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Re: [ccp4bb] Ligand insertion and orientation...
 

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CCP4bb <-- 2007 <-- May 2007 <-- 09 May 2007
Previous message:
Subject: Refmac and B factors
From: "Kolstoe S {- dot -} E {- dot -} " S {- dot -} E {- dot -} KOLSTOE {- at -} SOTON {- dot -} AC {- dot -} UK
Date: 2007-05-09 		Next message:
Subject: Re: Refmac and B factors
From: Eva Kirchner eva {- dot -} kirchner {- at -} UNI-TUEBINGEN {- dot -} DE
Date: 2007-05-09


Subject: Re: Ligand insertion and orientation...
From: Paul Emsley emsley {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-09
Thanks Juegen,


On Wed, May 09, 2007 at 08:45:16AM -0700, Juergen Bosch wrote:
> Hi James,
>
> start Coot, and read in your cif file plus a coordinate file containing
> your ligand. Read in your structure and read in your mtz file as Auto,
> then you end up with two maps FWTxPHWT and DELFWTxPHDELWT.
> Next go to Calculate / Other Modelling Tools and select Fit Ligand.
> Since you should have some nice extra density in you difference map
> select this map to search your ligand in that map. Let Coot do the rest.
> You can also select flexible ligand docking etc.

I would also add that for a difference map, I'd notch up the signigicance
level to 3 sigmas or so. And that should reduce spurious hits.

> Should work as advertised. Once your ligand is in the position you
> expect it to be you can run real space refinement using the difference
> density map at this point. Then go to Calculate/Merge Molecules and
> select which one you want to merge, save the new coordinates including
> your found ligand.
>
> Good luck,
>
> Juergen
>
> P.S. this is assuming Coot 0.31, and there's also a Coot BB :-)

0.3.1 (and not to be confused with 0.0.31)

>
> James Pauff wrote:
>
> >Good day all,
> >
> >I have what may be a very simple question. I am
> >trying to insert a substrate/ligand into the active
> >site of my enzyme using COOT, into electron density
> >that I have already utilized in "O" for this purpose.
> >I've created the substrate library file (*.cif) using
> >a pdb file from PRODRG in the ccp4 sketcher. In COOT,
> >I went to File->Get Monomer..., but when I type the 3
> >letter code, I get nothing.

OK, Coot should be more informative about what kind of nothing
you get.

> >Further, I have imported the substrate as a separate
> >pdb file, and can move it close to the active site,
> >but I have no idea how to orient/manipulate the ligand
> >into the electron density. If I can eventually get
> >the ligand as a monomer into the screen, I still don't
> >know how to manipulate its orientation prior to
> >writing it into the enzyme's pdb, so I guess that I'm
> >just generally stuck here.

If all else fails, there's alway Rotate/Translate Zone
(in the Model/Fit/Refine dialog). Using that you can drag
and rotate the fragment.

CCP4bb navigation

CCP4bb <-- 2007 <-- May 2007 <-- 09 May 2007
Previous message:
Subject: Refmac and B factors
From: "Kolstoe S {- dot -} E {- dot -} " S {- dot -} E {- dot -} KOLSTOE {- at -} SOTON {- dot -} AC {- dot -} UK
Date: 2007-05-09 		Next message:
Subject: Re: Refmac and B factors
From: Eva Kirchner eva {- dot -} kirchner {- at -} UNI-TUEBINGEN {- dot -} DE
Date: 2007-05-09


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