned off the both flags but the intra-models contacts are still recognized. it seems that in order to determine carefully the per-residual contacts between monomers, I should to make a backmapping of the CG models to AA. James 2017-11-27 9:23 GMT+01:00 <sdimicco@unisa.it>:
Grazie mille
Il 2017-11-23 04:47 James Starlight ha scritto:
Thank you for the suggestions, Elaine !
I have already tried "Find Clashes/Contacts" plugin. In generally, it works good, however its application on more complex oligomeric patterns (e.g if I deal with 10-20 GPCRs in one system) is a bit complicated. Briefly, if I select only one monomer and than try to find its contacts with the rest of the atoms ( I have changed the contact threshold to -1.2 for the MARTINI) - it works fine. However, If I selected all of the atoms (even excluding inter-residue and inter-molecular contacts) and changing the search criterium "against themselves" - it found alot of contacts within the monomers. Does anybody use any tricks for the MARTINI models to fascilitate the contact searching?
James
2017-11-22 17:52 GMT+01:00 Elaine Meng <meng@cgl.ucsf.edu>:
Dear James / Gleb, This question seems too broad, perhaps. I don't know that much about MARTINI, so I'm guessing instead of atoms you just have a bunch of points that each represent multiple atoms. In that case you could probably use any analysis that does not directly use exact atomic locations, atomic radii, or atomic point charges. Analyses that DO use those things include surface-area calculations, Find Clashes/Contacts, FindHBond.
Maybe you should just first think about what Chimera analysis you want to use, then just try it on your GC model and see if it works rather than trying to get some exhaustive list of what might work. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 22, 2017, at 2:23 AM, James Starlight <jmsstarlight@gmail.com> wrote:
Dear Chimera users!
I would like to make some analysis of the protein-protein binding established in coarse-grained MARTINI simulations. Briefly Chimera has recognized a coarse-grained pdb file of 16 martini models of GPCRs. What Chimera tools (e.g. contact maps, clustering of interphaces) should work with CG models? What tricks should be used to make this analysis easier? Because I am working with several proteins in one system, I would like to work with its CG models without the conversion to all atomistic representations.
I thank you so much for the help! James
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
One question regarding Find Clashes/Contacts. assuming that I have assigned the unique letters for each of the monomer in my CG system. Now I am using this selection ("the individual chain" vs "all other systems") to calculate contacts using -2.2 cutoff for MARTINI (operating with the backbone atoms only). Is it possible to run the same routine in batch mode i) for the individual pdb as input as well as ii) for the md trajectory (to calculate occurence of the contacts along the trajectory)? I would be very grateful for some example script file for batch Chimera! James 2017-11-27 12:03 GMT+01:00 James Starlight <jmsstarlight@gmail.com>:
Thank you so much for the suggestions, Elaine!
Indeed, I have turned off the both flags but the intra-models contacts are still recognized.
it seems that in order to determine carefully the per-residual contacts between monomers, I should to make a backmapping of the CG models to AA.
James
2017-11-27 9:23 GMT+01:00 <sdimicco@unisa.it>:
Grazie mille
Il 2017-11-23 04:47 James Starlight ha scritto:
Thank you for the suggestions, Elaine !
I have already tried "Find Clashes/Contacts" plugin. In generally, it works good, however its application on more complex oligomeric patterns (e.g if I deal with 10-20 GPCRs in one system) is a bit complicated. Briefly, if I select only one monomer and than try to find its contacts with the rest of the atoms ( I have changed the contact threshold to -1.2 for the MARTINI) - it works fine. However, If I selected all of the atoms (even excluding inter-residue and inter-molecular contacts) and changing the search criterium "against themselves" - it found alot of contacts within the monomers. Does anybody use any tricks for the MARTINI models to fascilitate the contact searching?
James
2017-11-22 17:52 GMT+01:00 Elaine Meng <meng@cgl.ucsf.edu>:
Dear James / Gleb, This question seems too broad, perhaps. I don't know that much about MARTINI, so I'm guessing instead of atoms you just have a bunch of points that each represent multiple atoms. In that case you could probably use any analysis that does not directly use exact atomic locations, atomic radii, or atomic point charges. Analyses that DO use those things include surface-area calculations, Find Clashes/Contacts, FindHBond.
