Re: [ccp4bb] Question about modeling SAM into a protein structure

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

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Subject: Re: Post-translational modification induced strcture
From: Paul Mcewan Paul {- dot -} Mcewan {- at -} NOTTINGHAM {- dot -} AC {- dot -} UK
Date: 2010-03-04

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Subject: Re: Question about modeling SAM into a protein structure
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-03-04

I presume you have a dictionary for both SAM and SAH? You need SAM at
least to use COOT.

My method is to calculate a difference map with the SAM density - xclude
all atoms like SAH or waters which might overlap SAM, then manually grad
the SAM to the right place and run real space refinement against thge
difference map.

You would probably get the same result more automatically by using the
Find Ligand tool after masking the map against "protein only"
Eleanor

move theYuan Cheng wrote:
> Hi everyone,
> I am trying to model a S-adenosylmethionine (SAM) molecule into the
> active site of a protein using the SAH (exists in the crystal structure)
> as the template.
>
> What I have already tried but failed so far are
> 1)Pymol: I loaded the pdbs of SAM and protein-SAH into pymol and copy
> SAH into a separate object. Then I tried to align SAM to SAH, but it
> didn't work and pymol said " Executivealign:Mobile selection must derive
> from one object only". Does anyone know what this mean?
>
> 2)Coot: I tried to superpose SAM to SAH in coot. Bot SSM superpose and
> LSQ superpose didn't work. when I did SSM superpose, coot said "can't
> make graph for SAH structure". when I did LSQ superpose, nothing
> happened after I run it. I also tried Extensions> modeling> superpose
> ligands, nothing happened too. Does anyone know what's wrong here?
>
> I know that I can probably manually move SAM to the position of SAH and
> change the bond angles to make SAM align to SAH. I am wondering if there
> is any program that can help to perform ligand alignment without the
> need for manual adjustment.
>
> Thank you very much for your suggestion!
>
> Yuan

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

Previous message:
Subject: Re: Post-translational modification induced strcture
From: Paul Mcewan Paul {- dot -} Mcewan {- at -} NOTTINGHAM {- dot -} AC {- dot -} UK
Date: 2010-03-04

Next message:
Subject: ´ð¸´: Post-translational modification induced strcture
From: Ëï±ø·¨ bfsun {- at -} SIBS {- dot -} AC {- dot -} CN
Date: 2010-03-04