I found that residue TRS has different dihedral target angles for the three hydroxyl oxygens, which are actually all equivalent. They have a periodicity of 1, but should have a periodicity of 3. What is the best way to handle such discrepancies? Most ligand parameters are probably auto-generated based on a reference structure, and there is probably a lot of conformation bias. In this case, it seems that parameterization should have been able to detect symmetry. It would be nice if parameters could include information about whether a human has done any validation. Actually, a ligand Wiki might be nice, where people can easily put comments, even if they are not sure about how to improve the parameters. Joe Krahn
Joe I think you may need to upgrade your version of PHENIX. In the current version, the periodicity is 3. I have recently been using eLBOW, the Chemical Components library and the Monomer Library to improve any residue restraints that have short comings. These are freely available at Source Forge from a project called GeoStd at http://sourceforge.net/projects/geostd Its included in more recent PHENIX versions in $PHENIX/chem_data/geostd Nigel On 9/28/09 11:45 AM, Joe Krahn wrote:
I found that residue TRS has different dihedral target angles for the three hydroxyl oxygens, which are actually all equivalent. They have a periodicity of 1, but should have a periodicity of 3. What is the best way to handle such discrepancies?
Most ligand parameters are probably auto-generated based on a reference structure, and there is probably a lot of conformation bias. In this case, it seems that parameterization should have been able to detect symmetry. It would be nice if parameters could include information about whether a human has done any validation. Actually, a ligand Wiki might be nice, where people can easily put comments, even if they are not sure about how to improve the parameters.
Joe Krahn _______________________________________________ phenixbb mailing list [email protected] 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 : [email protected] Web : CCI.LBL.gov
Nigel, I am using PHENIX 1.4-6, which is newer that the most recent version on the PHENIX web site, other than "nightly build" versions. Nigel W Moriarty wrote:
Joe
I think you may need to upgrade your version of PHENIX. In the current version, the periodicity is 3. I have recently been using eLBOW, the Chemical Components library and the Monomer Library to improve any residue restraints that have short comings. These are freely available at Source Forge from a project called GeoStd at http://sourceforge.net/projects/geostd
Its included in more recent PHENIX versions in $PHENIX/chem_data/geostd
Nigel
On 9/28/09 11:45 AM, Joe Krahn wrote:
I found that residue TRS has different dihedral target angles for the three hydroxyl oxygens, which are actually all equivalent. They have a periodicity of 1, but should have a periodicity of 3. What is the best way to handle such discrepancies?
Most ligand parameters are probably auto-generated based on a reference structure, and there is probably a lot of conformation bias. In this case, it seems that parameterization should have been able to detect symmetry. It would be nice if parameters could include information about whether a human has done any validation. Actually, a ligand Wiki might be nice, where people can easily put comments, even if they are not sure about how to improve the parameters.
Joe Krahn _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Joe It is in the nightly builds if you are inclined. You are also free to download the restraints from the GeoStd open source project. Nigel On 9/28/09 1:43 PM, Joe Krahn wrote:
Nigel, I am using PHENIX 1.4-6, which is newer that the most recent version on the PHENIX web site, other than "nightly build" versions.
Nigel W Moriarty wrote:
Joe
I think you may need to upgrade your version of PHENIX. In the current version, the periodicity is 3. I have recently been using eLBOW, the Chemical Components library and the Monomer Library to improve any residue restraints that have short comings. These are freely available at Source Forge from a project called GeoStd at http://sourceforge.net/projects/geostd
Its included in more recent PHENIX versions in $PHENIX/chem_data/geostd
Nigel
On 9/28/09 11:45 AM, Joe Krahn wrote:
I found that residue TRS has different dihedral target angles for the three hydroxyl oxygens, which are actually all equivalent. They have a periodicity of 1, but should have a periodicity of 3. What is the best way to handle such discrepancies?
