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