[phenixbb] real space refine generates non-compliant PDB files

[Pavel Afonine]

This is fixed in recent versions (nightly builds):

http://phenix-online.org/download/nightly_builds.cgi

Pavel

On 2/22/19 06:11, Edwin Pozharski wrote:
> Not sure whether anyone would care now that we got our marching orders 
> to abandon PDB format and move to mmCIF, but the output of 
> phenix.real_space_refine includes a number of lines that are not legit 
> PDB records, i.e. this section
>
> ...
> REMARK   3
>
> GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
> DEVIATIONS FROM IDEAL VALUES.
>   BOND      :  0.004   0.049  74053
>   ANGLE     :  0.747  12.299 100513
>   CHIRALITY :  0.052   0.232  11312
>   PLANARITY :  0.006   0.069  13125
>   DIHEDRAL  : 11.589 179.958  44947
>   MIN NONBONDED DISTANCE : 2.276
>
> MOLPROBITY STATISTICS.
>   ALL-ATOM CLASHSCORE : 5.04
>   RAMACHANDRAN PLOT:
>     OUTLIERS : 0.30  %
>     ALLOWED  : 8.63  %
>     FAVORED  : 91.06 %
>   ROTAMER OUTLIERS : 8.76 %
>   CBETA DEVIATIONS : 0
>   PEPTIDE PLANE:
>     CIS-PROLINE     : 3.7037037037
>     CIS-GENERAL     : 0.0
>     TWISTED PROLINE : 1.85185185185
>     TWISTED GENERAL : 0.316455696203
> REMARK   3
> ...
>
> This does result in errors when this output PDB file is used as input 
> to other software that is more stringent with format compliance.
>
> Cheers,
>
> Ed.
>
>
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