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Re: [ccp4bb] Preventing close contact between protein and ligand
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
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Subject: Re: Superposition of maps in diferent spacegroups
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-07-30		Next message:
Subject: Re: Meaning of sigma level of electron density map?
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2008-07-30


Subject: Re: Preventing close contact between protein and ligand
From: Sangeetha Vedula sangeetha {- dot -} bb {- at -} GMAIL {- dot -} COM
Date: 2008-07-30

I am looking at my ligand library file that ProDRG generated. I do not see
any column id that indicates that it is a restraints weight or such. Could
you tell me exactly which one I should edit?

Thanks,

Sangeetha.

On Tue, Jul 29, 2008 at 3:23 PM, Robert Immormino wrote:

> You're probably better off trying to change the restraints in the
> ligand .cif file. It sounds like you have some torsion angle or
> chiral center set wrong.
> -bob
>
> On Tue, Jul 29, 2008 at 10:24 AM, Sangeetha Vedula
> wrote:
> > Dear bb users,
> >
> > I am refining a protein-ligand complex (at 1.68 A resolution) in which
> the
> > ligand lies on a 2-fold crystallographic symmetry axis. The ligand
> occupancy
> > is, therefore, 0.5 in each asymmetric unit.
> >
> > I am almost at the end of the refinement but one problem has me stumped.
> > Refmac keeps moving a carbon in the ligand too close to a serine OG and
> an
> > oxygen too close to an arginine CD. Given that the ligand is at the
> > interface, the density is not perfect. However, I rebuild the ligand to
> > eliminate close contacts and still be within density and refmac pulls it
> > right back close to the protein. The refined position does not even look
> > better than the rebuilt one! It almost always looks worse! Would refmac
> put
> > less weight on close contacts with the ligand because it is only
> partially
> > occupied?
> >
> > I tried to use external restraints between the ligand and the residues so
> > that they are kept further away.
> >
> > Upon searching the net, I found this command line:
> >
> > external distance first chain [ch] residue [res] insertion [ins] -
> > atom [n] [altcode [a]] second chain [ch] residue [res] insertion [ins]-
> > atom [n] [altcode [a] ] value [v] sigma [s] [symm y/n]
> >
> > I thought (hoped) that the distance herein is the minimum distance of
> > approach between the specified atoms, I added these lines from within
> > "Developer options" in refmac interface:
> >
> > exte dist first chain A resi 59 atom CD seco chain X resi 2001 atom O1
> valu
> > 3.2 sigm 0.02 symm Y
> > exte dist first chain A resi 27 atom OG seco chain X resi 2001 atom C10
> valu
> > 3.2 sigm 0.02 symm Y
> >
> > It didn't recognize these restraints at all.
> >
> > However, when I change these lines to:
> >
> > exte dist first chain A resi 59 atom CA seco chain X resi 2001 atom O1
> valu
> > 3.2 sigm 0.02 symm Y
> > exte dist first chain A resi 27 atom OG seco chain X resi 2001 atom C10
> valu
> > 3.2 sigm 0.02 symm Y
> >
> > Refmac recognizes the first line but not the second - lines from log
> file:
> >
> > Bond distance deviations from the ideal >10.000Sigma will be monitored
> >
> > A 59 ARG CA . - X 2001 DIE O1 . mod.= 5.024 id.= 3.200 dev=
> -1.824
> > sig.= 0.020
> >
> > This raises two concerns:
> >
> > Concern 1: From the first line of output: the restraints here don't seem
> to
> > be minimizing close contact at all; it seems to think they are bonded
> > somehow (the distance between these atoms is not 5.024; it is 6.26 A; I
> > don't know what 5.024 A is!).
> >
> > I am missing something here. It'd be great if someone can tell me what
> that
> > is!
> >
> > Concern 2: This command only works when the first atom specified is a
> > C-alpha atom (or maybe a main chain atom; I didn't try using other main
> > chain atoms). Why is that?
> >
> > AND ULTIMATELY,
> >
> > is there some way I can tell refmac not to make the ligand and protein
> > clash?
> >
> > I'd really appreciate any help!
> >
> > Thanks,
> >
> > Sangeetha.
> >
>
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