[phenixbb] Low Resolution Density Modification Problems

Thomas C. Terwilliger terwilliger at lanl.gov
Tue May 10 14:45:46 PDT 2011


Hi Ian,

I don't know if this will help, as your resolution is pretty low for using
resolve density modification, but you can specify a model in density
modification to define where the solvent is not present. You have to run
resolve directly for this:

phenix.resolve<<EOD
hklin data_with_hl_coeffs.mtz
labin FP=FP PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD
model my_model_for_masking_protein.pdb
use_model_mask
solvent_content 0.5
no_build
EOD

Let me know if that doesn't work for you.

All the best,
Tom T

>> I am having a problem getting a decent DM map at lower resolutions (8, 10,
>> 12, 20). We have a model for the data (R-factor ~34) at 6.6 A (the model
>> is
>> based on different higher resolution data), and when I try and do DM at
>> anything worse than 6.6, the density no longer covers the model. Any
>> suggestions would be appreciated.
>>
>> Ian Slaymaker
>> USC
>> <http://www-scf.usc.edu/%7Eslaymake/>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>



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