Re: [ccp4bb] thread protein sequence using pdb coordinates that are not avaliable on RCSB?

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

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Subject: Re: Ion exchange protein lost
From: "Nadir T {- dot -} Mrabet" Nadir {- dot -} Mrabet {- at -} MEDECINE {- dot -} UHP-NANCY {- dot -} FR
Date: 2010-05-12

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Subject: Re: Micro-g Crystal Growth and the literature
From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2010-05-12

Subject: Re: thread protein sequence using pdb coordinates that are not avaliable on RCSB?
From: Kelly Daughtry kddaught {- at -} BU {- dot -} EDU
Date: 2010-05-12

Thanks for all the suggestions.

I was able to use swiss-pdb viewer to accomplish my goal within 2 minutes of
installing!

Very useful software in general! I didn't realize all of the tools present.

Thank you everyone!

Kelly
*******************************************************
Kelly Daughtry
PhD Candidate
Department of Physiology and Biophysics
Boston University School of Medicine
590 Commonwealth Ave
R 390
Boston MA, 02215
(P) 617-358-5548
*******************************************************

On Wed, May 12, 2010 at 12:46 PM, Scott Pegan wrote:

> Kelly,
>
> You can do it with swiss-model, just have to use the alignment mode. I
> will ask for a pdb or RCSB code. Also, in the past I have found Jigsaw 3D
> model server to be a comparable tool.
>
> Scott
>
>
> On Wed, May 12, 2010 at 10:10 AM, Kelly Daughtry wrote:
>
>> Hello all,
>> I would like to thread one protein sequence onto a structure I recently
>> solved, and has not been submitted to the pdb.
>>
>> I found the swiss-model website, which is an excellent tool for inputing a
>> template sequence and target sequence (which is what I want to do), but it
>> only allows you to select a PDB ID, and not to upload your own pdb file.
>>
>> Does anyone know where I can do this online? I'm thisclose to just
>> changing each amino acid in coot (with the amount of searching I've done,
>> it's about equal time!).
>>
>> Thanks in advance,
>> Kelly Daughtry
>>
>> *******************************************************
>> Kelly Daughtry
>> PhD Candidate
>> Department of Physiology and Biophysics
>> Boston University School of Medicine
>> 590 Commonwealth Ave
>> R 390
>> Boston MA, 02215
>> (P) 617-358-5548
>> *******************************************************
>>
>
>
>
> --
> Scott D. Pegan, Ph.D.
> Assistant Professor
> Chemistry & Biochemistry
> University of Denver
>

CCP4bb navigation

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

Previous message:
Subject: Re: Ion exchange protein lost
From: "Nadir T {- dot -} Mrabet" Nadir {- dot -} Mrabet {- at -} MEDECINE {- dot -} UHP-NANCY {- dot -} FR
Date: 2010-05-12

Next message:
Subject: Re: Micro-g Crystal Growth and the literature
From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2010-05-12