[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
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>
>   

-- 
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



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