[ccp4bb] 3D structure based alignment

Protein crystallography Programs for crystallography X-ray detectors
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Protein Peptide

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CCP4bb <-- 2008 <-- March 2008 <-- 28 March 2008

Previous message:
Subject: Re: program to draw 2D image of a peptide
From: "Kumar, Abhinav" abhinavk {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2008-03-28

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Subject: Re: program to draw 2D image of a peptide
From: Sandra Dias sd277 {- at -} CORNELL {- dot -} EDU
Date: 2008-03-28

Subject: 3D structure based alignment
From: Tânia_Oliveira taniao {- at -} ITQB {- dot -} UNL {- dot -} PT
Date: 2008-03-28

Hello,

I´m having a problem that I would like to know if someone could help me.

I want to do a 3D structure based alignment of my protein with another one.
The problem is that my protein has 2 domains, and the structure that I want
to superimpose just have one. I can do the structure superimposition by
hand, but I´m not being able to do the sequence alignment based on the 3D
structure, because the program that I´m using (SSM) starts to superimpose
the sequence of my second domain in the beginning of the sequence of my
reference model (exactly the same thing that it does with the sequence of
the first domain).

Do you know if there is any program where I can do this.

Thanks in advance,

Tânia Oliveira, PhD Student

Membrane Protein Crystallography and Microbial Biochemistry Laboratory -
ITQB-UNL

CCP4bb navigation

CCP4bb <-- 2008 <-- March 2008 <-- 28 March 2008

Previous message:
Subject: Re: program to draw 2D image of a peptide
From: "Kumar, Abhinav" abhinavk {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2008-03-28

Next message:
Subject: Re: program to draw 2D image of a peptide
From: Sandra Dias sd277 {- at -} CORNELL {- dot -} EDU
Date: 2008-03-28