Heavy atom refinement

Kay Diederichs dikay at sun1.ruf.uni-freiburg.de
Thu Apr 28 09:31:37 EST 1994

Dear reader of this mailing list -

if you are a protein crystallographer, you might occasionally have 
asked yourself: what is the best heavy atom refinement program?
There are quite a few around, and I list below the ones that I had to deal
with so far - the list is by no means complete:

MLPHARE - from the CCP4 distribution seems to be in wide-spread usage
          (I don't know much about the other refinement programs from CCP4)
GREF, PHASIT - from Bill Furey's PHASES package
PROTEIN - Steigemann
MIR     - originating from Rossmann's lab (?)
DICFAZ  - originating from Dickerson's lab (?)
DAREFI  - from Schulz's lab, originating from MPI Heidelberg (?)
XHEAVY  - part of McRee's XtalView

I believe that it would be quite interesting to find out the relative
merits of all these and other programs. We can do this in a combined effort,
using this great opportunity, the Internet, as a means of communciation.

Probably all the programs can calculate good phases if good derivatives are
available, but how is the situation when only crummy derivatives are at hand,
which is probably more the rule than the exception?

I have prepared a test case: native and four heavy-atom derivative data sets
of granulocyte-macrophage colony stimulating factor. The structure is solved
(Science 254 (1991), 1779-1782) and a coordinate set including water molecules 
available for purposes of map and phase comparison. The structure was solved 
with the help of the DAREFI program mentioned above using those 3.5A MIR data
that I will distribute. 
I believe that the data are quite adequate for two reasons: 
1) this is a small protein (two chains of 119 visible amino acid
   residues in the asymmetric unit) which is good in terms of your and your 
   computer's CPU time 
2) the derivatives are pretty bad - the structure could only be solved after 
   application of tricks like solvent flattening and non-crystallographic 
   symmetry averaging.

If you want to participate, please e-mail to me and I will send you the
data, together with a description and a list of heavy atom sites. Feed these
sites into your favourite refinement program(s), calculate difference fouriers
to find new/discard old sites and send the final, refined set of sites,
occupancies plus phases and figures of merit back to me. Furthermore, 
calculate SIR phases using only the first heavy atom data set and send them 
to me. 
I will collect all the data and compare to the phases calculated from the 
model, as well as get correlation coefficients between the SIR/MIR map and 
the 2Fobs-Fcalc map. DO NOT average and/or solvent flatten the maps that you 
calculate, as this adds a huge number of parameters and programs.
Finally, I will prepare a summary that will be sent to all participants. 
If the results warrant this, they may be published as well.
Kay Diederichs                      email: dikay at sun1.ruf.uni-freiburg.de 
Universitaet Freiburg, Institut fuer Biophysik, Albertstr. 23 
D-79104 Freiburg, Germany   Tel. +49/(0)761/2035391 FAX +49/(0)761/2035016

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