Atom Specification not working in exported PDB
Hello again Chimera Users So now that I have the “movie” command working decently, it turns out that I cannot export a PDB file from my MD simulation and retain the ability to select by residue or atom number. PDB files generated by other software (PACKMOL, AMBER) works fine though when I exported a PDB file from a fram in an AMBER MD simulation using chimera, I can open the file, I can select using residue names though trying to refer to atom or molecule numbers does not work. To be clear, the exported PDB file contains multiple molecules and solvent, all ar present and the file loads though trying to run commands like show :17 ~show @536-593 Affects EVERY atom and molecule in the system when it should only affect residue 17 (by specifying residue number OR all atoms in that residue). Using the show :XXX works as intended though this affects all residues XXX and I only want to affect residue 17. Am I doing something wrong or can I solve this in a simple way? Best regards // Gustaf
Hi Gustaf, I have every expectation that you should be able to refer to the residue by number, e.g. show :17 ~show :17 …or by atom serial numbers, e.g. (your syntax was wrong): show @/serialNumber>535 and serialNumber<594 It should be the same as when you have the original trajectory open. Can you use “show :17” in that case? We would need an example of your trajectory input to see how Chimera is interpreting it. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 30, 2018, at 4:33 AM, Gustaf Olsson <gustaf.olsson@lnu.se> wrote:
Hello again Chimera Users
So now that I have the “movie” command working decently, it turns out that I cannot export a PDB file from my MD simulation and retain the ability to select by residue or atom number.
PDB files generated by other software (PACKMOL, AMBER) works fine though when I exported a PDB file from a fram in an AMBER MD simulation using chimera, I can open the file, I can select using residue names though trying to refer to atom or molecule numbers does not work. To be clear, the exported PDB file contains multiple molecules and solvent, all ar present and the file loads though trying to run commands like
show :17 ~show @536-593
Affects EVERY atom and molecule in the system when it should only affect residue 17 (by specifying residue number OR all atoms in that residue). Using the
show :XXX
works as intended though this affects all residues XXX and I only want to affect residue 17.
Am I doing something wrong or can I solve this in a simple way?
Best regards // Gustaf
Hello again Elaine With regards to the atom serial number, yes this did work and I am now able to select a molecule by atom numbers, though this is not very convenient. With regard to the residue selection, no. It works on my original PDB file used to set up the simulation, it works on my loaded trajectory file though it does not work on my exported PDB file.
From what I can guess it has something to do with the format of the exported PDB file though I cannot figure out why chimera cannot find residue 17 in a PDB file, correctly numbered, that it produced itself. I might just need to modify my selection syntax though I can’t see why.
You should have received an invite to a shared BOX volume containing the files needed to (potentially) reproduce this issue. If you’d prefer I post a shared link here, pleas let me know. This is what I observe on my end: -> AMBER MD simulation open /amberSimulationFiles/filesRead.py # Just loads prmtop and mdcrd show :17 # Works -> PDB used to prepare amber input open packmolPDB.pdb show :17 # Works -> PDB exported from Chimera open chimeraExportedPDB.pdb show :17 # Does not work Any help solving this would be greatly appreciated of course. Best regards // Gustaf
On 30 May 2018, at 17:58, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Gustaf, I have every expectation that you should be able to refer to the residue by number, e.g.
show :17 ~show :17
…or by atom serial numbers, e.g. (your syntax was wrong):
show @/serialNumber>535 and serialNumber<594
It should be the same as when you have the original trajectory open. Can you use “show :17” in that case? We would need an example of your trajectory input to see how Chimera is interpreting it. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 30, 2018, at 4:33 AM, Gustaf Olsson <gustaf.olsson@lnu.se> wrote:
Hello again Chimera Users
So now that I have the “movie” command working decently, it turns out that I cannot export a PDB file from my MD simulation and retain the ability to select by residue or atom number.
PDB files generated by other software (PACKMOL, AMBER) works fine though when I exported a PDB file from a fram in an AMBER MD simulation using chimera, I can open the file, I can select using residue names though trying to refer to atom or molecule numbers does not work. To be clear, the exported PDB file contains multiple molecules and solvent, all ar present and the file loads though trying to run commands like
show :17 ~show @536-593
Affects EVERY atom and molecule in the system when it should only affect residue 17 (by specifying residue number OR all atoms in that residue). Using the
show :XXX
works as intended though this affects all residues XXX and I only want to affect residue 17.
Am I doing something wrong or can I solve this in a simple way?
Best regards // Gustaf
Hi Gustaf, After reading the exported PDB file back into Chimera, it works to use residue number if you also specify het chain, e.g. show :17.het I’m not sure exactly why (maybe a bug), but it’s probably related to the unexpected case of all the atoms being HETATM rather than ATOM because there are no standard residues in your system. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 30, 2018, at 11:54 PM, Gustaf Olsson <gustaf.olsson@lnu.se> wrote:
Hello again Elaine
With regards to the atom serial number, yes this did work and I am now able to select a molecule by atom numbers, though this is not very convenient.
With regard to the residue selection, no. It works on my original PDB file used to set up the simulation, it works on my loaded trajectory file though it does not work on my exported PDB file.
