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

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CCP4bb <-- 2007 <-- May 2007 <-- 09 May 2007
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Subject: Re: Ligand insertion and orientation...
From: James Pauff pauffjm {- at -} YAHOO {- dot -} COM
Date: 2007-05-09
Thank you all very much for your help. I am a
thousand miles farther than I was at the time I sent
out my question(s)!!



--- Paul Emsley wrote:

> 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.
>


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