[phenixbb] elbow builder / phenix question
Nigel W. Moriarty
nwmoriarty at lbl.gov
Thu Sep 20 10:07:58 PDT 2007
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
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
>
--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax : 510-486-5909
Email : NWMoriarty at LBL.gov
Web : CCI.LBL.gov
More information about the phenixbb
mailing list