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Dear Sam, May I suggest another way? Since 75% (poly-ALA/Gly) of the model has been built, you can use the model built to do fragment extension by OASIS-2004. Pick one good set of the MAD dataset, usually the peak wavelength, and put the data set and the model into OASIS-2004 to do fragment extension. After density modification by DM, you will get a new electron density map. Perhaps you can continue model building based on the new map. Since there are 2 molecules in the asymmetric unit, maybe they will have NCS. OASIS-2004 is available at website http://cryst.iphy.ac.cn/ and it is free. Good luck, Deqiang Yao ------------------------------------------------------------------------------ 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 combinedor 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 calculatexmin, xmax, ymin, ymax, zmin, zmaxas it requires as follows. {* limits in orthogonal angstroms for box m! ode 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. ThanksSam _______________________________________________! __________________Your Hotmail address already works to sign into Window! s 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
