Re: [ccp4bb] sequence from pdb

Fax: +1-404-727-2738 - Original Message > From: Miri Hirshberg > To: CCP4BB@JISCMAIL.AC.UK > Sent: Tue, April 6, 2010 3:24:57 AM > Subject: Re: [ccp4bb] sequence from pdb > > several options with no need for extra software: (1) goto > http://www.ebi.ac.uk/pdbe

Re: [ccp4bb] sequence from pdb

Mon., April 5th 2010 EBI several options with no need for extra software: (1) goto http://www.ebi.ac.uk/pdbe/ left handside under "Get PDB by ID" enter a pdb idcode for example 1mh1 you get http://www.ebi.ac.uk/pdbe-srv/view/entry/1mh1/summary goto Structure primary and click Fasta cut and past

Re: [ccp4bb] sequence from pdb

Mon., April 5th 2010 EBI several options with no need for extra software: (1) goto http://www.ebi.ac.uk/pdbe/ left handside under "Get PDB by ID" enter a pdb idcode for example 1mh1 you get http://www.ebi.ac.uk/pdbe-srv/view/entry/1mh1/summary goto Structure primary and click Fasta cut and past

Re: [ccp4bb] sequence from pdb

several options with no need for extra software: (1) goto http://www.ebi.ac.uk/pdbe/ left handside under "Get PDB by ID" enter a pdb idcode for example 1mh1 you get http://www.ebi.ac.uk/pdbe-srv/view/entry/1mh1/summary goto Structure primary and click Fasta cut and paste the sequence (2) pickup

Re: [ccp4bb] sequence from pdb

If you want the complete sequence of the material that was studied, rather than just a list of residues for which there are coordinates, then the information that you need is on the SEQRES records. So you could try grep "^SEQRES" followed by cut -c 20-70 with appropriate file names specified.

Re: [ccp4bb] sequence from pdb

Hi Rex, This can also be done in COOT, via the scripting interface: (print-sequence imol) best, Iain On 4/4/2010 6:55 AM, Rex Palmer wrote: Is there software that will extract a protein sequence in either 3 letter or single letter code from a given pdb file? Rex Palmer Birkbeck College No

Re: [ccp4bb] sequence from pdb

Hi Rex, Is there software that will extract a protein sequence in either 3 letter or single letter code from a given pdb file? yes. For example: phenix.print_sequence model.pdb More details: www.phenix-online.org Pavel.

Re: [ccp4bb] sequence from pdb

Hi Rex PDBSET (SEQUENCE keyword) does this, i.e. either 3 or 1 letter codes. Cheers -- Ian On Sun, Apr 4, 2010 at 2:55 PM, Rex Palmer wrote: > Is there software that will extract a protein sequence in either 3 letter or > single letter code from a given pdb file? > > Rex Palmer > Birkbeck Coll

[ccp4bb] sequence from pdb

Is there software that will extract a protein sequence in either 3 letter or single letter code from a given pdb file? Rex Palmer Birkbeck College