[sharp-discuss] where to find the overall FOM after solomon and DM

[Clemens Vonrhein]

Dear Yi,

I know that everyone puts the FOm after density modification into the
Table 1. Although I must say that these numbers are pretty
meaningless: the FO after (classical) density modification is always
high. So what does it actually tell us? I never look at these numbers
at all: the values after pure heavy atom phasing (i.e. from SHARP) are
the ones that are interesting to me.

Anyway, here is some explanation how to get the values if you need to
get them ;-) SFTOOLS is your friend:

1. get <FOM> from SHARP in 20 bins and overall:

sftools <<end_ip
mode batch
read eden_flat_56.5pc.mtz
plot col FOMsha versus resol shells 20
plot col FOMsha versus resol shells 1
quit
Y
end_ip

2. get <FOM> from SOLOMON in 20 bins and overall:

sftools <<end_ip
mode batch
read eden_flat_56.5pc.mtz
plot col FOMshasol versus resol shells 20
plot col FOMshasol versus resol shells 1
quit
Y
end_ip

3. get <FOM> from SOLOMON+DM in 20 bins and overall:

sftools <<end_ip
mode batch
read eden_flat_56.5pc.mtz
plot col FOMdm versus resol shells 20
plot col FOMdm versus resol shells 1
quit
Y
end_ip

Make sure you use the FOM column of the map you actually used (SOLOMON
map = FOMshasol; DM map = FOMdm)!

Note: I usually look at the maps after SOLOMON (I nearly always find
      them better, unless we're talking real low resolution like 5A or
      below). The final DM run is only done to get
      Hendrickson-Lattmann coefficients - something that the SOLOMON
      procedure doesn't give us directly. However, if you have NCS I
      would always use DM (from a script or the CCP4i) for doing the
      averaging - starting from the SOLOMON phases
      FBshasol/PHIBshasol.

Hope that helps.

Cheers

Clemens


On Tue, Oct 30, 2007 at 03:48:10PM -0500, Yi Xue wrote:
> Dear all:
>    I am trying to compile the statistics table, I used Se-SAD to solve the
> structure. I easily found the phasing statistics after SHARP. However, I
> could not find the phasing statistics (especially the overall FOM) after
> SOLOMON and DM. The DM log files only listed the FOM for each resolution
> bin. So, anyone knows, would you please give me some advices?
>    Additionally, for the phasing statistics after SHARP, the mean FOM of
> acentric and centric data are listed separately. Is there anyway to combine
> and average them? ( I might be wrong about how to compile these numbers, so,
> please correct me if you find something inappropriate).
> 
> thanks
> Yi
> 
> 
> 
> _______________________________________________
> sharp-discuss mailing list
> sharp-discuss at globalphasing.com
> https://www.globalphasing.com/mailman/listinfo/sharp-discuss
> 

-- 

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