[phenixbb] Autosol Feedback and questions

Partha Chakrabarti ppchak at gmail.com
Wed Jan 2 02:53:13 PST 2008

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

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?

2. How does PHASER know the different anomalous atoms? Does is use a
different scaling factor for SE and S?

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.

4. Lastly, is it possible to use multiple processors to run the job?

Best regards, Partha

MRC National Institute for Medical Research
Division of Molecular Structure
The Ridgeway, NW7 1AA, UK
Email: pchakra at nimr.mrc.ac.uk
Phone: + 44 208 816 2515
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