[phenixbb] elbow builder / phenix question

[Sudharsan Sridharan]

Hi all,

Is it ok to use the cif files generated by PRODRG server directly in
phenix refine ? I fit a ligand molecule in density in Coot using this
cif file. but after refinement in phenix using the same cif file the
ligand coordinates does not look right. Then I created a new cif file
using elbow.builder (with final geometry option) for the coordinates
fit in Coot. But I see differences in the bond properties in the new
cif file compared with the one from PRODRG server. e.g. please see
below for parts of the cif generated in these two.


could you please advice how to get the right cif file using the server
or phenix and do the refinement.

in a related question, is the command to use for building the cif in
phenix phenix.elbow or elbow.builder. the former is given in
http://www.phenix-online.org/new-site/documentation/elbow.htm

but didn't work (i'm using 1.3 beta)

and the latter does work (which is good !).

Thanks,
Sid.


from prodrg:

DRG      OAB    CAK       deloc       1.250    0.020
 DRG      CAK    OAD       deloc       1.250    0.020
 DRG      CAK    CAM       single      1.530    0.025
 DRG      CAM    CAA       double      1.390    0.020
 DRG      CAM    OAJ       single      1.360    0.022
 DRG      OAJ    CAO       single      1.435    0.033
 DRG      CAO    CAI       single      1.390    0.020
 DRG      CAO    CAP       single      1.530    0.025
 DRG      CAI    CAG       double      1.390    0.020
 DRG      CAG    CAH       single      1.390    0.020
 DRG      CAH    CAN       double      1.390    0.020
 DRG      CAN    CAL       single      1.530    0.025
 DRG      CAN    CAP       single      1.530    0.025
 DRG      CAL    OAE       deloc       1.250    0.020
 DRG      CAL    OAC       deloc       1.250    0.020
 DRG      CAP    OAF       single      1.430    0.025
 DRG      OAF    HAA       single      1.000    0.027
 DRG      CAA    1HAA      single      1.000    0.020
 DRG      CAA    2HAA      single      1.000    0.020
 DRG      CAO    1HAO      single      1.000    0.020
 DRG      CAI    1HAI      single      1.000    0.020
 DRG      CAG    1HAG      single      1.000    0.020
 DRG      CAH    1HAH      single      1.000    0.020
 DRG      CAP    1HAP      single      1.000    0.020


from elbow.builder:

ISC   OAB     CAK   double      1.23599 0.02
ISC   CAK     OAD   single      1.23956 0.02
ISC   CAK     CAM   single      1.51571 0.02
ISC   CAM     CAA   single      1.38593 0.02
ISC   CAM     OAJ   single      1.35985 0.02
ISC   OAJ     CAO   double      1.45557 0.02
ISC   CAO     CAI   aromatic    1.38350 0.02
ISC   CAO     CAP   aromatic    1.53664 0.02
ISC   CAI     CAG   aromatic    1.37763 0.02
ISC   CAG     CAH   aromatic    1.37668 0.02
ISC   CAH     CAN   aromatic    1.37587 0.02
ISC   CAN     CAL   single      1.53109 0.02
ISC   CAN     CAP   aromatic    1.52972 0.02
ISC   CAL     OAE   double      1.22830 0.02
ISC   CAL     OAC   single      1.23738 0.02
ISC   CAP     OAF   double      1.41071 0.02
ISC  1HAD     OAD   single      1.08000 0.02
ISC  1HAM     CAM   single      1.08000 0.02
ISC  1HAA     CAA   single      1.08000 0.02
ISC  2HAA     CAA   single      1.08000 0.02
ISC  3HAA     CAA   single      1.08000 0.02
ISC  1HAH     CAH   single      1.08000 0.02
ISC  1HAC     OAC   single      1.08000 0.02