[phenixbb] Se SAD data to include Sulphurs?

Thomas C. Terwilliger terwilliger at lanl.gov
Fri Dec 28 10:12:02 PST 2007

Hi Partha,

You can use phaser to choose what is sulfur and what is selenium.  Try
something like this:

phenix.autosol 3  Se data=sad.sca seq_file=seq.dat \
  sites_file=shelx.pdb \
  mad_ha_add_list="S"    \
  mad_ha_add_f_prime_list="0.3"   \

Phaser will first locate Se atoms (and add any to your shelx list if
appropriate), then it will look for S atoms as well.

All the best,
Tom T

> Hiya,
> I have a SAD dataset collected at 0.979A to very good completeness and
> redundancy, upto 2.1A. Two molecules in AU, each containing 2 Se and the
> solvent content is 40%. The Signal to noise is more than 1 upto 2.1A ,
> however solve resolve and phaser did not work.
> I am not an expert but what is getting somewhere is if I use SHELEX (or
> hyss) to find the sites, pick the best 3 of them, use MLPHARE or so to
> refine and Addsolve to find the other Se. However, looks like the fourth
> Se
> is less ordered. Now, the SHELEX file also finds several others which I
> guess are Sulphurs. I can see helix like density in the map after Addsolve
> (& resolve) or SHELEXE but have not been able to place any aromatic
> residue
> yet. I guess one problem is lack of proper NCS and low solvent content.
> Could someone point me to a method in which I can improve the map by
> including the Sulphurs? For example, using the already found Se as seeds?
> I
> am trying the autosol option anyway.
> Cheers, Partha
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

More information about the phenixbb mailing list