Sid If you use the SMILES string from the MSDChem website it will provide to correct bonding which can be ambiguous when using a PDB file. The new command in the most recent 1.3b versions is phenix.elbow, however elbow.builder will still work. Nigel On 9/18/2007 8:41 AM, Sudharsan Sridharan wrote:
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 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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