Dear CCP4BB users; Due to mixed state of a ligand conformation I wanted to use shelx, to refine it correctly at the end point of refinement.
My problem is, that I do not know how to control geometry in Shelx. After Shelx refinement, my bonds are very tight (rms 0.008), angles loose (rms ~1.9), R is lower (21.2) and Rfree (28.6) is much higher, comparing to Refmac results (R/Rf 22.9/27.6 rms Bond/Angle 0.011/1.1561) (statistics calculated doing 0 Refmac cycles on Shelx refined model, res 2A, refinement without water molecules). Is there an equivalent of Refmac's 'weighting' in Shelx? How to control X-ray vs geometry ratio? I have tried with different WGHT parameter, but in the best case there is no change in rms bonds and little in angles, Rf is getting better (to 27.9), while R drops a bit (20.2) - overfitting? . Different FVAR also make no big difference. How to deal with that? and my second question: Shelx complains that that I have too many atoms on a single SIMU/DELU instructions. Following FAQ, I should 'split the offending DELU (and possibly SIMU) instructions' f.ex. DELU N_1001> OT2_9999 DELU O_1 > O_999 but I am still not sure, what to feed Shelx instead of default: DELU $C_* $N_* $O_* $S_* Thanks for any help : ) Art.
