[ccp4bb] refmac vs shelx refinement

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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From: Sabuj Pattanayek sabuj {- dot -} pattanayek {- at -} VANDERBILT {- dot -} EDU
Date: 2007-03-06

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Subject: Re: refmac vs shelx refinement
From: "George M {- dot -} Sheldrick" gsheldr {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2007-03-07

Subject: refmac vs shelx refinement
From: Artur Matysik art {- dot -} matysik {- at -} GMAIL {- dot -} COM
Date: 2007-03-06

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.

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: OT: turbo frodo keys?
From: Sabuj Pattanayek sabuj {- dot -} pattanayek {- at -} VANDERBILT {- dot -} EDU
Date: 2007-03-06

Next message:
Subject: Re: refmac vs shelx refinement
From: "George M {- dot -} Sheldrick" gsheldr {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2007-03-07