Re: [ccp4bb] modified amino acids

2015-05-14 Thread Tristan Croll
; Cheers, Tristan From: CCP4 bulletin board on behalf of Debasish Chattopadhyay Sent: Friday, 15 May 2015 9:46 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] modified amino acids I am looking for a list of all modified amino acids found in protein structures (in PDB). Three lett

[ccp4bb] modified amino acids

2015-05-14 Thread Debasish Chattopadhyay
I am looking for a list of all modified amino acids found in protein structures (in PDB). Three letter codes and geometry files will be wonderful. Thanks Debasish

Re: [ccp4bb] AW: [ccp4bb] modified amino acids in the PDB

2013-07-09 Thread Engin Özkan
ienstag, 9. Juli 2013 16:23 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] modified amino acids in the PDB - really the only complicated case would be where a group is covalently linked to more than one amino acid, wouldn't it? Any case where only one covalent link with an is

Re: [ccp4bb] modified amino acids in the PDB

2013-07-09 Thread Dale Tronrud
k for explanations of these nomenclature features before they become hard-wired in the new pdb deposition system (however there may be time - I refer you to my previous posting ;). Cheers Martyn Dr Martyn Symmons Cambridge __________

Re: [ccp4bb] [ccp4bb] modified amino acids in the PDB

2013-07-09 Thread Peter Artymiuk
x27;Non-polymer' heterogens can turn up either linked or not. Once >>> they are in the residues they have to make a call on which kind of >>> backbone they will feature in within the pdb. >>> That is why there is 'D5M' for non-polymer deoxyAMP. Also known a

[ccp4bb] AW: [ccp4bb] modified amino acids in the PDB

2013-07-09 Thread Herman . Schreuder
: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] modified amino acids in the PDB - really the only complicated case would be where a group is covalently linked to more than one amino acid, wouldn't it? Any case where only one covalent link with an is present could (should?) be treated as a special

Re: [ccp4bb] modified amino acids in the PDB

2013-07-09 Thread MARTYN SYMMONS
starts at foo.pdb_1 in my example - still missing the authors original intent.     all the best    Martyn  From: Mark J van Raaij To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, 9 July 2013, 15:23 Subject: Re: [ccp4bb] modified amino acids in the PDB - really the only c

Re: [ccp4bb] modified amino acids in the PDB

2013-07-09 Thread Mark J van Raaij
;> when it >> is 'DNA-linking' but so far not fessing up to life under a third code as >> 'RNA-linking' >> Now is perhaps the time to ask for explanations of these nomenclature >> features before >> they become hard-wired in the new pdb deposition system (however there may >> be time - &g

Re: [ccp4bb] modified amino acids in the PDB

2013-07-09 Thread Frances C. Bernstein
efer you to my previous posting ;).      Cheers     Martyn     Dr Martyn Symmons Cambridge _ From: Michael Weyand To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, 8 July 2013, 10:03 Subject: [ccp4bb] modified amino acids in the PDB Dear collea

Re: [ccp4bb] modified amino acids in the PDB

2013-07-09 Thread MARTYN SYMMONS
o my previous posting ;).      Cheers     Martyn     Dr Martyn Symmons Cambridge From: Michael Weyand To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, 8 July 2013, 10:03 Subject: [ccp4bb] modified amino acids in the PDB Dear colleagues, We deposited protein struct

[ccp4bb] modified amino acids in the PDB

2013-07-08 Thread Michael Weyand
Dear colleagues, We deposited protein structures with modified lysine side chains and were surprised that the PDB treats the modification as an independent molecule, with a “LINK” record indicating the covalent bond – instead of defining a modified residue (that’s what we had uploaded to the PDB).