I believe Phaser places CRYST1 record at the top of an output
pdb-file... Yanming, did you try lower symmetry spacegroups?
Eleanor Dodson wrote:
It seems very odd..in fact almost impossible. You still have 3 correct
molecules
I wonder if there is some error in the coordinate file?
Errors I make are:
leaving and end record, between 2 parts. - many programs stop
reading coordinates at the first END
leaving CRYST1 and SCALE cards in the middle of the file..
Getting the CRYST record wrong somewhere - REFMAC does not seem to
check that the cell dimensions are consistent
Eleanor
Yanming Zhang wrote:
Dear all,
I am sorry to trouble you again because I am facing a very weird
situation:
Three copies from Phaser are the right solutions based upon:
1, Rfree 42% R 39%
2, No packing clash
3, The packing within the 3 makes good sense
4, Density evenly distributed among the 3 copies even without NCS
Then fix these 3, asking Phaser to find one more (here I adopt the
strategy one copy at a time). Phaser did find one more, So now I have
4 copies in total.
Using the phase calculated from the previous 3 copies(because Rfree
42%), the 4th copy can exactly match one junk of the density, even
the side chain matchs, demonstrating the 4th copy is correct.
Checking the crystallographic packing, The density which the 4th
occupies, is an extra density which did not account for by the
previous 3 copies or their symmetry mates.
No Clash exists
Then I use the 4 copies to do the refinement, forseeing that there
will be a huge Rfree drop from 42% because I account for the extra
density using the 4th copy. BUT TO MY SURPRISE, THE RFREE INCREASE TO
65%.
Can you teach me what is going wrong? Thank you
Yanming
--
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 /
