I'm attaching a pdb file of a protein ligand complex with a single conserve water molecule. The pdb file was constructed with Antechamber Leap. The water molecule is numbered as residue 127. When I try to select using: select :127 nothing happens. Selection works with: select :WAT The problem is that I need to monitor the distance between :127@O and a particular atom in the binding site of the protein during an MD trajectory. My question is if I'm doing something wrong with the residue selection. Many thanks in advance for your help Regards George
I don't know why that doesn't work, but: select :WAT@O seems to (if you only have the one water in your pdb file), as does: select :127.water@O (which would presumably limit the selection to the one water molecule) - Mark ________________________________ From: chimera-users-bounces@cgl.ucsf.edu [chimera-users-bounces@cgl.ucsf.edu] on behalf of George Tzotzos [gtzotzos@me.com] Sent: Thursday, November 14, 2013 8:08 AM To: chimera List Subject: [Chimera-users] Residue selection I'm attaching a pdb file of a protein ligand complex with a single conserve water molecule. The pdb file was constructed with Antechamber Leap. The water molecule is numbered as residue 127. When I try to select using: select :127 nothing happens. Selection works with: select :WAT The problem is that I need to monitor the distance between :127@O and a particular atom in the binding site of the protein during an MD trajectory. My question is if I'm doing something wrong with the residue selection. Many thanks in advance for your help Regards George _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Many thanks Mark, Much appreciated George On Nov 14, 2013, at 12:44 PM, Mark Girvin <mark.girvin@einstein.yu.edu> wrote:
I don't know why that doesn't work, but:
select :WAT@O
seems to (if you only have the one water in your pdb file), as does:
select :127.water@O
(which would presumably limit the selection to the one water molecule)
- Mark From: chimera-users-bounces@cgl.ucsf.edu [chimera-users-bounces@cgl.ucsf.edu] on behalf of George Tzotzos [gtzotzos@me.com] Sent: Thursday, November 14, 2013 8:08 AM To: chimera List Subject: [Chimera-users] Residue selection
I'm attaching a pdb file of a protein ligand complex with a single conserve water molecule. The pdb file was constructed with Antechamber Leap. The water molecule is numbered as residue 127. When I try to select using: select :127 nothing happens. Selection works with: select :WAT
The problem is that I need to monitor the distance between :127@O and a particular atom in the binding site of the protein during an MD trajectory.
My question is if I'm doing something wrong with the residue selection.
Many thanks in advance for your help
Regards
George
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Yeah, the :127@O behavior is deliberate. If you omit the chain ID, it only matches single-character chain IDs (i.e. not chain ID "water" or "het"). This choice was made so that if your structure has a bunch of waters that so happen to have the same numbers as various polymeric residues, :127 will get the polymeric residue(s) but not the waters. This behavior was more important before the PDB remediation a few years back where such occurrences were commonplace. Now, in standard PDB files waters are frequently assigned specific chain IDs and therefore have different numbers than the polymeric residues. Chimera's behavior still matters for non-standard PDB files generated by various programs. If I were making the decision about Chimera's behavior today, given that the issue no longer affects standard PDB files, it might go the other way (it might not), but I don't feel strongly enough to change anything. A bunch of complaining could change my mind. :-) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Nov 14, 2013, at 7:44 AM, Mark Girvin <mark.girvin@einstein.yu.edu> wrote:
I don't know why that doesn't work, but:
select :WAT@O
seems to (if you only have the one water in your pdb file), as does:
select :127.water@O
(which would presumably limit the selection to the one water molecule)
- Mark From: chimera-users-bounces@cgl.ucsf.edu [chimera-users-bounces@cgl.ucsf.edu] on behalf of George Tzotzos [gtzotzos@me.com] Sent: Thursday, November 14, 2013 8:08 AM To: chimera List Subject: [Chimera-users] Residue selection
I'm attaching a pdb file of a protein ligand complex with a single conserve water molecule. The pdb file was constructed with Antechamber Leap. The water molecule is numbered as residue 127. When I try to select using: select :127 nothing happens. Selection works with: select :WAT
The problem is that I need to monitor the distance between :127@O and a particular atom in the binding site of the protein during an MD trajectory.
My question is if I'm doing something wrong with the residue selection.
Many thanks in advance for your help
Regards
George
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Eric Pettersen -
George Tzotzos -
Mark Girvin