Maybe you should just first think about what Chimera analysis you want to use, then just try it on your GC model and see if it works rather than trying to get some exhaustive list of what might work. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 22, 2017, at 2:23 AM, James Starlight <jmsstarlight@gmail.com> wrote:
Dear Chimera users!
I would like to make some analysis of the protein-protein binding established in coarse-grained MARTINI simulations. Briefly Chimera has recognized a coarse-grained pdb file of 16 martini models of GPCRs. What Chimera tools (e.g. contact maps, clustering of interphaces) should work with CG models? What tricks should be used to make this analysis easier? Because I am working with several proteins in one system, I would like to work with its CG models without the conversion to all atomistic representations.
I thank you so much for the help! James
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi James, I don’t know how you have assigned these letters (as aliases? chain IDs? residue names?) but first figure out the “findclash” command that does the same thing you were doing with the Find Clashes/Contacts GUI. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> There are two main kinds of Chimera scripts, Chimera commands and Python. Python can have Chimera commands embedded, and is generally needed if you want to substitute arguments into the commands or loop through many variations of the command or a large set of PDB files. Python is also needed for actions for which no Chimera command is available. I’m not a programmer myself so I can only point to information others have generated… there’s always the programmer’s guide: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/index.html> In this case after figuring out the findclash command options you want, I guess you could write a python script to substitute in the letters into the command to loop through the monomers. There is a page on how to loop through multiple different structures, which is different, but may still be helpful: <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> There are lot of example Chimera python scripts for miscellaneous tasks here: <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> After you figured out a script for an individual PDB, you could adapt it to specify a per-frame script in MD Movie for your trajectory. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 4, 2017, at 5:37 AM, James Starlight <jmsstarlight@gmail.com> wrote:
One question regarding Find Clashes/Contacts.
assuming that I have assigned the unique letters for each of the monomer in my CG system. Now I am using this selection ("the individual chain" vs "all other systems") to calculate contacts using -2.2 cutoff for MARTINI (operating with the backbone atoms only). Is it possible to run the same routine in batch mode i) for the individual pdb as input as well as ii) for the md trajectory (to calculate occurence of the contacts along the trajectory)? I would be very grateful for some example script file for batch Chimera!
James
Thank you so much for the suggestions, Elaine! In fact I have assigned chains (I guess as chain IDs) using Chimera's GUI interface, which I have mentioned in the another topic. For the simplicity I would use Chimera's scripting interface for the batch mode (will be grateful for the example of the script because I am also very bad in the programming!) e.g to check the contacts between chain A and "all other atoms" in only one pdb file (not a trajectory). BTW, via bash I can produce several such scripts (for each of the chains) and execute them in a loop manner, doesn't it? e.g to check contacts between chain B and "all other atoms". between chain C and "all other atoms" etc .. James 2017-12-04 18:57 GMT+01:00 Elaine Meng <meng@cgl.ucsf.edu>:
Hi James, I don’t know how you have assigned these letters (as aliases? chain IDs? residue names?) but first figure out the “findclash” command that does the same thing you were doing with the Find Clashes/Contacts GUI. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
There are two main kinds of Chimera scripts, Chimera commands and Python. Python can have Chimera commands embedded, and is generally needed if you want to substitute arguments into the commands or loop through many variations of the command or a large set of PDB files. Python is also needed for actions for which no Chimera command is available.
I’m not a programmer myself so I can only point to information others have generated… there’s always the programmer’s guide: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/index.html>
In this case after figuring out the findclash command options you want, I guess you could write a python script to substitute in the letters into the command to loop through the monomers. There is a page on how to loop through multiple different structures, which is different, but may still be helpful: <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
There are lot of example Chimera python scripts for miscellaneous tasks here: <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts>
After you figured out a script for an individual PDB, you could adapt it to specify a per-frame script in MD Movie for your trajectory. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 4, 2017, at 5:37 AM, James Starlight <jmsstarlight@gmail.com> wrote:
One question regarding Find Clashes/Contacts.
assuming that I have assigned the unique letters for each of the monomer in my CG system. Now I am using this selection ("the individual chain" vs "all other systems") to calculate contacts using -2.2 cutoff for MARTINI (operating with the backbone atoms only). Is it possible to run the same routine in batch mode i) for the individual pdb as input as well as ii) for the md trajectory (to calculate occurence of the contacts along the trajectory)? I would be very grateful for some example script file for batch Chimera!
