phenix.refine: including modifications
Hi all, I'm starting to use phenix.refine and have some questions about defining modifications during refinement: I want to refine a structure that includes several alpha-D-mannose residues. I see that mon_lib_list.cif contains, under the "LIST OF RECOGNIZED MODIFIED MONOMERS," the following line: MAN-a-D MAN-b-D SUG-a-D MAN alpha_D_mannose D-pyranose Question: Where/how do I invoke this modification? I.e., how do I tell the refinement program that a particular sugar is an alpha, and not a beta, mannose? Clearly I can't label the residue MAN-a-D in the PDB file, as this would step on the chain identifier. I'm guessing that I label each sugar MAN in the PDB file, and then insert some instructions about applying the modification in the CIF file that I supply to the refinement program. However, I'm not able to find an example of the appropriate syntax. Thanks, Pat Loll ------------------------------------------------------------------------ --------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 [email protected]
Hi Patrick, Let me give my best shot, I don't have my files with me. There might be some mistakes. You can give phenix.refine the .cif file on command line for MAN-a-D.cif, which you can get from ccp4 sketcher (and I think under phenix, somewhere close to where you found mon_lib_list.cif). Then you should describe the linkage as an alpha linkage by data_link = ALPHA1-4 if you have 1-4 linkage, by something like this. In the mon_lib_list.cif, I believe they have all recognized linkage types somewhere down the file, where you can see the proper description for ALPHA1-4, ALPHA1-6, BETA1-4, and other common sugar linkages. refinement.pdb_interpretation.apply_cif_link { data_link = ALPHA1-4 residue_selection_1 = chain X and resname MAN and resid 905 residue_selection_2 = chain X and resname MAN and resid 906 } I also delete hydrogens and the removed O1 in coot before I do refinement in phenix, but I am not sure if this is necessary (Phenix supposedly knows the deletion, it is in the description of the bond). Good luck, Engin Patrick Loll wrote:
Hi all,
I'm starting to use phenix.refine and have some questions about defining modifications during refinement:
I want to refine a structure that includes several alpha-D-mannose residues.
I see that mon_lib_list.cif contains, under the "LIST OF RECOGNIZED MODIFIED MONOMERS," the following line:
MAN-a-D MAN-b-D SUG-a-D MAN alpha_D_mannose D-pyranose
Question:
Where/how do I invoke this modification? I.e., how do I tell the refinement program that a particular sugar is an alpha, and not a beta, mannose?
Clearly I can't label the residue MAN-a-D in the PDB file, as this would step on the chain identifier.
I'm guessing that I label each sugar MAN in the PDB file, and then insert some instructions about applying the modification in the CIF file that I supply to the refinement program. However, I'm not able to find an example of the appropriate syntax.
Thanks,
Pat Loll
---------------------------------------------------------------------------------------
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA 19102-1192 USA
(215) 762-7706
[email protected] mailto:[email protected]
------------------------------------------------------------------------
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
OK, so I think you are implying that if I feed phenix.refine the MAN- a-D.cif, it will assume that any MAN residue it encounters in the PDB file is alpha. Is that right? Does this mean that if you have examples of both alpha and beta mannose residues in a structure, you would need to give one of them a different residue name? Thanks, Pat On 16 Oct 2008, at 4:52 PM, Engin Ozkan wrote:
Hi Patrick,
Let me give my best shot, I don't have my files with me. There might be some mistakes.
You can give phenix.refine the .cif file on command line for MAN-a-D.cif, which you can get from ccp4 sketcher (and I think under phenix, somewhere close to where you found mon_lib_list.cif). Then you should describe the linkage as an alpha linkage by data_link = ALPHA1-4 if you have 1-4 linkage, by something like this. In the mon_lib_list.cif, I believe they have all recognized linkage types somewhere down the file, where you can see the proper description for ALPHA1-4, ALPHA1-6, BETA1-4, and other common sugar linkages.
refinement.pdb_interpretation.apply_cif_link { data_link = ALPHA1-4 residue_selection_1 = chain X and resname MAN and resid 905 residue_selection_2 = chain X and resname MAN and resid 906 }
I also delete hydrogens and the removed O1 in coot before I do refinement in phenix, but I am not sure if this is necessary (Phenix supposedly knows the deletion, it is in the description of the bond).
Good luck,
Engin
Patrick Loll wrote:
Hi all,
I'm starting to use phenix.refine and have some questions about defining modifications during refinement:
I want to refine a structure that includes several alpha-D-mannose residues.
I see that mon_lib_list.cif contains, under the "LIST OF RECOGNIZED MODIFIED MONOMERS," the following line:
MAN-a-D MAN-b-D SUG-a-D MAN alpha_D_mannose D- pyranose
Question:
Where/how do I invoke this modification? I.e., how do I tell the refinement program that a particular sugar is an alpha, and not a beta, mannose?