From what I can guess it has something to do with the format of the exported PDB file though I cannot figure out why chimera cannot find residue 17 in a PDB file, correctly numbered, that it produced itself. I might just need to modify my selection syntax though I can’t see why.
You should have received an invite to a shared BOX volume containing the files needed to (potentially) reproduce this issue. If you’d prefer I post a shared link here, pleas let me know. This is what I observe on my end:
-> AMBER MD simulation open /amberSimulationFiles/filesRead.py # Just loads prmtop and mdcrd show :17 # Works
-> PDB used to prepare amber input open packmolPDB.pdb show :17 # Works
-> PDB exported from Chimera open chimeraExportedPDB.pdb show :17 # Does not work
Any help solving this would be greatly appreciated of course.
Best regards // Gustaf
On 30 May 2018, at 17:58, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Gustaf, I have every expectation that you should be able to refer to the residue by number, e.g.
show :17 ~show :17
…or by atom serial numbers, e.g. (your syntax was wrong):
show @/serialNumber>535 and serialNumber<594
It should be the same as when you have the original trajectory open. Can you use “show :17” in that case? We would need an example of your trajectory input to see how Chimera is interpreting it. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 30, 2018, at 4:33 AM, Gustaf Olsson <gustaf.olsson@lnu.se> wrote:
Hello again Chimera Users
So now that I have the “movie” command working decently, it turns out that I cannot export a PDB file from my MD simulation and retain the ability to select by residue or atom number.
PDB files generated by other software (PACKMOL, AMBER) works fine though when I exported a PDB file from a fram in an AMBER MD simulation using chimera, I can open the file, I can select using residue names though trying to refer to atom or molecule numbers does not work. To be clear, the exported PDB file contains multiple molecules and solvent, all ar present and the file loads though trying to run commands like
show :17 ~show @536-593
Affects EVERY atom and molecule in the system when it should only affect residue 17 (by specifying residue number OR all atoms in that residue). Using the
show :XXX
works as intended though this affects all residues XXX and I only want to affect residue 17.
Am I doing something wrong or can I solve this in a simple way?
Best regards // Gustaf
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaine, hope you had a nice weekend. Thank you for this workaround which solves my immediate issue, I can no select and modify the presentation using both a script and the GUI menus. I did play around with editing the PDB file to resemble the layout of a working PDB file, using ATOM, including “TER” and so forth though without any real success. This, however, might also have been caused bu a lack of time and energy invested. Again, a high thank you fo you time and effort, much appreciated. Best regards // Gustaf
On 1 Jun 2018, at 18:50, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Gustaf, After reading the exported PDB file back into Chimera, it works to use residue number if you also specify het chain, e.g.
show :17.het
I’m not sure exactly why (maybe a bug), but it’s probably related to the unexpected case of all the atoms being HETATM rather than ATOM because there are no standard residues in your system.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 30, 2018, at 11:54 PM, Gustaf Olsson <gustaf.olsson@lnu.se> wrote:
Hello again Elaine
With regards to the atom serial number, yes this did work and I am now able to select a molecule by atom numbers, though this is not very convenient.
With regard to the residue selection, no. It works on my original PDB file used to set up the simulation, it works on my loaded trajectory file though it does not work on my exported PDB file.
From what I can guess it has something to do with the format of the exported PDB file though I cannot figure out why chimera cannot find residue 17 in a PDB file, correctly numbered, that it produced itself. I might just need to modify my selection syntax though I can’t see why.
You should have received an invite to a shared BOX volume containing the files needed to (potentially) reproduce this issue. If you’d prefer I post a shared link here, pleas let me know. This is what I observe on my end:
-> AMBER MD simulation open /amberSimulationFiles/filesRead.py # Just loads prmtop and mdcrd show :17 # Works
-> PDB used to prepare amber input open packmolPDB.pdb show :17 # Works
-> PDB exported from Chimera open chimeraExportedPDB.pdb show :17 # Does not work
Any help solving this would be greatly appreciated of course.
Best regards // Gustaf
On 30 May 2018, at 17:58, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Gustaf, I have every expectation that you should be able to refer to the residue by number, e.g.
show :17 ~show :17
…or by atom serial numbers, e.g. (your syntax was wrong):
show @/serialNumber>535 and serialNumber<594
It should be the same as when you have the original trajectory open. Can you use “show :17” in that case? We would need an example of your trajectory input to see how Chimera is interpreting it. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 30, 2018, at 4:33 AM, Gustaf Olsson <gustaf.olsson@lnu.se> wrote:
Hello again Chimera Users
So now that I have the “movie” command working decently, it turns out that I cannot export a PDB file from my MD simulation and retain the ability to select by residue or atom number.
PDB files generated by other software (PACKMOL, AMBER) works fine though when I exported a PDB file from a fram in an AMBER MD simulation using chimera, I can open the file, I can select using residue names though trying to refer to atom or molecule numbers does not work. To be clear, the exported PDB file contains multiple molecules and solvent, all ar present and the file loads though trying to run commands like
show :17 ~show @536-593
Affects EVERY atom and molecule in the system when it should only affect residue 17 (by specifying residue number OR all atoms in that residue). Using the
show :XXX
works as intended though this affects all residues XXX and I only want to affect residue 17.
Am I doing something wrong or can I solve this in a simple way?
Best regards // Gustaf
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
-
Elaine Meng -
Gustaf Olsson