Most ligand parameters are probably auto-generated based on a reference structure, and there is probably a lot of conformation bias. In this case, it seems that parameterization should have been able to detect symmetry. It would be nice if parameters could include information about whether a human has done any validation. Actually, a ligand Wiki might be nice, where people can easily put comments, even if they are not sure about how to improve the parameters.
Joe Krahn _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] 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 : [email protected] Web : CCI.LBL.gov
GeoStd seems not to have an files. Is it only available via SVN for now? The GeoStd parameters still need some work. The equivalent hydroxyls are not symmetric. One of the dihedrals has a base angle of -175.0 instead of 180 (or +/-60). One has an esd of 30.0, and the others have an esd of 20.0. The hydrogen ESDs also seem a bit too tight, and probably should have a periodicity of 3. They are an improvement, but I don't think automated parameterization will ever be perfect. Joe Nigel W Moriarty wrote:
Joe
It is in the nightly builds if you are inclined. You are also free to download the restraints from the GeoStd open source project.
Nigel
On 9/28/09 1:43 PM, Joe Krahn wrote:
Nigel, I am using PHENIX 1.4-6, which is newer that the most recent version on the PHENIX web site, other than "nightly build" versions.
Nigel W Moriarty wrote:
Joe
I think you may need to upgrade your version of PHENIX. In the current version, the periodicity is 3. I have recently been using eLBOW, the Chemical Components library and the Monomer Library to improve any residue restraints that have short comings. These are freely available at Source Forge from a project called GeoStd at http://sourceforge.net/projects/geostd
Its included in more recent PHENIX versions in $PHENIX/chem_data/geostd
Nigel
On 9/28/09 11:45 AM, Joe Krahn wrote:
I found that residue TRS has different dihedral target angles for the three hydroxyl oxygens, which are actually all equivalent. They have a periodicity of 1, but should have a periodicity of 3. What is the best way to handle such discrepancies?
Most ligand parameters are probably auto-generated based on a reference structure, and there is probably a lot of conformation bias. In this case, it seems that parameterization should have been able to detect symmetry. It would be nice if parameters could include information about whether a human has done any validation. Actually, a ligand Wiki might be nice, where people can easily put comments, even if they are not sure about how to improve the parameters.
Joe Krahn
Joe I guess you are correct. I'll have a closer look. Nigel On 9/28/09 4:18 PM, Joe Krahn wrote:
GeoStd seems not to have an files. Is it only available via SVN for now?
The GeoStd parameters still need some work. The equivalent hydroxyls are not symmetric. One of the dihedrals has a base angle of -175.0 instead of 180 (or +/-60). One has an esd of 30.0, and the others have an esd of 20.0. The hydrogen ESDs also seem a bit too tight, and probably should have a periodicity of 3.
They are an improvement, but I don't think automated parameterization will ever be perfect.
Joe
Nigel W Moriarty wrote:
Joe
It is in the nightly builds if you are inclined. You are also free to download the restraints from the GeoStd open source project.
Nigel
On 9/28/09 1:43 PM, Joe Krahn wrote:
Nigel, I am using PHENIX 1.4-6, which is newer that the most recent version on the PHENIX web site, other than "nightly build" versions.
Nigel W Moriarty wrote:
Joe
I think you may need to upgrade your version of PHENIX. In the current version, the periodicity is 3. I have recently been using eLBOW, the Chemical Components library and the Monomer Library to improve any residue restraints that have short comings. These are freely available at Source Forge from a project called GeoStd at http://sourceforge.net/projects/geostd
Its included in more recent PHENIX versions in $PHENIX/chem_data/geostd
Nigel
On 9/28/09 11:45 AM, Joe Krahn wrote:
I found that residue TRS has different dihedral target angles for the three hydroxyl oxygens, which are actually all equivalent. They have a periodicity of 1, but should have a periodicity of 3. What is the best way to handle such discrepancies?
Most ligand parameters are probably auto-generated based on a reference structure, and there is probably a lot of conformation bias. In this case, it seems that parameterization should have been able to detect symmetry. It would be nice if parameters could include information about whether a human has done any validation. Actually, a ligand Wiki might be nice, where people can easily put comments, even if they are not sure about how to improve the parameters.
