Dear all, thanks to the phenix team which helped me a lot to resolve all issues regarding the correct link definitions. I have summarised a few things which one might consider if nonstandard links are necessary. Try phenix ready set to get your links out of the pdb. Do not forget to change the possible LINKR to LINK! Inspect the links and decide if they are useful! Peptide links are automatically incorporated if residues are close (inspect geo file) Non standard peptide links could be created using using an now available alpha release script: elbow.ligand_linking model.pdb Inspect the generated cif file and correct angles and incorporate dihedrals and so on if necessary. Sugar links which exists in the mon_lib.cif should be incorporated using the apply_cif link option like refinement.pdb_interpretation.apply_cif_link { data_link = ALPHA1-4 residue_selection_1 = chain B and resname GLC and resseq 1 residue_selection_2 = chain B and resname GLC and resseq 2 } According to the link definition the C1 oxygen of the following sugar with the higher number must be removed. The automatic incorporation of sugar links will be probably soon available in phenix. Nigel is already working on this. If one want use hydrogens in the refinement, they have to be added previously with ready_set and afterwards the OH4 sugar hydrogen has to be removed before the refinement. For links with symmetry related atoms the symmetry operator must be included in a custom bond definition efinement.geometry_restraints.edits { bond { action = *add delete change atom_selection_1 = chain A and resname HEM and resid 154 and name FE atom_selection_2 = chain A and resname MTO and resid 155 and name O symmetry_operation = -x,y,-z distance_ideal = 2.2 sigma = 0.01 } } The operator can be obtained using iotbx.show_distances your.pdb > all_distances Search for keyword "sym" or from Coot clicking on the symm option. Coot print out the operator and the translation term separately. Both has to be merged in the final operator used in phenix! Christian
Hi - I was trying to resolve some issues where I have an acetyl group at the N-terminus. Historically it appears, these are treated as a residue (say "ACE 0"). To provide phenix.refine with angles and bonds, I made a file similar to a metal.edits file: One example of an angle between the acetyl and the first amino acid in my file: refinement.geometry_restraints.edits { angle { action = *add atom_selection_1 = name C and chain A and resname ACE and resseq 0 atom_selection_2 = name N and chain A and resname ALA and resseq 1 atom_selection_3 = name CA and chain A and resname ALA and resseq 1 angle_ideal = 121.6367 sigma = 5 } } The problem I'm having is defining a plane such that what would appear to be a peptide bond is flat: ACE O - ACE C - ALA N - ALA H I'm just not sure if it's being taken care of, there is a slight bend after refinement, but this also matches the electron density somewhat. I tried to run elbow.ligand_linking , but appears to be missing from the release I have: phenix-1.8.2-1309 Anything help appreciated. Thanks, Dave On Mon, Jan 30, 2012 at 12:36 AM, Christian Roth < [email protected]> wrote:
Dear all,
thanks to the phenix team which helped me a lot to resolve all issues regarding the correct link definitions.
I have summarised a few things which one might consider if nonstandard links are necessary.
Try phenix ready set to get your links out of the pdb. Do not forget to change the possible LINKR to LINK! Inspect the links and decide if they are useful! Peptide links are automatically incorporated if residues are close (inspect geo file) Non standard peptide links could be created using using an now available alpha release script:
elbow.ligand_linking model.pdb
Inspect the generated cif file and correct angles and incorporate dihedrals and so on if necessary.
Sugar links which exists in the mon_lib.cif should be incorporated using the apply_cif link option like refinement.pdb_interpretation.apply_cif_link { data_link = ALPHA1-4 residue_selection_1 = chain B and resname GLC and resseq 1 residue_selection_2 = chain B and resname GLC and resseq 2 } According to the link definition the C1 oxygen of the following sugar with the higher number must be removed. The automatic incorporation of sugar links will be probably soon available in phenix. Nigel is already working on this. If one want use hydrogens in the refinement, they have to be added previously with ready_set and afterwards the OH4 sugar hydrogen has to be removed before the refinement.
