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 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov http://cci.lbl.gov/ On Thu, Feb 22, 2018 at 9:25 AM, Pavel Afonine mailto:[email protected]> 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-... http://phenix-online.org/documentation/reference/refinement.html#definition-...

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

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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: USA: 001 901 491 4649 2018-02-26 12:41 GMT-06:00 Christian Roth :

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 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov http://cci.lbl.gov/

On Thu, Feb 22, 2018 at 9:25 AM, Pavel Afonine 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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