James
Just try the Chimera findclash command and figure out what options you want. When you have one command that works the way you want, you can use bash to make a plain text file containing many such commands (Chimera command script file, *.com). The command would be something like findclash :.b test other … but you would have to give additional options with the values you want to use (overlapCutoff, hbondAllowance etc.). See the documentation: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile> We can’t do the exact script for you because everybody’s situation is slightly different. You have actually try entering some commands. Elaine
On Dec 5, 2017, at 1:24 AM, James Starlight <jmsstarlight@gmail.com> wrote:
Thank you so much for the suggestions, Elaine!
In fact I have assigned chains (I guess as chain IDs) using Chimera's GUI interface, which I have mentioned in the another topic. For the simplicity I would use Chimera's scripting interface for the batch mode (will be grateful for the example of the script because I am also very bad in the programming!) e.g to check the contacts between chain A and "all other atoms" in only one pdb file (not a trajectory).
BTW, via bash I can produce several such scripts (for each of the chains) and execute them in a loop manner, doesn't it? e.g to check contacts between chain B and "all other atoms". between chain C and "all other atoms" etc ..
James
2017-12-04 18:57 GMT+01:00 Elaine Meng <meng@cgl.ucsf.edu>:
Hi James, I don’t know how you have assigned these letters (as aliases? chain IDs? residue names?) but first figure out the “findclash” command that does the same thing you were doing with the Find Clashes/Contacts GUI. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
There are two main kinds of Chimera scripts, Chimera commands and Python. Python can have Chimera commands embedded, and is generally needed if you want to substitute arguments into the commands or loop through many variations of the command or a large set of PDB files. Python is also needed for actions for which no Chimera command is available.
I’m not a programmer myself so I can only point to information others have generated… there’s always the programmer’s guide: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/index.html>
In this case after figuring out the findclash command options you want, I guess you could write a python script to substitute in the letters into the command to loop through the monomers. There is a page on how to loop through multiple different structures, which is different, but may still be helpful: <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
There are lot of example Chimera python scripts for miscellaneous tasks here: <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts>
After you figured out a script for an individual PDB, you could adapt it to specify a per-frame script in MD Movie for your trajectory. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 4, 2017, at 5:37 AM, James Starlight <jmsstarlight@gmail.com> wrote:
One question regarding Find Clashes/Contacts.
assuming that I have assigned the unique letters for each of the monomer in my CG system. Now I am using this selection ("the individual chain" vs "all other systems") to calculate contacts using -2.2 cutoff for MARTINI (operating with the backbone atoms only). Is it possible to run the same routine in batch mode i) for the individual pdb as input as well as ii) for the md trajectory (to calculate occurence of the contacts along the trajectory)? I would be very grateful for some example script file for batch Chimera!
James
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Elaine, the question was related not to the bash script for this routine but instead to the input file for the batch chimera. E.g. I have indentified the following command which works in command line of Chimera GUI. It finds the contacts between chain A and others and save the outputs to the log file in the same dir. findclash :.a test other overlapCutoff -3.0 intraMol false saveFile ./test_cont.log Now when I had put the same line into the input.batch and executed it with the batch_chimera, i have recieved the following error message from python: chimera_batch ./rep2.pdb ./xz.batch Opening rep2.pdb.. Traceback (most recent call last): File "/home/t-iris2-011/.local/UCSF-Chimera64-batch/share/chimeraInit.py", line 708, in init chimera.openModels.open(a, prefixableType=1) File "/home/t-iris2-011/.local/UCSF-Chimera64-batch/share/chimera/__init__.py", line 1916, in open raise ValueError, "Unknown model type" ValueError: Unknown model type Error while processing ./xz.batch: ValueError: Unknown model type File "/home/t-iris2-011/.local/UCSF-Chimera64-batch/share/chimera/__init__.py", line 1916, in open raise ValueError, "Unknown model type" See reply log for Python traceback. does it the problems with the python variables? In my *.bashrc file I have sourced the pathways to both chimeras in the following manner: export PATH=$PATH:/home/t-iris2-011/.local/UCSF-Chimera64-1.12/bin:/home/t-iris2-011/.local/UCSF-Chimera64-batch/bin James 2017-12-05 20:32 GMT+01:00 Elaine Meng <meng@cgl.ucsf.edu>:
Just try the Chimera findclash command and figure out what options you want. When you have one command that works the way you want, you can use bash to make a plain text file containing many such commands (Chimera command script file, *.com). The command would be something like
findclash :.b test other
… but you would have to give additional options with the values you want to use (overlapCutoff, hbondAllowance etc.). See the documentation: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile>
We can’t do the exact script for you because everybody’s situation is slightly different. You have actually try entering some commands. Elaine
On Dec 5, 2017, at 1:24 AM, James Starlight <jmsstarlight@gmail.com> wrote:
Thank you so much for the suggestions, Elaine!
