[phenixbb] refining a covalent-bound ligand

Maxime Cuypers maximecuypers at gmail.com
Mon Feb 26 11:08:18 PST 2018


Hi,
one solution would be to create a custom link/angle... using a .param file
with the restrains as in below example.

on the phenix website:
Definition of custom bonds and angles
<http://www.phenix-online.org/documentation/reference/refinement.html#id49>

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



Dr. Maxime Cuypers
Post-Doctoral Research Associate, Structural Biology
St Jude Children s Research Hospital,
262 Danny Thomas Place
Memphis, TN 38105-3678, USA

or

3000 Eagle Dr.
Memphis, TN 38115, USA

Mobile phone:
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2018-02-26 12:41 GMT-06:00 Christian Roth <christianroth034 at gmail.com>:

> 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 at 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 Bioimaging
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709     Email : NWMoriarty at LBL.gov <NWMoriarty at LBL.gov>
> Fax   : 510-486-5909       Web  : CCI.LBL.gov <http://cci.lbl.gov/>
>
> On Thu, Feb 22, 2018 at 9:25 AM, Pavel Afonine <pafonine at 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 <+39%2002%209437%205167>
>> fax +39 02 9437 5990 <+39%2002%209437%205990>
>> web http://is.gd/IEOXtalUnit
>>
>>
>>
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>
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