[phenixbb] assign multiple ligand conformations
tg at shelx.uni-ac.gwdg.de
Tue Feb 11 05:21:17 PST 2014
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the refinement menu (Calculate -> Model/Fit/Refine...) contains "Add
Alt Conf..." which, when applied to a ligand, splits the entire ligand
into two (or three on the second go).
You can modify occupancies and B-values with "Measures->Reside Info"
On 02/11/2014 02:00 PM, Wei Shi wrote:
> 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
>>> current position look possible according to the blue density in
>>> Coot. I
>>> 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
>> -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4
>> D-37077 Goettingen
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Dr Tim Gruene
Institut fuer anorganische Chemie
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