[phenixbb] adding sutrates in phenix.refine

Nigel W Moriarty NWMoriarty at lbl.gov
Thu Aug 13 07:44:08 PDT 2009


Rune

Folmer was correct in his instructions about using the restraints file.  
You can also run the refinement from the GUI.  Just type

phenix2

The eLBOW instruction you used initially would most likely have worked 
but ReadySet! has additional features and uses eLBOW internally will all 
the available information.

Nigel

On 8/13/09 1:38 AM, Rune wederkinck Andersen wrote:
> Hi Nigel
> Tanks for your quick answer
> I have tried what you suggested. and ran
> phenix.ready_set ssp.pdb   (ssp.pdb is my hole protein with my two 
> ligands AMP and RP5)
>
> This generate ssp.updated.pdb and ssp.ligands.cif
>
> I asume that ssp.ligands.cif is the file containing restraints.
>
> This i similar to the  cif file that I  generated  with the comand
> phenix.elbow  ssp.pdb  --do-all
>
> My problem is that I don't know how to  use both files in my later 
> phenix.refine command.
> I use a in_refine.def file in my refinement command
>
> phenix.refine in_refine.def
>
> In this in_refine.def file there is a section with the command:
>
>   pdb_interpretation {
>     apply_cif_modification {
>       data_mod = None
>       residue_selection = None
>     }
>
> sould anything by added in this section?
>
> Cheers
> Rune
>
>
>
> ------------------------------------------------------------------------
> Date: Wed, 12 Aug 2009 08:20:08 -0700
> From: NWMoriarty at lbl.gov
> To: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] adding sutrates in phenix.refine
>
> Rune
>
> You are correct that the ligand RP5 is in the Chemical Components 
> library but the ChemComp is a library of ligand chemical data not 
> ligand geometry restraints.  An additional step needs to be performed 
> to convert to restraints for a refinement.
>
> The simplest solution is the run ReadySet! on your model.
>
> phenix.ready_set model.pdb
>
> will generate a new model with hydrogens and ligands with hydrogens 
> and a restraints CIF file for any ligands not in the Monomer library.
>
> Contact me again if you still have difficulty.
>
> Nigel
>
> On 8/12/09 5:11 AM, Rune wederkinck Andersen wrote:
>
>     Hi everyone
>     I'm running a refinement in phenix.refine. I'm now trying to ad
>     two subtrates AMP and RP5. The phenix.refine  seams  to reconise
>     AMP but not the RP5 molecules. It seams as if this molecules is
>     well known for the program 
>     (phenix-1.4-3/ext_ref_files/chemical_components/r/data_RP5.cif).
>     In my PDB file the two molecules are described like this:
>     ...
>     HETATM   19  C6  AMP A 301      35.852  19.986  36.427  1.00
>     22.32      A
>     HETATM   20  N6  AMP A 301      35.448  19.736  37.693  1.00
>     24.44      A
>     HETATM   21  N7  AMP A 301      36.400  17.540  35.616  1.00
>     23.01      A
>     HETATM   22  C8  AMP A 301      36.853  17.097  34.416  1.00
>     21.98      A
>     HETATM   23  N9  AMP A 301      37.034  18.126  33.560  1.00
>     19.84      A
>     HETATM    1  P'  RP5 A 302      30.291  24.910  31.815  0.25
>     10.66      A
>     HETATM    2  C5' RP5 A 302      32.348  25.416  30.301  0.25
>     14.76      A
>     HETATM    3  O5' RP5 A 302      31.481  24.448  30.868  0.25
>     12.67      A
>     HETATM    4  C4' RP5 A 302      33.260  24.753  29.307  0.25
>     15.58      A
>     HETATM    5  C3' RP5 A 302      33.017  25.227  27.872  0.25
>     15.17      A
>     HETATM    6  O3' RP5 A 302      33.951  26.264  27.522  0.25
>     14.15      A
>     HETATM    7  C2' RP5 A 302      33.282  23.935  27.083  0.25
>     16.11      A
>     HETATM    8  O2' RP5 A 302      34.571  23.963  26.478  0.25
>     13.68      A
>     HETATM    9  C1' RP5 A 302      33.351  22.848  28.160  0.25
>     16.92      A
>     HETATM   10  O1' RP5 A 302      32.775  23.415  29.296  0.25
>     16.62      A
>     HETATM   11  O1  RP5 A 302      32.631  21.639  27.867  0.25
>     20.12      A
>     HETATM   12  O1X RP5 A 302      29.112  25.373  30.809  0.25
>     10.53      A
>     HETATM   13  O2X RP5 A 302      29.912  23.844  32.781  0.25
>     10.59      A
>     HETATM   14  O3X RP5 A 302      30.793  26.258  32.567  0.25 
>     9.63      A
>     ATOM      1  N   MET B   1      63.305   2.511  45.667  1.00
>     64.80      B
>     ATOM      2  CA  MET B   1      62.528   3.463  46.463  1.00
>     68.29      B
>     ATOM      3  C   MET B   1      62.555   4.863  45.882  1.00
>     65.73      B
>     ATOM      4  O   MET B   1      63.607   5.325  45.446  1.00
>     64.47      B
>     ...
>
>     I have tried with phenix.elbow as well but didn't work...
>
>     Please help...
>
>     Rune
>
>
>
>     ------------------------------------------------------------------------
>     check out the rest of the Windows Live™. More than mail–Windows
>     Live™ goes way beyond your inbox. More than messages
>     <http://www.microsoft.com/windows/windowslive/>
>
>     ------------------------------------------------------------------------
>
>     _______________________________________________
>     phenixbb mailing list
>     phenixbb at phenix-online.org <mailto: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 <mailto:NWMoriarty at LBL.gov>
> Web   : CCI.LBL.gov
>
> ------------------------------------------------------------------------
> What can you do with the new Windows Live? Find out 
> <http://www.microsoft.com/windows/windowslive/default.aspx>
> ------------------------------------------------------------------------
>
> _______________________________________________
> 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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20090813/9b88ec78/attachment-0003.htm>


More information about the phenixbb mailing list