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ExcitedStates / qfit-3.0

qFit: Automated and unbiased multi-conformer models from X-ray and EM maps.
MIT License
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what about anisotropic waters? #416

Closed mysecondnameisdanger closed 2 months ago

mysecondnameisdanger commented 2 months ago

If resolution is 1.2 (some say 1.1) or better, should we refine waters as anisotropic, right?

Looking at 

#__________________________________DETERMINE RESOLUTION AND (AN)ISOTROPIC REFINEMENT__________________________________
mtzmetadata=`phenix.mtz.dump "${pdb_name}.mtz"`
resrange=`grep "Resolution range:" <<< "${mtzmetadata}"`

echo "${resrange}"

res=`echo "${resrange}" | cut -d " " -f 4 | cut -c 1-5`
res1000=`echo $res | awk '{tot = $1*1000}{print tot }'`

if (( $res1000 < 1550 )); then
  adp='adp.individual.anisotropic="not (water or element H)"'
else
  adp='adp.individual.isotropic=all'
fi

in qfit_final_refine_xray.sh ...

stephaniewankowicz commented 2 months ago

We do not automatically anisotropically refine waters at high resolution (only protein heavy atoms), but we welcome people to edit and/or re-refine the final structures with the parameters they see best fit.