Hi Partha, At 03:53 AM 1/2/2008, you wrote:
Happy new year everybody,
I had quite a bit of difficulty with a SAD dataset which also showed Sulphur. Previously I had tried SHELEX to find sites, MLPHARE to refine, AddSOLVE to find more , and both SOLVE and PHASER to solve but it did not get to a point where I could do manual building. Autosol worked beautifully, the input files were scalepack merged data, ha.pdb (from addsolve step), and the sequence. PHASER to solve and TEXTAL & RESOLVE with through build option.
This actually leave me with some confusions / questions:
1. When I compare the other "solutions", they look like the right one, just not good enough. Where exactly is the autosol making a difference? Is it the ability of of TEXTAL to build something more meaningful when the solution is not good or number of iterations?
Autosol uses the quality of the model built as a score, if any model is built (R-factor if < 0.40; number of residues built less 2 * number of chains otherwise).. If no model is built, it uses the standard 4 or 5 criteria that are printed out on the AutoSol wizard screen (CC and R-factor for density modification; skew of electron density histograms, FOM, CC of NCS).
2. How does PHASER know the different anomalous atoms? Does is use a different scaling factor for SE and S?
It can tell by the ratio of anomalous to real scattering corresponding to each atom.
3. I see that phenix.refine has been used in the internal runs, I have used phenix.refine earlier. But after playing with the side chains in Coot, when I tried to use the modified pdb file and resolve.mtz, it complained about the good old Free_R flag. However, it ran directly in Refmac. Is it a known problem or maybe I did something stupid? I could do a dry run and change the read mtz and not cns if that would solve the problem.
As Pavel and Ralf have mentioned, this is because AutoSol has tossed a few (usually blank) reflections from your reflection file when it created the refinement file exptl_fobs_phases_freeR_flags_15.mtz # or something similar. Without the "_15" if from AutoBuild The solution is to either (1) use the refinement file from AutoSol (exptl_fobs_phases_freeR_flags_15.mtz), or to delete the MD5 remark record from the AutoSol/AutoBuild PDB file.
4. Lastly, is it possible to use multiple processors to run the job?
As Pavel mentioned...we are thinking about this but do not have anything yet. -Tom T Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB