[Chimera-users] Residue selection

[Mark Girvin]

Thanks for the info Eric,

 - Mark
________________________________
From: Eric Pettersen [pett at cgl.ucsf.edu]
Sent: Thursday, November 14, 2013 3:43 PM
To: Mark Girvin
Cc: George Tzotzos ‎[gtzotzos at me.com]‎
Subject: Re: [Chimera-users] Residue selection

Yeah, waters with a blank chain ID are put in chain "water" and similarly residues in HETATM records with a blank chain ID are put in chain "het".  If the chain ID is non-blank, both get assigned the given chain ID rather than "water" or "het".

--Eric

On Nov 14, 2013, at 12:22 PM, Mark Girvin <mark.girvin at einstein.yu.edu<mailto:mark.girvin at einstein.yu.edu>> wrote:

Got it.  And no problem - just not quite expected.

So then chimera sets up internal chain names (like "water") for some entries in PDB files? I don't think George's file had any internal chain entries, or HETATM lines.

 - Mark
________________________________
From: Eric Pettersen [pett at cgl.ucsf.edu<mailto:pett at cgl.ucsf.edu>]
Sent: Thursday, November 14, 2013 2:50 PM
To: Mark Girvin
Cc: George Tzotzos; chimera List
Subject: Re: [Chimera-users] Residue selection

Yeah, the :127 at 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<http://www.cgl.ucsf.edu/>


On Nov 14, 2013, at 7:44 AM, Mark Girvin <mark.girvin at einstein.yu.edu<mailto:mark.girvin at einstein.yu.edu>> wrote:

I don't know why that doesn't work, but:

select :WAT at O

seems to (if you only have the one water in your pdb file), as does:

select :127.water at O

(which would presumably limit the selection to the one water molecule)

 - Mark
________________________________
From: chimera-users-bounces at cgl.ucsf.edu<mailto:chimera-users-bounces at cgl.ucsf.edu> [chimera-users-bounces at cgl.ucsf.edu<mailto:chimera-users-bounces at cgl.ucsf.edu>] on behalf of George Tzotzos [gtzotzos at me.com<mailto:gtzotzos at 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 at 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

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