In fact I have assigned chains (I guess as chain IDs) using Chimera's GUI interface, which I have mentioned in the another topic. For the simplicity I would use Chimera's scripting interface for the batch mode (will be grateful for the example of the script because I am also very bad in the programming!) e.g to check the contacts between chain A and "all other atoms" in only one pdb file (not a trajectory).
BTW, via bash I can produce several such scripts (for each of the chains) and execute them in a loop manner, doesn't it? e.g to check contacts between chain B and "all other atoms". between chain C and "all other atoms" etc ..
James
2017-12-04 18:57 GMT+01:00 Elaine Meng <meng@cgl.ucsf.edu>:
Hi James, I don’t know how you have assigned these letters (as aliases? chain IDs? residue names?) but first figure out the “findclash” command that does the same thing you were doing with the Find Clashes/Contacts GUI. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
There are two main kinds of Chimera scripts, Chimera commands and Python. Python can have Chimera commands embedded, and is generally needed if you want to substitute arguments into the commands or loop through many variations of the command or a large set of PDB files. Python is also needed for actions for which no Chimera command is available.
I’m not a programmer myself so I can only point to information others have generated… there’s always the programmer’s guide: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/index.html>
In this case after figuring out the findclash command options you want, I guess you could write a python script to substitute in the letters into the command to loop through the monomers. There is a page on how to loop through multiple different structures, which is different, but may still be helpful: <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
There are lot of example Chimera python scripts for miscellaneous tasks here: <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts>
After you figured out a script for an individual PDB, you could adapt it to specify a per-frame script in MD Movie for your trajectory. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 4, 2017, at 5:37 AM, James Starlight <jmsstarlight@gmail.com> wrote:
One question regarding Find Clashes/Contacts.
assuming that I have assigned the unique letters for each of the monomer in my CG system. Now I am using this selection ("the individual chain" vs "all other systems") to calculate contacts using -2.2 cutoff for MARTINI (operating with the backbone atoms only). Is it possible to run the same routine in batch mode i) for the individual pdb as input as well as ii) for the md trajectory (to calculate occurence of the contacts along the trajectory)? I would be very grateful for some example script file for batch Chimera!
James
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
P.S. is it possible to make a complex task script for batch chimera e.g to find contacts between all of the chains and other atoms in the sequential manner adding the results within the same log? # an example of such workflow within one batch input file for the batch chimera findclash :.a test other overlapCutoff -3.0 intraMol false saveFile ./test_cont.log findclash :.b test other overlapCutoff -3.0 intraMol false saveFile ./test_cont.log ... findclash :.p test other overlapCutoff -3.0 intraMol false saveFile ./test_cont.log 2017-12-06 15:02 GMT+01:00 James Starlight <jmsstarlight@gmail.com>:
Elaine,
the question was related not to the bash script for this routine but instead to the input file for the batch chimera.
E.g. I have indentified the following command which works in command line of Chimera GUI. It finds the contacts between chain A and others and save the outputs to the log file in the same dir.
findclash :.a test other overlapCutoff -3.0 intraMol false saveFile ./test_cont.log
Now when I had put the same line into the input.batch and executed it with the batch_chimera, i have recieved the following error message from python:
chimera_batch ./rep2.pdb ./xz.batch Opening rep2.pdb.. Traceback (most recent call last): File "/home/t-iris2-011/.local/UCSF-Chimera64-batch/share/chimeraInit.py", line 708, in init chimera.openModels.open(a, prefixableType=1) File "/home/t-iris2-011/.local/UCSF-Chimera64-batch/share/chimera/__init__.py", line 1916, in open raise ValueError, "Unknown model type" ValueError: Unknown model type
Error while processing ./xz.batch: ValueError: Unknown model type
File "/home/t-iris2-011/.local/UCSF-Chimera64-batch/share/chimera/__init__.py", line 1916, in open raise ValueError, "Unknown model type"
See reply log for Python traceback.
