Sun., June 21st 2015
Good evening,
adding several general points to the thread.
(1) Fundamentally PDB unlike other chemical databases
insists that all equal structures should have the same 3-letter
code and the same atom names - obviously for amino acids and say ATP.
(1.1) Needless to say t
Miri raises important points about issues in the PDB Chemical
Component Dictionary - I think part of the problem is that this is
published completely separately from the actual PDB - so for example I
don't think we have an archive of the CCD for comparison alongside the
PDB snapshots? This makes it
I can't imagine a journal doing that can you? When I work on my
supplementary material in a paper I don't expect that the journal will
take a bit out and publish it separately to support the work of my
competitors. Not out of spite that I was beaten - but because I don't
want to take the respon
Well the problem is there is a lot more to a ligand than PDB
coordinates - little things like bond orders... In addition people can
publish ligands with atoms for which they have no density - so
zero-occupancy is allowed too. So who should get priority - the group
who publishes a ligand first, or t
board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Martyn
Symmons
Sent: 22 June 2015 23:39
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [Fwd: Re: [ccp4bb] FW: New ligand 3-letter code
(help-7071)]
Well the problem is there is a lot more to a ligand than PDB coordinates -
little things li
smithkline>
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> -Original Message-----
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
> ] On Behalf Of Martyn Symmons
> Sent: 22 June 2015 23:39
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] [Fwd: Re: [ccp4bb] FW:
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> -Original Message-----
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
> Behalf Of Martyn Symmons
> Sent: 22 June 2015 23:39
> To: CCP4BB@JISCMAIL.AC.UK
> Subj
