Chimera: Amber to PDB
Hi, I am Boris TOUZEAU, actually a PhD student at the National Taiwanese University (NTU) based in Taipei. I had a question about chimera; Is it possible to output pdb files having amber residues naming convention instead of pdb residues naming convention ? I saw it was possible to do it for the atoms (ligands) but I would be more interested to do it for residues. Best wishes, Boris TOUZEAU
Hi Boris, Well, not directly. If you run the AddCharge tool (or ‘addcharge’ command), which will in turn add hydrogens if any are missing, then the “Amber name” of the residue is computed and put into the ‘amberName’ attribute of each residue. So, if you then run the Python script below (simply by opening it with File→Open or the “open” command), then the regular name of the residue will be overwritten with the amberName attribute and if you then save a PDB file, the residue names will use the Amber convention. —Eric Eric Pettersen UCSF Computer Graphics Lab
On Aug 27, 2018, at 2:00 AM, Boris TOUZEAU <boris.touzeau@gmail.com> wrote:
Hi,
I am Boris TOUZEAU, actually a PhD student at the National Taiwanese University (NTU) based in Taipei.
I had a question about chimera; Is it possible to output pdb files having amber residues naming convention instead of pdb residues naming convention ? I saw it was possible to do it for the atoms (ligands) but I would be more interested to do it for residues.
Best wishes,
Boris TOUZEAU _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Eric, Thank you for the quick answer, I tried to use the addcharge command indeed but I think that my HIS residues were still HIS residues for all the histidines and not HID nor HIE. I expected that one could not do it directly and was prepared to write a script but I did not expected you to write it for me. Still I thank you as it is much much shorter than what I envisioned. Best wishes, Boris TOUZEAU Le mar. 28 août 2018 à 04:59, Eric Pettersen <pett@cgl.ucsf.edu> a écrit :
Hi Boris, Well, not directly. If you run the AddCharge tool (or ‘addcharge’ command), which will in turn add hydrogens if any are missing, then the “Amber name” of the residue is computed and put into the ‘amberName’ attribute of each residue. So, if you then run the Python script below (simply by opening it with File→Open or the “open” command), then the regular name of the residue will be overwritten with the amberName attribute and if you then save a PDB file, the residue names will use the Amber convention.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Aug 27, 2018, at 2:00 AM, Boris TOUZEAU <boris.touzeau@gmail.com> wrote:
Hi,
I am Boris TOUZEAU, actually a PhD student at the National Taiwanese University (NTU) based in Taipei.
I had a question about chimera; Is it possible to output pdb files having amber residues naming convention instead of pdb residues naming convention ? I saw it was possible to do it for the atoms (ligands) but I would be more interested to do it for residues.
Best wishes,
Boris TOUZEAU _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi, I have another issue with the script, correct me if I am wrong but it goes inside my own chimera names residues depositery and fetch the name right ? However it fails to fetch the cystein residue CYM. Is chimera name library up to date ? Best wishes, Boris TOUZEAU Le mar. 28 août 2018 à 04:59, Eric Pettersen <pett@cgl.ucsf.edu> a écrit :
Hi Boris, Well, not directly. If you run the AddCharge tool (or ‘addcharge’ command), which will in turn add hydrogens if any are missing, then the “Amber name” of the residue is computed and put into the ‘amberName’ attribute of each residue. So, if you then run the Python script below (simply by opening it with File→Open or the “open” command), then the regular name of the residue will be overwritten with the amberName attribute and if you then save a PDB file, the residue names will use the Amber convention.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Aug 27, 2018, at 2:00 AM, Boris TOUZEAU <boris.touzeau@gmail.com> wrote:
Hi,
I am Boris TOUZEAU, actually a PhD student at the National Taiwanese University (NTU) based in Taipei.
I had a question about chimera; Is it possible to output pdb files having amber residues naming convention instead of pdb residues naming convention ? I saw it was possible to do it for the atoms (ligands) but I would be more interested to do it for residues.
Best wishes,
Boris TOUZEAU _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Boris, You can put the script wherever you want. You just need to run it (by opening it with File→Open or the “open” command) after running ‘addcharge’ on your structures. If you do this a lot, you might want to consult the documentation for the ‘alias command (i.e. “help alias”) to make the process more convenient. Chimera will basically never consider the cysteine sulphur to be deprotonated by default. Therefore, you never get the Amber residue type CYM. You would have to force Chimera to consider the sulphur to be deprotonated by changing its IDATM type to ‘S3-‘ (negatively charged sp3 sulphur). You would do this (before adding hydrogens!) by selecting the sulphurs you want to change and then using this command: setattr a idatmType S3- sel —Eric Eric Pettersen UCSF Computer Graphics Lab
On Sep 4, 2018, at 1:22 AM, Boris TOUZEAU <boris.touzeau@gmail.com> wrote:
Hi, I have another issue with the script, correct me if I am wrong but it goes inside my own chimera names residues depositery and fetch the name right ? However it fails to fetch the cystein residue CYM. Is chimera name library up to date ?
Best wishes,
Boris TOUZEAU
Le mar. 28 août 2018 à 04:59, Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> a écrit : Hi Boris, Well, not directly. If you run the AddCharge tool (or ‘addcharge’ command), which will in turn add hydrogens if any are missing, then the “Amber name” of the residue is computed and put into the ‘amberName’ attribute of each residue. So, if you then run the Python script below (simply by opening it with File→Open or the “open” command), then the regular name of the residue will be overwritten with the amberName attribute and if you then save a PDB file, the residue names will use the Amber convention.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Aug 27, 2018, at 2:00 AM, Boris TOUZEAU <boris.touzeau@gmail.com <mailto:boris.touzeau@gmail.com>> wrote:
Hi,
I am Boris TOUZEAU, actually a PhD student at the National Taiwanese University (NTU) based in Taipei.
I had a question about chimera; Is it possible to output pdb files having amber residues naming convention instead of pdb residues naming convention ? I saw it was possible to do it for the atoms (ligands) but I would be more interested to do it for residues.
Best wishes,
Boris TOUZEAU _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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Eric Pettersen