For links with symmetry related atoms the symmetry operator must be included in a custom bond definition efinement.geometry_restraints.edits { bond { action = *add delete change atom_selection_1 = chain A and resname HEM and resid 154 and name FE atom_selection_2 = chain A and resname MTO and resid 155 and name O symmetry_operation = -x,y,-z distance_ideal = 2.2 sigma = 0.01 } } The operator can be obtained using
iotbx.show_distances your.pdb > all_distances
Search for keyword "sym" or from Coot clicking on the symm option. Coot print out the operator and the translation term separately. Both has to be merged in the final operator used in phenix!
Christian _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- David Shin, Ph.D Lawrence Berkeley National Labs 1 Cyclotron Road MS 83-R0101 Berkeley, CA 94720 USA
Send me the PDB file and I'll work on getting the correct links for you.
You can send just the two residues involved off-list if you like.
Nigel
NB. Any files sent to me will be held in strictest confidence.
On Wed, Apr 3, 2013 at 8:11 PM, David Shin
Hi -
I was trying to resolve some issues where I have an acetyl group at the N-terminus. Historically it appears, these are treated as a residue (say "ACE 0"). To provide phenix.refine with angles and bonds, I made a file similar to a metal.edits file:
One example of an angle between the acetyl and the first amino acid in my file: refinement.geometry_restraints.edits { angle { action = *add atom_selection_1 = name C and chain A and resname ACE and resseq 0 atom_selection_2 = name N and chain A and resname ALA and resseq 1 atom_selection_3 = name CA and chain A and resname ALA and resseq 1 angle_ideal = 121.6367 sigma = 5 } }
The problem I'm having is defining a plane such that what would appear to be a peptide bond is flat: ACE O - ACE C - ALA N - ALA H I'm just not sure if it's being taken care of, there is a slight bend after refinement, but this also matches the electron density somewhat.
I tried to run elbow.ligand_linking , but appears to be missing from the release I have: phenix-1.8.2-1309
Anything help appreciated.
Thanks,
Dave
On Mon, Jan 30, 2012 at 12:36 AM, Christian Roth < [email protected]> wrote:
Dear all,
thanks to the phenix team which helped me a lot to resolve all issues regarding the correct link definitions.
I have summarised a few things which one might consider if nonstandard links are necessary.
Try phenix ready set to get your links out of the pdb. Do not forget to change the possible LINKR to LINK! Inspect the links and decide if they are useful! Peptide links are automatically incorporated if residues are close (inspect geo file) Non standard peptide links could be created using using an now available alpha release script:
elbow.ligand_linking model.pdb
Inspect the generated cif file and correct angles and incorporate dihedrals and so on if necessary.
Sugar links which exists in the mon_lib.cif should be incorporated using the apply_cif link option like refinement.pdb_interpretation.apply_cif_link { data_link = ALPHA1-4 residue_selection_1 = chain B and resname GLC and resseq 1 residue_selection_2 = chain B and resname GLC and resseq 2 } According to the link definition the C1 oxygen of the following sugar with the higher number must be removed. The automatic incorporation of sugar links will be probably soon available in phenix. Nigel is already working on this. If one want use hydrogens in the refinement, they have to be added previously with ready_set and afterwards the OH4 sugar hydrogen has to be removed before the refinement.
For links with symmetry related atoms the symmetry operator must be included in a custom bond definition efinement.geometry_restraints.edits { bond { action = *add delete change atom_selection_1 = chain A and resname HEM and resid 154 and name FE atom_selection_2 = chain A and resname MTO and resid 155 and name O symmetry_operation = -x,y,-z distance_ideal = 2.2 sigma = 0.01 } } The operator can be obtained using
iotbx.show_distances your.pdb > all_distances
Search for keyword "sym" or from Coot clicking on the symm option. Coot print out the operator and the translation term separately. Both has to be merged in the final operator used in phenix!
Christian _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- David Shin, Ph.D Lawrence Berkeley National Labs 1 Cyclotron Road MS 83-R0101 Berkeley, CA 94720 USA
_______________________________________________ phenixbb mailing list [email protected] http://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 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov
participants (3)
-
Christian Roth -
David Shin -
Nigel Moriarty