does it the problems with the python variables? In my *.bashrc file I have sourced the pathways to both chimeras in the following manner:
export PATH=$PATH:/home/t-iris2-011/.local/UCSF-Chimera64-1.12/bin:/home/t-iris2-011/.local/UCSF-Chimera64-batch/bin
James
2017-12-05 20:32 GMT+01:00 Elaine Meng <meng@cgl.ucsf.edu>:
Just try the Chimera findclash command and figure out what options you want. When you have one command that works the way you want, you can use bash to make a plain text file containing many such commands (Chimera command script file, *.com). The command would be something like
findclash :.b test other
… but you would have to give additional options with the values you want to use (overlapCutoff, hbondAllowance etc.). See the documentation: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile>
We can’t do the exact script for you because everybody’s situation is slightly different. You have actually try entering some commands. Elaine
On Dec 5, 2017, at 1:24 AM, James Starlight <jmsstarlight@gmail.com> wrote:
Thank you so much for the suggestions, Elaine!
In fact I have assigned chains (I guess as chain IDs) using Chimera's GUI interface, which I have mentioned in the another topic. For the simplicity I would use Chimera's scripting interface for the batch mode (will be grateful for the example of the script because I am also very bad in the programming!) e.g to check the contacts between chain A and "all other atoms" in only one pdb file (not a trajectory).
BTW, via bash I can produce several such scripts (for each of the chains) and execute them in a loop manner, doesn't it? e.g to check contacts between chain B and "all other atoms". between chain C and "all other atoms" etc ..
James
2017-12-04 18:57 GMT+01:00 Elaine Meng <meng@cgl.ucsf.edu>:
Hi James, I don’t know how you have assigned these letters (as aliases? chain IDs? residue names?) but first figure out the “findclash” command that does the same thing you were doing with the Find Clashes/Contacts GUI. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
There are two main kinds of Chimera scripts, Chimera commands and Python. Python can have Chimera commands embedded, and is generally needed if you want to substitute arguments into the commands or loop through many variations of the command or a large set of PDB files. Python is also needed for actions for which no Chimera command is available.
I’m not a programmer myself so I can only point to information others have generated… there’s always the programmer’s guide: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/index.html>
In this case after figuring out the findclash command options you want, I guess you could write a python script to substitute in the letters into the command to loop through the monomers. There is a page on how to loop through multiple different structures, which is different, but may still be helpful: <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
There are lot of example Chimera python scripts for miscellaneous tasks here: <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts>
After you figured out a script for an individual PDB, you could adapt it to specify a per-frame script in MD Movie for your trajectory. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 4, 2017, at 5:37 AM, James Starlight <jmsstarlight@gmail.com> wrote:
One question regarding Find Clashes/Contacts.
assuming that I have assigned the unique letters for each of the monomer in my CG system. Now I am using this selection ("the individual chain" vs "all other systems") to calculate contacts using -2.2 cutoff for MARTINI (operating with the backbone atoms only). Is it possible to run the same routine in batch mode i) for the individual pdb as input as well as ii) for the md trajectory (to calculate occurence of the contacts along the trajectory)? I would be very grateful for some example script file for batch Chimera!
James
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Instead of saving to a log file with each command (which is better if you want a different file each time), save to the Reply Log with “findclash” option “log true”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> ...and then at the end, after multiple calculations, save the Reply Log to a file. You could save it “manually”, menu Favorites… Reply Log, and then use the Save button on the Reply Log, or save it with python in the script as described at the bottom of this page: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 6, 2017, at 6:37 AM, James Starlight <jmsstarlight@gmail.com> wrote:
P.S. is it possible to make a complex task script for batch chimera e.g to find contacts between all of the chains and other atoms in the sequential manner adding the results within the same log?
