Sam, May I suggest TEXTAL. It is available as part of the PHENIX (http://www.phenix-online.org/) package. TEXTAL is very good at fitting lower resolution maps. Also do not forget to provide TEXTAL or RESOLVE with a sequence file, so that it can try to do an automated sequence alignment and side-chain fitting.
Good Luck, Mark On Tue, 2006-12-19 at 21:17 +0000, U Sam wrote: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > > 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 > > _________________________________________________________________ > Your Hotmail address already works to sign into Windows Live Messenger! Get > it now > http://clk.atdmt.com/MSN/go/msnnkwme0020000001msn/direct/01/?href=http://get.live.com/messenger/overview Sincerely yours, Mark A. White, Ph.D. Assistant Professor, Dept. Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics X-ray Crystallography Laboratory, Basic Science Building, Room 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Fax. (409) 747-4745 mailto://[EMAIL PROTECTED] http://xray.utmb.edu http://xray.utmb.edu/~white
