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[sameeta bilgrami <sameeta_b@yahoo.co.in>]

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dear all,
     I am trying to solve a structure through MIR. I
have got 3 derivatives Hg Th and Ur. All the
derivatives as well as the native have data upto 2.5 A
resolution.
     I tried SOLVE. The FOM for the Phases finallly
obtained is 0.48 till 3.74 A resolution. The overall
Phasing power for the Hg derivative is 0.91, for Th it
is 0.21 and that for Ur it is 0.28.The final map that
i get after running solomon has an sfall reliability
index of 0.31 till 2.5 A resolution. 
     I am new to the method of MIR (it is being done
for the first time in our lab). I have the following
doubts that i know only a novice can have. I hope you
will all bear with me:
1) I have read people saying that they can see the
protein and solvent boundary clearly or they can see
the outline of two domains. But in O the maps can be
seen upto a certain radii mostly upto 8 A radii. How
do we see the entire Electron density together in
O...will it help if i just increase the radii of the
map that has to be drawn...or is there another program
to visualize the whole electron density of an
assymetric unit together.
2) From what i have read people first start putting in
sec. str. elements (mostly helices)...and model the
loops only in the end. But my protein has no helices
and very little B-sheet and mostly loops. The nmr
model of a similar protein shows that even the
B-sheets dont have standard ramachandran values. What
will be the best way to start modeling this protein. I
am seeing certain portions in the density which seem
like continuos strand of a protein. Should i start
putting something there.
3) The phasing power for Hg is just Ok and that for Ur
and Th is bad. Is phasing power the property of the
derivative as such or it depends on the program that
has found out the sites and refined them. Even the FOM
are  not good. On what does FOM and R-cullis depend.
4) The ccp4 has a documentation for all the programs
with detailed descriptions of the keywords used in the
program. Is there a similar manual for understanding
the logfiles. 
            Thnking you all for your kind attention
                              Yours sinecerely,
                              Sameeta Bilgrami


 

=====
Sameeta Bilgrami
Research Scolar
Deptt. of biophysics
All India Instt. of Medical Scs.
India

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