# an example of such workflow within one batch input file for the batch chimera findclash :.a test other overlapCutoff -3.0 intraMol false saveFile ./test_cont.log findclash :.b test other overlapCutoff -3.0 intraMol false saveFile ./test_cont.log ... findclash :.p test other overlapCutoff -3.0 intraMol false saveFile ./test_cont.log
Hi David, I am not feeling good at all today and would like to get a sick day tomorrow if this is OK with you. The Arctica autoloader part arrived today and the FEI engineers will replace and test the equipment. Once they replace the part it may take up to two days for the column to pump down. Either way I will be first thing on Friday to check with them. I will put the request in people soft shortly. Best, Svetla ________________________________ From: Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, December 6, 2017 12:40 PM To: James Starlight Cc: Chimera BB Subject: Re: [Chimera-users] Analysis of the protein-protein binding interphaces in MARTINI models Instead of saving to a log file with each command (which is better if you want a different file each time), save to the Reply Log with “findclash” option “log true”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> findclash - rbvi.ucsf.edu<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> www.rbvi.ucsf.edu Chimera Commands Index Usage: findclash atom-spec options Usage: ~findclash. Findclash identifies interatomic clashes and contacts based on VDW radii and user ... ...and then at the end, after multiple calculations, save the Reply Log to a file. You could save it “manually”, menu Favorites… Reply Log, and then use the Save button on the Reply Log, or save it with python in the script as described at the bottom of this page: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 6, 2017, at 6:37 AM, James Starlight <jmsstarlight@gmail.com> wrote:
P.S. is it possible to make a complex task script for batch chimera e.g to find contacts between all of the chains and other atoms in the sequential manner adding the results within the same log?
# an example of such workflow within one batch input file for the batch chimera findclash :.a test other overlapCutoff -3.0 intraMol false saveFile ./test_cont.log findclash :.b test other overlapCutoff -3.0 intraMol false saveFile ./test_cont.log ... findclash :.p test other overlapCutoff -3.0 intraMol false saveFile ./test_cont.log
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Thank you, Elaine! One question: where the Reply Log will be saved after execution of the batch chimera, assuming that I'am using cmd script without python? # this is chimera.cmd" findclash :.${i} test other overlapCutoff -3.0 intraMol false saveFile log true" Thank you! James 2017-12-06 18:40 GMT+01:00 Elaine Meng <meng@cgl.ucsf.edu>:
Instead of saving to a log file with each command (which is better if you want a different file each time), save to the Reply Log with “findclash” option “log true”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> ...and then at the end, after multiple calculations, save the Reply Log to a file. You could save it “manually”, menu Favorites… Reply Log, and then use the Save button on the Reply Log, or save it with python in the script as described at the bottom of this page: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 6, 2017, at 6:37 AM, James Starlight <jmsstarlight@gmail.com> wrote:
P.S. is it possible to make a complex task script for batch chimera e.g to find contacts between all of the chains and other atoms in the sequential manner adding the results within the same log?
# an example of such workflow within one batch input file for the batch chimera findclash :.a test other overlapCutoff -3.0 intraMol false saveFile ./test_cont.log findclash :.b test other overlapCutoff -3.0 intraMol false saveFile ./test_cont.log ... findclash :.p test other overlapCutoff -3.0 intraMol false saveFile ./test_cont.log
There is no “saveFile” in the command. “log true” is a separate option that only means to show information in the Reply Log without saving any file. Please see the description of all the findclash options in the manpage: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> Then, AFTER all the calculations, you would save the Reply Log contents to a file either manually or with python, as explained in my previous message. Elaine
On Dec 7, 2017, at 6:54 AM, James Starlight <jmsstarlight@gmail.com> wrote:
Thank you, Elaine!
One question: where the Reply Log will be saved after execution of the batch chimera, assuming that I'am using cmd script without python?
# this is chimera.cmd" findclash :.${i} test other overlapCutoff -3.0 intraMol false saveFile log true"
Thank you!
James
2017-12-06 18:40 GMT+01:00 Elaine Meng <meng@cgl.ucsf.edu>:
Instead of saving to a log file with each command (which is better if you want a different file each time), save to the Reply Log with “findclash” option “log true”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> ...and then at the end, after multiple calculations, save the Reply Log to a file. You could save it “manually”, menu Favorites… Reply Log, and then use the Save button on the Reply Log, or save it with python in the script as described at the bottom of this page: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 6, 2017, at 6:37 AM, James Starlight <jmsstarlight@gmail.com> wrote:
P.S. is it possible to make a complex task script for batch chimera e.g to find contacts between all of the chains and other atoms in the sequential manner adding the results within the same log?
# an example of such workflow within one batch input file for the batch chimera findclash :.a test other overlapCutoff -3.0 intraMol false saveFile ./test_cont.log findclash :.b test other overlapCutoff -3.0 intraMol false saveFile ./test_cont.log ... findclash :.p test other overlapCutoff -3.0 intraMol false saveFile ./test_cont.log
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Dear Chimera, Is it possible to mix scenes and morphs in the animation timeline? Thanks H.