Joe Krahn
phenixbb mailing list [email protected] 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 : [email protected] Web : CCI.LBL.gov
Hi all, I'm having what I believe is a simple problem defining custom bond restraints between a side chain in my protein model and a ligand (non-covalent bond). Here is a minimal form of my custom bond definition file that suffers from the error: refinement.geometry_restraints.edits { Atom1 = chain F and resid 1 and name FE1 Atom2 = chain A and resid 69 and name SG bond { action = *add atom_selection_1 = Atom1 atom_selection_2 = Atom2 distance_ideal = 2.35 sigma = 0.1 slack = None } } I'm using phenix 1.4-153 and I get the following error: ERROR: Unused parameter definitions: refinement.geometry_restraints.edits.Atom1 (file "/HOME/andrew/PHENIX_paramfiles/test.edits", line 5) refinement.geometry_restraints.edits.Atom2 (file "/HOME/andrew/PHENIX_paramfiles/test.edits", line 6) I've checked through the online manual and I believe my syntax is correct, but I'm not sure why my custom bond restraint is being ignored. A second question is: once I get the custom bond/angle restraints correctly implemented, is there a better or more convenient place to look and confirm that the restraints have been imposed other than the .geo file phenix.refine outputs? Thank you very much for your help, -Andy
atom_selection_1 = Atom1 atom_selection_2 = Atom2
This should fix it: atom_selection_1 = $Atom1 atom_selection_2 = $Atom2
A second question is: once I get the custom bond/angle restraints correctly implemented, is there a better or more convenient place to look and confirm that the restraints have been imposed other than the .geo file phenix.refine outputs?
The custom restraints will also be listed in the .log file. Ralf
Alternatively, you can do simply this: refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = chain F and resid 1 and name FE1 atom_selection_2 = chain A and resid 69 and name SG distance_ideal = 2.35 sigma = 0.1 slack = None } } Pavel. On 9/29/09 8:54 AM, Andrew T. Torelli wrote:
Hi all,
I'm having what I believe is a simple problem defining custom bond restraints between a side chain in my protein model and a ligand (non-covalent bond). Here is a minimal form of my custom bond definition file that suffers from the error:
refinement.geometry_restraints.edits { Atom1 = chain F and resid 1 and name FE1 Atom2 = chain A and resid 69 and name SG bond { action = *add atom_selection_1 = Atom1 atom_selection_2 = Atom2 distance_ideal = 2.35 sigma = 0.1 slack = None } }
I'm using phenix 1.4-153 and I get the following error: ERROR: Unused parameter definitions: refinement.geometry_restraints.edits.Atom1 (file "/HOME/andrew/PHENIX_paramfiles/test.edits", line 5) refinement.geometry_restraints.edits.Atom2 (file "/HOME/andrew/PHENIX_paramfiles/test.edits", line 6)
I've checked through the online manual and I believe my syntax is correct, but I'm not sure why my custom bond restraint is being ignored.
A second question is: once I get the custom bond/angle restraints correctly implemented, is there a better or more convenient place to look and confirm that the restraints have been imposed other than the .geo file phenix.refine outputs?
Thank you very much for your help, -Andy
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thanks Pavel, that works well. Best, -Andy On 9/29/2009 12:21 PM, Pavel Afonine wrote:
Alternatively, you can do simply this:
refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = chain F and resid 1 and name FE1 atom_selection_2 = chain A and resid 69 and name SG distance_ideal = 2.35 sigma = 0.1 slack = None } }
Pavel.
