[phenixbb] question on the missing fobs filled maps

Thomas C. Terwilliger terwilliger at lanl.gov
Mon Nov 8 15:50:52 PST 2010

Hi Fengyun,

The one with 81% completeness is likely to be fine, but do compare results
with the unfilled map. The one with 45% completeness is going to be very
difficult for model-building...unless your starting model is almost
correct to start with.

I would recommend trying in both cases: instead of using these maps, use
density-modified maps which can replace this model information with
information based on solvent flattening or (better yet, if you have NCS),
ncs averaging.

You can do this with

phenix.autobuild data=data.mtz model=coords.pdb \
   maps_only=True seq_file=seq.dat resolve_command_list=" 'fill' "

which will fill in missing reflections with information from the density
modification process.

All the best,
Tom T

>> Hi all,
>> I have two datasets, one of which the completeness is only about 81%,
>> the other one is even lower, about 45%.
>> The resulting "missing fobs filled map" is much better than the
>> unfilled map in the loop region. I read one file of Pavel on the fact
>> of maps, the concern of using missing fobs filled map is that the risk
>> of the mdoel bias.
>> My question is that could the missing fobs filled map be used for the
>> model building?
>> Thanks!
>> Fengyun
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb

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