Hi Hernando, The short answer is to try it and see what you get. If by morphing you mean atomic structure morphing, yes you can play parts of the morphing trajectory (previously calculated from morphing) within the timeline. When you save the scene it would have to be showing the trajectory frame of interest for that scene. See the mentions of “trajectory” in the Animation documentation for more details on how that works. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/animation/frameanimation.html> However, morphing maps is a different matter and I doubt it would work. For including map morphing, or for more elaborate interleaving of events in the movie with the atomic-morph trajectory playback than the simple Animation interface allows, you may need to use a Chimera command script instead. I hope this helps, Elaine —— Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 8, 2017, at 10:51 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Dear Chimera, Is it possible to mix scenes and morphs in the animation timeline? Thanks H.
The message is saying that Chimera does not know what kind of file “xz.batch” is. If it is a Chimera command file it should be named ending with .cmd or .com, and if it is a Python file, it should be named ending with .py <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#command> Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 6, 2017, at 6:02 AM, James Starlight <jmsstarlight@gmail.com> wrote:
Elaine,
the question was related not to the bash script for this routine but instead to the input file for the batch chimera.
E.g. I have indentified the following command which works in command line of Chimera GUI. It finds the contacts between chain A and others and save the outputs to the log file in the same dir.
findclash :.a test other overlapCutoff -3.0 intraMol false saveFile ./test_cont.log
Now when I had put the same line into the input.batch and executed it with the batch_chimera, i have recieved the following error message from python:
chimera_batch ./rep2.pdb ./xz.batch Opening rep2.pdb.. Traceback (most recent call last): File "/home/t-iris2-011/.local/UCSF-Chimera64-batch/share/chimeraInit.py", line 708, in init chimera.openModels.open(a, prefixableType=1) File "/home/t-iris2-011/.local/UCSF-Chimera64-batch/share/chimera/__init__.py", line 1916, in open raise ValueError, "Unknown model type" ValueError: Unknown model type
Error while processing ./xz.batch: ValueError: Unknown model type
File "/home/t-iris2-011/.local/UCSF-Chimera64-batch/share/chimera/__init__.py", line 1916, in open raise ValueError, "Unknown model type"
See reply log for Python traceback.
does it the problems with the python variables? In my *.bashrc file I have sourced the pathways to both chimeras in the following manner:
export PATH=$PATH:/home/t-iris2-011/.local/UCSF-Chimera64-1.12/bin:/home/t-iris2-011/.local/UCSF-Chimera64-batch/bin
James
Dear Users, I have created long ( 100 mer ) polymer strands which when laid side to side, create a usable surface. This model is “recyclable”.. Hwever each time I use it, it goes through a long PARMChk. Is there an output or file of this composite I can save that obviates this step ? thanks Paul
Hi Paul, It ain’t easy. You would need to modify Chimera’s Python code. First you would need to squirrel the “frcmod" file computed by parmchk away so it could be used later. You can find the file by looking at the Reply Log and in the parmchk command it’s the file after the “-o” parmchk option. Probably some horrible path to a file in a temporary folder (for example on my Mac it was "/var/folders/mz/q5nthjsn13gcb04mw0xnxkcc0000gn/T/tmpLLQnFV/frcmod.0-1”). Then you would need to change line 471 of <your chimera>/share/MMMD/MMTKinter.py from: rtype2frcmod = {} to: rtype2frcmod = { ‘your-res-name’: ‘full-path-to-squirreled-frcmod’ } (e.g. rtype2frcmod = { ‘GLC’: ‘/Users/pett/frcmods/GLC.frcmod’ }) On a Mac, “<your chimera>” is Chimera.app/Contents/Resources. —Eric Eric Pettersen UCSF Computer Graphics Lab
On Feb 8, 2018, at 4:58 PM, Paul Buscemi <busce004@umn.edu> wrote:
Dear Users,
I have created long ( 100 mer ) polymer strands which when laid side to side, create a usable surface. This model is “recyclable”.. Hwever each time I use it, it goes through a long PARMChk. Is there an output or file of this composite I can save that obviates this step ?
thanks Paul _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (6)
-
Elaine Meng -
Eric Pettersen -
Hernando J Sosa -
James Starlight -
Paul Buscemi -
Stoilova-McPhie, Svetla