Re: [ccp4bb]: Se-SAD problems

[Noinaj]

phx,   sg is C2, with no twinning.  Yep, the peak dataset was collected first and I have been focusing on the SAD phasing, but now am focusing more on the MAD procedures.  Thanks for the ideas, keep 'em coming!      cheers Nick     ----- Original Message ----- From: Frank von Delft To: 'Noinaj' ; ccp4bb@dl.ac.uk Sent: Friday, June 30, 2006 4:20 PM Subject: RE: [ccp4bb]: Se-SAD problems Hi Nick   What's the spacegroup?  If it's twinned and you're unlucky (but not particularly), the phasing would be iffy.   But far more likely is you killed the crystal collecting all that data;  try phasing only on the first (peak) dataset, provided you did collect that to completion first (and not by interleaving wavelengths).   Just two possibilities.  phx     From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Noinaj Sent: 30 June 2006 21:08 To: ccp4bb@dl.ac.uk Subject: [ccp4bb]: Se-SAD problems Hi,   I recently collected Se-MAD data (resolution --> p=2.4, e=2.8, hr=2.7) and currently attempting to find the heavy atom sites, but have experienced several problems.  I expect 20 Se sites in my protein (~99 KDa).    Initially, I just used the peak dataset (2.4 angstroms) for SAD Phasing procedures in CNS, AutoSol and Solve (via PHENIX), BnP, and CCP4.  With CNS, I found ~20 sites and they all showed up very nicely in the maps.  But when I did the density modification of both hands, neither map seemed to be better than the other, which was very disappointing.  Next, I tried AutoSOL strategy in PHENIX, which found the sites also, but listed varying degrees of occupancy for the sites, ranging from 0.7 to 0.05.  Not being that familiar with PHENIX, I used the sites from AutoSOL and made maps using CNS, but, map quality wasn't improved at all.  I have also tried using CCP4 and BnP to find the sites, hoping for better results, but these programs failed to find all the sites, typically fewer than 6 or so, depending on the program.  If they did list more sites, the signal for the sites wasn't significant over background.  My boss' friend used SHELX to found all the sites with much improved occupancies.  Using these sites, the maps looked a bit better, but still, no real discernable secondary structure, and still, alot of fragmented density.   I am currently working on MAD phasing procedures, which have so far, produced about the same results.   This is my first experimental phasing experiment, so I would like some advice or guidance about either SAD or MAD phasing procedures in general.  For example, what programs do people typically use, and why choose one program over another?  Which is most reliable?  I had expected the experimental phases to give me a map with good enough quality to at least build a rough model, but so far, this isn't the case.  So what steps can be taken now to improve the quality of the maps or phases to at least get to a map with some discernable features?    Thanks in advance for your feedback and guidance.         Cheers, Nicholas