Dear Bei, 

  Since you have multiple HA data sets you can also try using dmmulti, which
can be used to data from one or more crystal forms simultaneously. 

Best of luck,
Sridhar

-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Phoebe
Rice
Sent: Wednesday, April 29, 2015 12:07 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] experimental phasing at low resolution

Dear Bei,
  It can sometimes be difficult to tell a real molecular replacement
solution from noise at low resolution.  
  In addition to Eleanor's excellent advice, you might try to use your
potential derivative data to test the top molrep solutions, even if their
statistics are crappy.  Try making derivative minus native and anomalous
difference maps phased with possible molrep solutions, and see if you get
peaks that agree (another nice reality check is to see if those peaks are
bigger than the holes).
  Also, don't despair until you've tried solvent flattening (or more
sophisticated solvent massaging).  Also remember that your first map will
probably be at somewhere around 6A, so beta sheets at best will look like
walls and helices will look like tubes (or, as my post doc advisor called
the very first map I calculated all by myself, dog turds).  Again, don't
despair: if you have a map that shows you where the helices are, molecular
replacement with those phases, or simple manual placement of the model,
should be easy.
  Good luck,
   Phoebe


> On Apr 27, 2015, at 7:51 PM, joy yang <[log in to unmask]> wrote:
> 
> Hi All,
> 
> I am looking for some advices on experimental phasing at low resolution,
any advices will be highly appreciated.
> 
> I have 3 data sets, with similar but not identical cell parameters,
Redundancy of each dataset is larger than 6  for overall and 2.5 for
anomalous signal, completeness >95% for overall and >90% for anomalous
signal:
> 
> peak: 72.12, 92.07, 128.05, 90, 95.56, 90,  P12(1)1, overall Res: 4.5 A,
ano signal 7.13 A (cc>0.15), HA=TaBr, f''=20.99
> 
> edge: 72.34, 92.28, 127.47, 90, 95.61, 90,  P12(1)1, overall Res: 4.1 A,
ano signal 8.31 A (cc>0.15), HA=TaBr , f'=-24.17
> 
> high remote:  72.18, 92.43, 128.11, 90, 95.60, 90,  P12(1)1, overall Res:
4.2 A, ano signal 12.48 A (cc>0.15), HA=TaBr 
> 
> When I tried phenix autosol, the Hyss search gives out a FOM at around
0.30, which is on the boarder line, however the BayesCC is always between
10-20 (meaning handiness not distinguishable?), the SKEW is some where
between 0.01-0.05, when it is 0.05, clear solvent boundary could be seen,
but the map is not traceable if it is meaningful at all.
> 
> As I have no idea of how many TaBr cluster could bind, I have tried
everything from 1 to 8, and all I got are similar FOM, SKEW and BAYESCC
values, with the FOM at sites=5 or 6 better than the others.
> 
> I am wondering if anybody have any experience with such kind of data:
> 1. what is a better software (maybe SHAPR or SHELEX?) to use in such a
case?
> 
> 2. What parameters should I change to make Phenix autosol to work? 
> 
> 3. I also have multiple native datasets and peak datasets (TaBr or Pt)
which have quite different cell parameters than these MAD datasets, could
these datasets be of any help? 
> 
> 4. What is more, a homolog structure is available, though can not solve
the structure through MR, is there anyway to use the homolog structure as a
aid for experimental phasing?
> 
> Thank you very much in advance!
> 
> Bei 
>