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

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

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Subject: Re: Anomalous correlation plot in scala
From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2008-10-01

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From: ANDY DODDS andy {- dot -} dodds6 {- at -} GOOGLEMAIL {- dot -} COM
Date: 2008-10-01

Subject: Re: to extract protein sequence from a rebuilt pdb file
From: Mark Brooks mark {- dot -} x {- dot -} brooks {- at -} GMAIL {- dot -} COM
Date: 2008-10-01

You can do this quickly in Coot:
Calculate>Scripting>Scheme
And a scripting window opens.
See the Coot user manual (1) for detailed scheme instructions, but the
command now is in the form:
(print-sequence imol)
"imol" comes from the number shown in the display manager to the left
of the model name.
e.g.:
(print-sequence 0)
...for imol 0.
The sequences of each chain are output to the terminal.

If you have only python support in Coot:
Calculate>Scripting>Python
print_sequence(0) is the pythonized version of the command for imol 0.

(1) http://www.ysbl.york.ac.uk/~emsley/coot/doc/user-manual.html#SEC79

2008/10/1 Jane Bailey
>
> 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

--
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
Institut de Biochmie et de Biophysique Moleculaire et Cellulaire
UMR8619 - Bât 430 - Université de Paris-Sud
91405 Orsay CEDEX
Skype: markabrooks

CCP4bb navigation

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

Previous message:
Subject: Re: Anomalous correlation plot in scala
From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2008-10-01

Next message:
Subject: resuspending precipitated protein
From: ANDY DODDS andy {- dot -} dodds6 {- at -} GOOGLEMAIL {- dot -} COM
Date: 2008-10-01