Hi Ed,

Reset occupancies that are outside the [0,1] range at every step of minimization.

this simply will not work: this will invalidate the internal memory of LBFGS minimizer that we use in phenix.refine and as result it will drive it crazy. Pavel.

But nothing will prevent the sum of the two occupancies to exceed 1, right? But this may work in some cases. On Fri, 2010-07-16 at 09:31 -0700, Nathaniel Echols wrote:

On Thu, Jul 15, 2010 at 3:27 PM, Ed Pozharski wrote: Am I missing something or the only way to get this done is to refine twice - once only for ligand occupancy, and then for the rest of the model.

And what if total occupancy of the ligand is unknown? Is there a way to allow sum(occ) to be anywhere between 0 and 1?

I may be wildly off base here, but if you give each conformation a different residue number as well as different altlocs, and set the occupancies below 1, won't this remove the sum constraint? It's a little clumsy, but you just need to change the residue numbers back before you deposit in the PDB.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore ---------------------------------------------- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. ------------------------------ / Lao Tse /

After thinking on this some more (thanks jetlag), I believe I have a (relatively clean) solution in mind. It will take me 3-5 days to implement, so I will do it once I have those spare 3-5 days. The upper limit for the sum of occupancies of present conformers will be determined automatically and it will set individually (per involved residue group - ensemble of conformers) as constraint target for the sum. Thanks Ed for stimulating discussion -:) I'm sure once it's available this will raise another waive of questions like "why the sum of occupancies of my alternative conformers is not 1?" . Pavel. On 7/16/10 10:28 AM, Nathaniel Echols wrote:

On Fri, Jul 16, 2010 at 10:15 AM, Ed Pozharski mailto:[email protected]> wrote:

But nothing will prevent the sum of the two occupancies to exceed 1, right? But this may work in some cases.

Good point - the additive effect of the conformers probably wouldn't be considered, so both would be refined to something like the total occupancy.

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb