Glycan Links/Restraints
Sorry to bring up an old topic again but I can't find any documentation of glycan refinement on the Phenix website and previous threads don't seem to answer my question. I am refining a structure with N-linked glycans. I have inserted several "apply_cif_link" records to my .eff file to define the glycan topologies (see below) and fed in a cif file for BMA. After fiddling for quite some time now, I have managed to get around all the error messages people have described previously to disappear. Yet, 1) none of my linkages appear to be enforced and 2) even the restraints on the individual sugars appear to be unenforced (or at least, insufficiently so). For example, some rings are rendered almost flat, or flipped into boat or otherwise distorted conformations, and glycosidic bonds stretch to >2 A. No obvious signs of trouble in the log file, running the latest version (1.7, also tried 1.6.4), but my glycans look terrible (despite some of the best density I have ever seen! :-) ) Any suggestions would be appreciated! Thanks, Damian Ekiert
From my .eff file:
apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain X and resname NAG and resid 401 residue_selection_2 = chain A and resname ASN and resid 91 } apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain Y and resname NAG and resid 401 residue_selection_2 = chain C and resname ASN and resid 91 } apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain Z and resname NAG and resid 401 residue_selection_2 = chain E and resname ASN and resid 91 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain X and resname NAG and resid 402 residue_selection_2 = chain X and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Y and resname NAG and resid 402 residue_selection_2 = chain Y and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Z and resname NAG and resid 402 residue_selection_2 = chain Z and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Y and resname BMA and resid 403 residue_selection_2 = chain Y and resname NAG and resid 402 } apply_cif_link { data_link = ALPHA1-3 residue_selection_1 = chain Y and resname MAN and resid 404 residue_selection_2 = chain Y and resname BMA and resid 403 }
Dear Damien, Let me make a guess: You have the BETA1-4 linkages in the wrong order. If you look in the mon_lib_list.cif file, you can find the line where it says: BETA1-4 1 O4 2 C1 single 1.439 0.020 which tells me that the residue to be defined (residue_selection_1) ought to be the atom atom connecting with the O4 atom (the inner glycan) and the second residue is the one with the C1 atom (the outer glycan). So try switching residue_selection_1 and _2 for your BETA1-4 linkages. I know you are probably thinking BETA1-4 should go 1 to 4, but that is not how it is defined in the monomer library. By the way, your NAG-ASN linkages do look correct, and you have the correct anomers for beta-mannose (BMA) and alpha-mannose (MAN), which is where most people seem to get stuck. One stylistic question I have for you is, why are you naming your protein and glycans with different chain IDs; aren't they actually covalently linked? There apparently is no right way for numbering glycan residues, and everybody seems to be do a different thing... Good luck, Engin On 2/28/11 6:39 PM, Damian Ekiert wrote:
Sorry to bring up an old topic again but I can't find any documentation of glycan refinement on the Phenix website and previous threads don't seem to answer my question.
I am refining a structure with N-linked glycans. I have inserted several "apply_cif_link" records to my .eff file to define the glycan topologies (see below) and fed in a cif file for BMA. After fiddling for quite some time now, I have managed to get around all the error messages people have described previously to disappear. Yet, 1) none of my linkages appear to be enforced and 2) even the restraints on the individual sugars appear to be unenforced (or at least, insufficiently so). For example, some rings are rendered almost flat, or flipped into boat or otherwise distorted conformations, and glycosidic bonds stretch to>2 A.
No obvious signs of trouble in the log file, running the latest version (1.7, also tried 1.6.4), but my glycans look terrible (despite some of the best density I have ever seen! :-) )
Any suggestions would be appreciated!
Thanks,
Damian Ekiert
From my .eff file:
apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain X and resname NAG and resid 401 residue_selection_2 = chain A and resname ASN and resid 91 } apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain Y and resname NAG and resid 401 residue_selection_2 = chain C and resname ASN and resid 91 } apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain Z and resname NAG and resid 401 residue_selection_2 = chain E and resname ASN and resid 91 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain X and resname NAG and resid 402 residue_selection_2 = chain X and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Y and resname NAG and resid 402 residue_selection_2 = chain Y and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Z and resname NAG and resid 402 residue_selection_2 = chain Z and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Y and resname BMA and resid 403 residue_selection_2 = chain Y and resname NAG and resid 402 } apply_cif_link { data_link = ALPHA1-3 residue_selection_1 = chain Y and resname MAN and resid 404 residue_selection_2 = chain Y and resname BMA and resid 403 } _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
Also, I just remembered that Phenix/monomer library may still not have BMA and MAN right. You may have to provide MAN and/or BMA cif files with the correct stereochemistries. Monomer library does not necessarily follow the standards of the PDB chemical component library (but obviously, PDB enforces them). Finally, you can always check the .geo file that phenix.refine produces, and you will find all the applied restraints. That should definitively tell you your problem. Engin On 2/28/11 10:36 PM, Engin Özkan wrote:
Dear Damien,
Let me make a guess: You have the BETA1-4 linkages in the wrong order. If you look in the mon_lib_list.cif file, you can find the line where it says: BETA1-4 1 O4 2 C1 single 1.439 0.020 which tells me that the residue to be defined (residue_selection_1) ought to be the atom atom connecting with the O4 atom (the inner glycan) and the second residue is the one with the C1 atom (the outer glycan). So try switching residue_selection_1 and _2 for your BETA1-4 linkages. I know you are probably thinking BETA1-4 should go 1 to 4, but that is not how it is defined in the monomer library. By the way, your NAG-ASN linkages do look correct, and you have the correct anomers for beta-mannose (BMA) and alpha-mannose (MAN), which is where most people seem to get stuck.
One stylistic question I have for you is, why are you naming your protein and glycans with different chain IDs; aren't they actually covalently linked? There apparently is no right way for numbering glycan residues, and everybody seems to be do a different thing...
Good luck, Engin
On 2/28/11 6:39 PM, Damian Ekiert wrote:
Sorry to bring up an old topic again but I can't find any documentation of glycan refinement on the Phenix website and previous threads don't seem to answer my question.
I am refining a structure with N-linked glycans. I have inserted several "apply_cif_link" records to my .eff file to define the glycan topologies (see below) and fed in a cif file for BMA. After fiddling for quite some time now, I have managed to get around all the error messages people have described previously to disappear. Yet, 1) none of my linkages appear to be enforced and 2) even the restraints on the individual sugars appear to be unenforced (or at least, insufficiently so). For example, some rings are rendered almost flat, or flipped into boat or otherwise distorted conformations, and glycosidic bonds stretch to>2 A.
No obvious signs of trouble in the log file, running the latest version (1.7, also tried 1.6.4), but my glycans look terrible (despite some of the best density I have ever seen! :-) )
Any suggestions would be appreciated!
Thanks,
Damian Ekiert
From my .eff file:
apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain X and resname NAG and resid 401 residue_selection_2 = chain A and resname ASN and resid 91 } apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain Y and resname NAG and resid 401 residue_selection_2 = chain C and resname ASN and resid 91 } apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain Z and resname NAG and resid 401 residue_selection_2 = chain E and resname ASN and resid 91 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain X and resname NAG and resid 402 residue_selection_2 = chain X and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Y and resname NAG and resid 402 residue_selection_2 = chain Y and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Z and resname NAG and resid 402 residue_selection_2 = chain Z and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Y and resname BMA and resid 403 residue_selection_2 = chain Y and resname NAG and resid 402 } apply_cif_link { data_link = ALPHA1-3 residue_selection_1 = chain Y and resname MAN and resid 404 residue_selection_2 = chain Y and resname BMA and resid 403 } _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
Engin, Thanks for your help. Initially, I tried the order you are suggesting for the links ("inner first, outer second"), but Phenix quits with the following output: Sorry: Traceback (most recent call last): File "/jcsg/software/phenix/phenix-1.7/phenix-1.7-650/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 972, in apply_mod mod_mon = self.monomer.apply_mod(mod_mod_id) File "/jcsg/software/phenix/phenix-1.7/phenix-1.7-650/cctbx_project/mmtbx/monomer_library/cif_types.py", line 387, in apply_mod result.delete_atom_in_place(mod_atom.atom_id) File "/jcsg/software/phenix/phenix-1.7/phenix-1.7-650/cctbx_project/mmtbx/monomer_library/cif_types.py", line 304, in delete_atom_in_place raise RuntimeError("delete_atom_in_place: unknown atom_id: %s" % atom_id) RuntimeError: delete_atom_in_place: unknown atom_id: O1 apply_mod failure: pdbres="ASN A 91 " comp id: ASN mod id: DEL-O1 This sounded to me like it was trying to delete O1 from my Asn instead of the GlcNAc, which I figured meant that I should reverse the order (i.e., outer residue first, inner residue second). When I did this, phenix completed refinement with no obvious problems in the log file. I initially took this to mean that all was well, until I looked at my coordinates. As for glycans in the same chain or different chains, I agree with you completely. I actually split them into separate chains to try to get around another apparent problem that was cropping up near the top of my log file: Chain: "C" Number of atoms: 5065 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 5018 Unusual residues: {'MAN%DEL-HO3': 1, 'MAN%DEL-HO4%DEL-O1': 1, 'NAG%DEL-O1': 1, 'NAG%DEL-HO4%DEL-O1': 1} Classifications: {'undetermined': 4, 'peptide': 323} Modifications used: {'DEL-HD22': 1, 'DEL-HO3': 1, 'DEL-O1': 3, 'DEL-HO4': 2} Link IDs: {'PTRANS': 18, None: 4, 'TRANS': 304} Not linked: pdbres="NAG C 401 " pdbres="NAG C 402 " Not linked: pdbres="NAG C 402 " pdbres="BMA C 403 " Not linked: pdbres="BMA C 403 " pdbres="MAN C 404 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 These "Not linked" sections went away when I moved the glycans to separate chains, so I figured that Phenix might only allow one polymer type in a given chain (not sure if this is true or not). As for the monomer cif files, I don't see an major differences between the cifs from Phenix and those from CCP4 that I have used previously for refinement in Refmac, but I will look into this further. Best, Damian On Feb 28, 2011, at 11:44 PM, Engin Özkan wrote:
Also, I just remembered that Phenix/monomer library may still not have BMA and MAN right. You may have to provide MAN and/or BMA cif files with the correct stereochemistries. Monomer library does not necessarily follow the standards of the PDB chemical component library (but obviously, PDB enforces them).
Finally, you can always check the .geo file that phenix.refine produces, and you will find all the applied restraints. That should definitively tell you your problem.
Engin
On 2/28/11 10:36 PM, Engin Özkan wrote:
Dear Damien,
Let me make a guess: You have the BETA1-4 linkages in the wrong order. If you look in the mon_lib_list.cif file, you can find the line where it says: BETA1-4 1 O4 2 C1 single 1.439 0.020 which tells me that the residue to be defined (residue_selection_1) ought to be the atom atom connecting with the O4 atom (the inner glycan) and the second residue is the one with the C1 atom (the outer glycan). So try switching residue_selection_1 and _2 for your BETA1-4 linkages. I know you are probably thinking BETA1-4 should go 1 to 4, but that is not how it is defined in the monomer library. By the way, your NAG-ASN linkages do look correct, and you have the correct anomers for beta-mannose (BMA) and alpha-mannose (MAN), which is where most people seem to get stuck.
One stylistic question I have for you is, why are you naming your protein and glycans with different chain IDs; aren't they actually covalently linked? There apparently is no right way for numbering glycan residues, and everybody seems to be do a different thing...
Good luck, Engin
On 2/28/11 6:39 PM, Damian Ekiert wrote:
Sorry to bring up an old topic again but I can't find any documentation of glycan refinement on the Phenix website and previous threads don't seem to answer my question.
I am refining a structure with N-linked glycans. I have inserted several "apply_cif_link" records to my .eff file to define the glycan topologies (see below) and fed in a cif file for BMA. After fiddling for quite some time now, I have managed to get around all the error messages people have described previously to disappear. Yet, 1) none of my linkages appear to be enforced and 2) even the restraints on the individual sugars appear to be unenforced (or at least, insufficiently so). For example, some rings are rendered almost flat, or flipped into boat or otherwise distorted conformations, and glycosidic bonds stretch to>2 A.
No obvious signs of trouble in the log file, running the latest version (1.7, also tried 1.6.4), but my glycans look terrible (despite some of the best density I have ever seen! :-) )
Any suggestions would be appreciated!
Thanks,
Damian Ekiert
From my .eff file:
apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain X and resname NAG and resid 401 residue_selection_2 = chain A and resname ASN and resid 91 } apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain Y and resname NAG and resid 401 residue_selection_2 = chain C and resname ASN and resid 91 } apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain Z and resname NAG and resid 401 residue_selection_2 = chain E and resname ASN and resid 91 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain X and resname NAG and resid 402 residue_selection_2 = chain X and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Y and resname NAG and resid 402 residue_selection_2 = chain Y and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Z and resname NAG and resid 402 residue_selection_2 = chain Z and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Y and resname BMA and resid 403 residue_selection_2 = chain Y and resname NAG and resid 402 } apply_cif_link { data_link = ALPHA1-3 residue_selection_1 = chain Y and resname MAN and resid 404 residue_selection_2 = chain Y and resname BMA and resid 403 } _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Dear Damian, On 3/1/11 2:09 PM, Damian Ekiert wrote:
Engin,
Thanks for your help.
Initially, I tried the order you are suggesting for the links ("inner first, outer second"), but Phenix quits with the following output:
Sorry: Traceback (most recent call last): File "/jcsg/software/phenix/phenix-1.7/phenix-1.7-650/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 972, in apply_mod mod_mon = self.monomer.apply_mod(mod_mod_id) File "/jcsg/software/phenix/phenix-1.7/phenix-1.7-650/cctbx_project/mmtbx/monomer_library/cif_types.py", line 387, in apply_mod result.delete_atom_in_place(mod_atom.atom_id) File "/jcsg/software/phenix/phenix-1.7/phenix-1.7-650/cctbx_project/mmtbx/monomer_library/cif_types.py", line 304, in delete_atom_in_place raise RuntimeError("delete_atom_in_place: unknown atom_id: %s" % atom_id) RuntimeError: delete_atom_in_place: unknown atom_id: O1 apply_mod failure: pdbres="ASN A 91 " comp id: ASN mod id: DEL-O1
This sounded to me like it was trying to delete O1 from my Asn instead of the GlcNAc, which I figured meant that I should reverse the order (i.e., outer residue first, inner residue second). When I did this, phenix completed refinement with no obvious problems in the log file. I initially took this to mean that all was well, until I looked at my coordinates.
As for glycans in the same chain or different chains, I agree with you completely. I actually split them into separate chains to try to get around another apparent problem that was cropping up near the top of my log file:
Chain: "C" Number of atoms: 5065 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 5018 Unusual residues: {'MAN%DEL-HO3': 1, 'MAN%DEL-HO4%DEL-O1': 1, 'NAG%DEL-O1': 1, 'NAG%DEL-HO4%DEL-O1': 1} Classifications: {'undetermined': 4, 'peptide': 323} Modifications used: {'DEL-HD22': 1, 'DEL-HO3': 1, 'DEL-O1': 3, 'DEL-HO4': 2} Link IDs: {'PTRANS': 18, None: 4, 'TRANS': 304} Not linked: pdbres="NAG C 401 " pdbres="NAG C 402 " Not linked: pdbres="NAG C 402 " pdbres="BMA C 403 " Not linked: pdbres="BMA C 403 " pdbres="MAN C 404 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1
These "Not linked" sections went away when I moved the glycans to separate chains, so I figured that Phenix might only allow one polymer type in a given chain (not sure if this is true or not). I never heard of that. And I have refined many structures with multiple
You misunderstood me. There is no logic as outer first, inner later. Every link description is what it is; you have to carefully read the monomer library description file. As I said in my previous email, your NAG-ASN linkages were right in your first email, only the BETA1-4s were wrong. polymer types in single chains (with versions 1.6.4 and before).
As for the monomer cif files, I don't see an major differences between the cifs from Phenix and those from CCP4 that I have used previously for refinement in Refmac, but I will look into this further. That is not surprising. The monomer libraries are common to both. I suggest that you check your refmac-refined model for beta-linked BMAs and alpha-linked MANs. As a reminder, beta-NAG and beta-MAN (BMA) have equitorial linkages at their C1, and alpha-MAN has axial. Best,
Damian
On Feb 28, 2011, at 11:44 PM, Engin Özkan wrote:
Also, I just remembered that Phenix/monomer library may still not have BMA and MAN right. You may have to provide MAN and/or BMA cif files with the correct stereochemistries. Monomer library does not necessarily follow the standards of the PDB chemical component library (but obviously, PDB enforces them).
Finally, you can always check the .geo file that phenix.refine produces, and you will find all the applied restraints. That should definitively tell you your problem.
Engin
On 2/28/11 10:36 PM, Engin Özkan wrote:
Dear Damien,
Let me make a guess: You have the BETA1-4 linkages in the wrong order. If you look in the mon_lib_list.cif file, you can find the line where it says: BETA1-4 1 O4 2 C1 single 1.439 0.020 which tells me that the residue to be defined (residue_selection_1) ought to be the atom atom connecting with the O4 atom (the inner glycan) and the second residue is the one with the C1 atom (the outer glycan). So try switching residue_selection_1 and _2 for your BETA1-4 linkages. I know you are probably thinking BETA1-4 should go 1 to 4, but that is not how it is defined in the monomer library. By the way, your NAG-ASN linkages do look correct, and you have the correct anomers for beta-mannose (BMA) and alpha-mannose (MAN), which is where most people seem to get stuck.
One stylistic question I have for you is, why are you naming your protein and glycans with different chain IDs; aren't they actually covalently linked? There apparently is no right way for numbering glycan residues, and everybody seems to be do a different thing...
Good luck, Engin
On 2/28/11 6:39 PM, Damian Ekiert wrote:
Sorry to bring up an old topic again but I can't find any documentation of glycan refinement on the Phenix website and previous threads don't seem to answer my question.
I am refining a structure with N-linked glycans. I have inserted several "apply_cif_link" records to my .eff file to define the glycan topologies (see below) and fed in a cif file for BMA. After fiddling for quite some time now, I have managed to get around all the error messages people have described previously to disappear. Yet, 1) none of my linkages appear to be enforced and 2) even the restraints on the individual sugars appear to be unenforced (or at least, insufficiently so). For example, some rings are rendered almost flat, or flipped into boat or otherwise distorted conformations, and glycosidic bonds stretch to>2 A.
No obvious signs of trouble in the log file, running the latest version (1.7, also tried 1.6.4), but my glycans look terrible (despite some of the best density I have ever seen! :-) )
Any suggestions would be appreciated!
Thanks,
Damian Ekiert
From my .eff file:
apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain X and resname NAG and resid 401 residue_selection_2 = chain A and resname ASN and resid 91 } apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain Y and resname NAG and resid 401 residue_selection_2 = chain C and resname ASN and resid 91 } apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain Z and resname NAG and resid 401 residue_selection_2 = chain E and resname ASN and resid 91 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain X and resname NAG and resid 402 residue_selection_2 = chain X and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Y and resname NAG and resid 402 residue_selection_2 = chain Y and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Z and resname NAG and resid 402 residue_selection_2 = chain Z and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Y and resname BMA and resid 403 residue_selection_2 = chain Y and resname NAG and resid 402 } apply_cif_link { data_link = ALPHA1-3 residue_selection_1 = chain Y and resname MAN and resid 404 residue_selection_2 = chain Y and resname BMA and resid 403 } _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Engin Özkan Post-doctoral Scholar Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
Engin I would like to see the restraints for MAN and BMA that are correct compared to the monomer lib. I'd be interested in making it available in PHENIX. Damian You can check if the ASN and NAG are connected using the alpha script elbow.refine_geo_display model_refine.geo NAG ASN Nigel -- 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
Nigel and Engin, The script shows the NAG-ANS linkage being enforced, thanks. Engin, thanks for pointing out the inversion of my BETA1-4 links, that fixed the problem. As Phenix struggled to enforce my backwards restraints, it was distorting everything. Now my glycans look great! Best, Damian On Mar 1, 2011, at 2:58 PM, Nigel Moriarty wrote:
Engin
I would like to see the restraints for MAN and BMA that are correct compared to the monomer lib. I'd be interested in making it available in PHENIX.
Damian
You can check if the ASN and NAG are connected using the alpha script
elbow.refine_geo_display model_refine.geo NAG ASN
Nigel
-- 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (3)
-
Damian Ekiert -
Engin Özkan -
Nigel Moriarty