Hi -
I thought that both phenix and refmac output map coefficients
corresponding to de-twinned data - or do I get this wrong?
I am also wondering what is the context of "poor" and if it has to do
with twinning,
or simply if the starting model is not so good. In what was are these
"poor" maps
different than the refmac5 "model biased" maps?
From what I have seen also from your previous email its hard to advice.
Its not clear if the Phaser solution is correct, how good the search
model was,
how the refinement goes. I would suggest to post these details so maybe
we could send more detailed comments.
Tassos
On Mar 16, 2009, at 11:24, Clemens Steegborn wrote:
Hi Walter,
You should definitely detwin data for map calculation if you have a
significant twinning fraction (and only for maps; keep using the
twinned
data set for refinement). We use the CCP4 program detwin. BUT if
Shelxl
gives bad density, maybe that's simply what you have, a bad density
map -
because output from Shelx is already detwinned!
BTW, we observed that different programs handled different cases
differently
well; I would suggest ALWAYS to try more than one program, and also
to try
Phenix ...
Best
Clemens
-----Ursprüngliche Nachricht-----
Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von
Walter Kim
Gesendet: Monday, March 16, 2009 7:22 AM
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Twinned data and maps
Hi again,
Thanks for your insight into refinement tools for twinned data. I
have a
couple of twinned data sets that are nearly perfectly
pseudomerohedrally
twinned. I've begun to refine my data in Refmac5 (using the
automated twin
refinement), CNS (using the twin inputs) and Shelxl; I'm testing out
the
different refinement programs to evaluate the best strategy for the
refinement. However, I would like to start making maps.
1. Refmac5 - outputs an mtz that is model-biased
2. CNS - maps made via model_map_twin.inp are poor
3. Shelxl - the maps generated in coot from the.fcf file are poor
Are there better ways to make cleaner maps with my twinnned data
that are
less model-biased that I can try to build into? Should I detwin the
data and
make maps from that (but continue to refine against the twinned data)?
Thanks,
Walter
P please don't print this e-mail unless you really need to
Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
Department of Biochemistry (B8)
Netherlands Cancer Institute,
Dept. B8, 1066 CX Amsterdam, The Netherlands
Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
