Re: [phenixbb] assign multiple ligand conformations

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Wei, 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" Regards, Tim 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 wrote:

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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

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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

On 02/11/2014 05:35 AM, Wei Shi wrote: the

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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

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