Re: [ccp4bb] to extract protein sequence from a rebuilt pdb file

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: mtz library in windows
From: "Stein, ND (Norman)" n {- dot -} d {- dot -} stein {- at -} DL {- dot -} AC {- dot -} UK
Date: 2008-10-01

Next message:
Subject: Re: to extract protein sequence from a rebuilt pdb file
From: Jane Bailey jbailey {- dot -} xtal {- at -} GOOGLEMAIL {- dot -} COM
Date: 2008-10-01

Subject: Re: to extract protein sequence from a rebuilt pdb file
From: "Miller, Mitchell D {- dot -} " mmiller {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2008-10-01

Hi Jane,
Qingping Xu wrote a python script that will extract the
sequence from the PDB file and align it with a fasta file.
The script depends on biopython and clustalw.
Regards,
Mitch

-----Original Message-----
From: owner-ccp4bb@dl.ac.uk [mailto:owner-ccp4bb@dl.ac.uk] On Behalf Of Miller, Mitchell D.
Sent: Tuesday, October 03, 2006 1:57 PM
To: Bottomley, Matthew; ccp4bb@ccp4.ac.uk
Subject: RE: [ccp4bb]: PDB to 1 letter code

*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***

Hi Matt,
Qingping Xu wrote a python script that will compare a PDB file with
a fasta file and corrects ala/gly to the correct amino acid on output.
The script depends on biopython and clustalw. If you are interested I
made a copy available,
http://smb.slac.stanford.edu/~mmiller/seqcheck.py

http://biopython.org/
http://www.ebi.ac.uk/clustalw/

Regards,
Mitch

________________________________

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jane Bailey
Sent: Wednesday, October 01, 2008 1:40 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] to extract protein sequence from a rebuilt pdb file

Hi, all

I am currently rebuilting my structure in coot, and the protein sequence is around 98% rebuilt yet. I am looking for a way to extract protein sequence from the rebuilt.pdb so that I could see clearly which part need to be rebuilt by sequence alignment. Any ideas about this? thanks

Best
Jane

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: mtz library in windows
From: "Stein, ND (Norman)" n {- dot -} d {- dot -} stein {- at -} DL {- dot -} AC {- dot -} UK
Date: 2008-10-01

Next message:
Subject: Re: to extract protein sequence from a rebuilt pdb file
From: Jane Bailey jbailey {- dot -} xtal {- at -} GOOGLEMAIL {- dot -} COM
Date: 2008-10-01