On 9/29/09 8:54 AM, Andrew T. Torelli wrote:
Hi all,
I'm having what I believe is a simple problem defining custom bond restraints between a side chain in my protein model and a ligand (non-covalent bond). Here is a minimal form of my custom bond definition file that suffers from the error:
refinement.geometry_restraints.edits { Atom1 = chain F and resid 1 and name FE1 Atom2 = chain A and resid 69 and name SG bond { action = *add atom_selection_1 = Atom1 atom_selection_2 = Atom2 distance_ideal = 2.35 sigma = 0.1 slack = None } }
I'm using phenix 1.4-153 and I get the following error: ERROR: Unused parameter definitions: refinement.geometry_restraints.edits.Atom1 (file "/HOME/andrew/PHENIX_paramfiles/test.edits", line 5) refinement.geometry_restraints.edits.Atom2 (file "/HOME/andrew/PHENIX_paramfiles/test.edits", line 6)
I've checked through the online manual and I believe my syntax is correct, but I'm not sure why my custom bond restraint is being ignored.
A second question is: once I get the custom bond/angle restraints correctly implemented, is there a better or more convenient place to look and confirm that the restraints have been imposed other than the .geo file phenix.refine outputs?
Thank you very much for your help, -Andy
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Dear All, I am trying to make a custom bond with an inhibitor compound and my protein. Plesae see the attached file for restraints file. But phenix is returning this error. Please help. Sorry: No atom selected: 'chain S and resid 501 and name C7 I am using version1.6-289 Thanks. Jobi
Dear All, I am trying to make a custom covalent bond with an inhibitor compound and my protein. Plesae see the attached file for restraints file. But phenix is returning this error. Please help. Sorry: No atom selected: 'chain S and resid 501 and name C7 I am using version1.6-289 Thanks. Jobi refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = chain S and resid 501 and name C7 atom_selection_2 = chain A and resid 25 and name SG distance_ideal = 2.35 sigma = 0.1 slack = None } }
Hi Jobi,
Your selection syntax looks correct to me. Would you be willing to
send me your coordinates and data (directly to me, not to the list) so
that I can have a closer look at what is going on?
The version of PHENIX you are using is also quite old, so I would
recommend upgrading to a more recent installer.
Thanks,
Jeff
On Thu, Oct 21, 2010 at 1:49 AM, Jobichen Chacko
Dear All, I am trying to make a custom covalent bond with an inhibitor compound and my protein. Plesae see the attached file for restraints file. But phenix is returning this error. Please help. Sorry: No atom selected: 'chain S and resid 501 and name C7 I am using version1.6-289 Thanks. Jobi
refinement.geometry_restraints.edits {
bond {
action = *add
atom_selection_1 = chain S and resid 501 and name C7
atom_selection_2 = chain A and resid 25 and name SG
distance_ideal = 2.35
sigma = 0.1
slack = None
}
}
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Jobi, I hope Jeff has helped you already. So just as a remark of how you can quickly debug it... Just type this from your command line: phenix.pdb_atom_selection model.pdb "chain S and resid 501 and name C7" and that will print the lines from PDB file that you have selected with the above atoms selection syntax. Similarly do for another one: phenix.pdb_atom_selection model.pdb "chain A and resid 25 and name SG" If it doesn't print anything or complaints, that means that either your atom selection syntax is not right (which is NOT your case since it appears to me correct), or simply you are trying to select atoms that are NOT present in your PDB file (empty selection). Pavel. On 10/20/10 10:49 PM, Jobichen Chacko wrote:
Dear All, I am trying to make a custom covalent bond with an inhibitor compound and my protein. Plesae see the attached file for restraints file. But phenix is returning this error. Please help. Sorry: No atom selected: 'chain S and resid 501 and name C7
I am using version1.6-289 Thanks. Jobi refinement.geometry_restraints.edits {
bond {
action = *add
atom_selection_1 = chain S and resid 501 and name C7
atom_selection_2 = chain A and resid 25 and name SG
distance_ideal = 2.35
sigma = 0.1
slack = None
}
}
participants (9)
-
Andrew T. Torelli -
Andy Torelli
-
Jeff Headd -
Jobichen Chacko -
Joe Krahn -
Nigel W Moriarty -
Pavel Afonine -
Pavel Afonine
-
Ralf W. Grosse-Kunstleve