Dear Rune 2009/8/13 Rune wederkinck Andersen :

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

You could simply add the cif file to that line: phenix.refine in_refine.def spp.ligands.cif That should work... If you want to use the updated pdb file (with hydrogens) I would: Start by stripping your def file: phenix.refine --diff-params "in_refine.def" To get just your corrections. Change the input pdb file in your .def file and then run this as mentioned above. Regards, Folmer Fredslund

Hi, I am trying to use GUI for the refinement for the first time. Where do you give the cif_link_param file for the covalent substrate? I was able to give only the ligands.cif file. Maia

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: [email protected] To: [email protected] 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

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