[phenixbb] assign multiple ligand conformations

[Wei Shi]

Dear Tim,
Thank you so much for the suggestions. How can I split the entire ligand in
Coot? By adding "Ter" in the pdb text file? Thank you!

Best,
Wei


On Tue, Feb 11, 2014 at 3:55 AM, Tim Gruene <tg at shelx.uni-ac.gwdg.de> wrote:

> Dear Wei,
>
> I would split the entire ligand in coot twice, not only the head. You
> can set the initial occupancy with coot, too.
> This has the advantage that the three conformation gain greater
> flexibility than what you might expect from the current density and, if
> the putatively non-disordered tail does not refine stably, you have a
> good indicator that you are overfitting and that e.g. your data are not
> strong enough for occupancy refinement.
>
> Best,
> Tim
>
> On 02/11/2014 05:35 AM, Wei Shi wrote:
> > Hi everyone,
> > I am working with protein-ligand complex structure. For the head group in
> > one of the ligands in the structure, two more positions in addition to
> the
> > current position look possible according to the blue density in Coot. I
> am
> > thinking of assigning multiple occupancies/positions to this head group.
> > So, I am wondering what I should do to achieve this. Is the following
> > strategy right?
> > 1. Fit the head group to the density at three different positions
> > separately in Coot and save them separately.
> > 2. Find out the atoms that are different among the three ligand positions
> > and combine the same atoms with different positions and change the
> > occupancy of those atoms to something between 0 to 1.
> > 3. Use Phenix. refine to refine. The occupancy refinement should be
> > automatically on, right?
> > Is this the best way to assign multiple occupancies/positions to the head
> > group? Thank you so much!
> > Also, anything to look after refinement which can tell me whether I am
> > assigning the right multiple conformations to the ligand?
> > Thank you so much!
> >
> > Best,
> > Wei
> >
> >
> >
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> >
>
> --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20140211/2e6bc1f9/attachment.htm>