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Dear Everybody,
I have a 2.7A MAD data o f Hg derivative. By SOLVE I got the phase and by
RESOLVE I got initial model (50%) which I modelled upto 75% (poly-ALA/Gly)
but some of the fragments are not contineous. C2 space group and 2 molecules
in the asymmetric init, 400 residues per monomer.
In order to extend and complete the model (poly ALA) I tired to refine the
model by REFMAC5 (CCP4i) and CNS.
In REFMAC5 I used "no restrain" and varied weight from 0.3 (default) to
0.05. In all cases I got the output PDB where mainchain residues are not
regularized as seen both in O and COOT. In O I could at least see CA trace,
but in COOT CA trace is brocken (maximum 4-5 resides contineous).
Thereafter I used "restrain" and in library gave a monomer Alanine, then I
got a output PDB which is better than before. I can get CA trace in both O
and COOT. But some of the mainchain atoms and CB are not regularized. I
included Hg atom in the input PDB. But in the output PDB I donot get Hg.
I would appreciate if somebody advice me how to overcome this.
Then I tried CNS "model_map.inp" to get the map for improving the model.
(a) generate.inp gave me output (generate.pdb) but I still miss the Hg atoms
in the output.
(b) then I added Hg atoms manually in generate.pdb and ran "minimize.inp".
In the output (minimize.pdb) after minimize I am also not getting Hg atoms.
(c) However, taking the minimize.pdb (with protein residues poly ALA/Gly
only) I am trying to run "model_map.inp". I would like to know how I can get
HL co-efficients from .SCA file (created by HKL2000) as it requires as
follows.
{* Hendrickson-Lattman coefficients A,B,C,D *}
{* required for the "mlhl" target and phase combined
or observed maps *}
{+ table: rows=1 "HL coefficients" cols=4 "A" "B" "C" "D" +}
{===>} obs_pa="pa";
{===>} obs_pb="pb";
{===>} obs_pc="pc";
{===>} obs_pd="pd";
Then I would like to know how can I calculate
xmin, xmax, ymin, ymax, zmin, zmax
as it requires as follows.
{* limits in orthogonal angstroms for box mode or fractional coordinates
for fract mode *}
{+ table: rows=3 "x" "y" "z" cols=2 "minimum" "maximum" +}
{===>} xmin="";
{===>} xmax="";
{===>} ymin="";
{===>} ymax="";
{===>} zmin="";
{===>} zmax="";
If I run "model_map.inp" without above parameters, then I get the map but
that does not cover the model and model chains (with helices and strands)
are also not going through the electron density.
d) I assessed in the model that there are 3 Cys residues per monomer, so
total 6 Cys residues per Asymmetric unit.
When I checked generate.pdb in COOT after (a) above, I see there are
straight lines (25 to 50A) between CYS residues of two monomers in the
Asymmetric unit. Is COOT assuming something here between Cys residues of two
monomers in the Asymmetric unit or I needed to do something so that I can
avoid these kinds of straight line btween Cys residues.
I would appreciate comments and suggestions to short out above problems.
Thanks
Sam
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