[phenixbb] question on bad geometry
Thomas C. Terwilliger
terwilliger at lanl.gov
Tue Aug 31 19:08:27 PDT 2010
Hi Fengyun,
That does look like a lot of outliers to me. You could try improving the
model by "rebuilding in place" with autobuild with the keyword
"rebuild_in_place=True" which will try to rebuild your model without
changing the sequence alignment. This procedure takes a while and it is
useful to use a multiprocessor machine with nproc=5.
You should also have a careful look at your model, as some manual
rebuilding might improve it a lot.
All the best,
Tom T
>> Hi everyone,
>>
>> I have a structure at 2.3 A refined in phenix to R/Rfree=0.23/0.28.
>> However, the geometry is not that good, the followings are the output
>> from phenix.model_vs_data,
>>
>> Stereochemistry statistics (mean, max, count):
>> bonds : 0.0080 0.0547 3244
>> angles : 1.1669 12.1085 4374
>> dihedrals : 15.7241 85.6280 1202
>> chirality : 0.0706 0.2831 536
>> planarity : 0.0036 0.0246 573
>> non-bonded (min) : 2.1217
>> Ramachandran plot, number of:
>> outliers : 17 (4.02 %)
>> allowed : 37 (8.75 %)
>> favored : 369 (87.23 %)
>> Rotamer outliers : 30 (8.62 %) goal: < 1%
>> Cbeta deviations >0.25A : 0
>> All-atom clashscore : 40.51 (steric overlaps >0.4A per 1000
>> atoms)
>>
>> I tried to use fix_rotamer=True, but it doesn't help at all. As to the
>> rotamer outliers, the value is far higher than the ideal one. Does
>> that mean I need to manually adjust the model? Or will autobuild help
>> improve the geometry?
>>
>> Thanks!
>> Fengyun
>>
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