[phenixbb] elbow builder / phenix question
Sudharsan Sridharan
sudhaarsan at gmail.com
Tue Sep 18 08:41:21 PDT 2007
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
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