Most geometry restraints (bonds, angles, etc.) are generated automatically based on the CCP4 monomer library. Additional custom bond and angle restraints, e.g. between protein and a ligand or ion, can be specified in this way:
refinement.geometry_restraints.edits {
zn_selection = chain X and resname ZN and resid 200 and name ZN
his117_selection = chain X and resname HIS and resid 117 and name NE2
asp130_selection = chain X and resname ASP and resid 130 and name OD1
bond {
action = *add
atom_selection_1 = $zn_selection
atom_selection_2 = $his117_selection
symmetry_operation = None
distance_ideal = 2.1
sigma = 0.02
slack = None
}
bond {
action = *add
atom_selection_1 = $zn_selection
atom_selection_2 = $asp130_selection
symmetry_operation = None
distance_ideal = 2.1
sigma = 0.02
slack = None
}
angle {
action = *add
atom_selection_1 = $his117_selection
atom_selection_2 = $zn_selection
atom_selection_3 = $asp130_selection
angle_ideal = 109.47
sigma = 5
}
}
cheers
Maxime
You could add the link description to your dictionary, import that in coot and it should work.
The non phenix way would be to create the link in jligand, write out the dictionary description and merge it with your ligand dictionary. The link statement needs to be in the pdb of course.
There might be also a way in phenix to do this, but I'm not aware of it at the moment. Maybe Pavel or Nigel can help out here.
Cheers
Christian
Am 26.02.2018 um 10:45 schrieb Sebastiano Pasqualato:
Dear Nigel and Pavel,thank you very much for you feedback and precious advice.It is a compound with a C=C double bond that gets attacked by the S of a Cys, hence I think it’s normal that the program is not recognising automatically the bond.I have changed the C=C bond to C-C and recreated the CIF file for the compound, than provided phenix the bond restrains (bond length and angles) for the C-S bond.It all seems to work very nicely.Thanks.
Any idea on how to tell Coot the same things? ;-)(I guess this one should go to the Coot_bb though ;-))
Thanks again,ciao,S
On 22 Feb 2018, at 18:35, Nigel Moriarty <nwmoriarty@lbl.gov> wrote:
Sebastiano
As Pavel said, send me the inputs if you are having issues.
Cheers
Nigel
---Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated BioimagingLawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty@LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
On Thu, Feb 22, 2018 at 9:25 AM, Pavel Afonine <pafonine@lbl.gov> wrote:
Hi Sebastiano,
if the ligand in PDB file is placed correctly and distance between atoms that are supposed to have a bond is within reasonable then it should be linked automatically. Otherwise you can use custom bonds as described here (available in GUI and command line):
http://phenix-online.org/documentation/reference/refinement. html#definition-of-custom- bonds-and-angles
Phenix does not recognize LINK records.
To verify the link, check .geo file that lists all the restraints used in refinement.
Let us know if you more questions or need help!
Pavel
On 2/22/18 05:13, Sebastiano Pasqualato wrote:
Hi there,
I have a pretty basic question.I am refining a structure in which a drug has been covalently linked to a Cys of the protein.I have generated the .cif fie for the ligand, but I don’t know how to tell the program that carbon C04 has to be covalently linked to the SG of the Cys. Is that sufficient to insert a LINK record in the pdb file? What is the correct syntax for that?Thanks a lot for the feedback and sorry for the naive question,ciao,Sebastiano
--
Sebastiano Pasqualato, PhD
Crystallography Unit
Department of Experimental Oncology
European Institute of Oncology
IFOM-IEO Campus
via Adamello, 16
20139 - Milano
Italy
tel +39 02 9437 5167
fax +39 02 9437 5990
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