Clearly I can't label the residue MAN-a-D in the PDB file, as this would step on the chain identifier.
I'm guessing that I label each sugar MAN in the PDB file, and then insert some instructions about applying the modification in the CIF file that I supply to the refinement program. However, I'm not able to find an example of the appropriate syntax.
Thanks,
Pat Loll
--------------------------------------------------------------------- ------------------
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA 19102-1192 USA
(215) 762-7706
[email protected] mailto:[email protected]
--------------------------------------------------------------------- ---
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------------------------------------------------------------------------ --------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 [email protected]
I don't have access to phenix, ccp4, or any of my files right now (our systems are being upgraded), but I'll make some guesses that may help you, I might be off the mark. I think the data_link determines the linkage type, so you should have ALPHA1-4 and BETA1-4 for different mannoses in your parameter file. You can also call alpha and beta mannoses different names, I think MAN is usually alpha mannose, and BMA is beta, and give phenix different cif files to phenix. I suggest you look into the cif descriptions, runs a few phenix runs, and convince yourself that everything checks out chemically. Engin Patrick Loll wrote:
OK, so I think you are implying that if I feed phenix.refine the MAN-a-D.cif, it will assume that any MAN residue it encounters in the PDB file is alpha. Is that right?
Does this mean that if you have examples of both alpha and beta mannose residues in a structure, you would need to give one of them a different residue name?
Thanks,
Pat
On 16 Oct 2008, at 4:52 PM, Engin Ozkan wrote:
Hi Patrick,
Let me give my best shot, I don't have my files with me. There might be some mistakes.
You can give phenix.refine the .cif file on command line for MAN-a-D.cif, which you can get from ccp4 sketcher (and I think under phenix, somewhere close to where you found mon_lib_list.cif). Then you should describe the linkage as an alpha linkage by data_link = ALPHA1-4 if you have 1-4 linkage, by something like this. In the mon_lib_list.cif, I believe they have all recognized linkage types somewhere down the file, where you can see the proper description for ALPHA1-4, ALPHA1-6, BETA1-4, and other common sugar linkages.
refinement.pdb_interpretation.apply_cif_link { data_link = ALPHA1-4 residue_selection_1 = chain X and resname MAN and resid 905 residue_selection_2 = chain X and resname MAN and resid 906 }
I also delete hydrogens and the removed O1 in coot before I do refinement in phenix, but I am not sure if this is necessary (Phenix supposedly knows the deletion, it is in the description of the bond).
Good luck,
Engin
Patrick Loll wrote:
Hi all,
I'm starting to use phenix.refine and have some questions about defining modifications during refinement:
I want to refine a structure that includes several alpha-D-mannose residues.
I see that mon_lib_list.cif contains, under the "LIST OF RECOGNIZED MODIFIED MONOMERS," the following line:
MAN-a-D MAN-b-D SUG-a-D MAN alpha_D_mannose D-pyranose
Question:
Where/how do I invoke this modification? I.e., how do I tell the refinement program that a particular sugar is an alpha, and not a beta, mannose?
Clearly I can't label the residue MAN-a-D in the PDB file, as this would step on the chain identifier.
I'm guessing that I label each sugar MAN in the PDB file, and then insert some instructions about applying the modification in the CIF file that I supply to the refinement program. However, I'm not able to find an example of the appropriate syntax.
Thanks,
Pat Loll
---------------------------------------------------------------------------------------
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA 19102-1192 USA
(215) 762-7706
[email protected] mailto:[email protected]
------------------------------------------------------------------------
_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
---------------------------------------------------------------------------------------
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA 19102-1192 USA
(215) 762-7706
[email protected] mailto:[email protected]
------------------------------------------------------------------------
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi All, the file ending with ".geo" has a complete footprint of all the geometry restraints used in phenix.refine run. For example, if you want to check that atom A is bonded to atom B with given bond length, bond angle, corresponding sigmas, and so on, just find the corresponding record in ".geo" file. If you don't see it there, then it means this particular bond (angle, ...) was not restrained. Pavel. On 10/16/2008 3:16 PM, Engin Ozkan wrote:
I don't have access to phenix, ccp4, or any of my files right now (our systems are being upgraded), but I'll make some guesses that may help you, I might be off the mark. I think the data_link determines the linkage type, so you should have ALPHA1-4 and BETA1-4 for different mannoses in your parameter file. You can also call alpha and beta mannoses different names, I think MAN is usually alpha mannose, and BMA is beta, and give phenix different cif files to phenix.
I suggest you look into the cif descriptions, runs a few phenix runs, and convince yourself that everything checks out chemically.
Engin
Patrick Loll wrote:
OK, so I think you are implying that if I feed phenix.refine the MAN-a-D.cif, it will assume that any MAN residue it encounters in the PDB file is alpha. Is that right?
Does this mean that if you have examples of both alpha and beta mannose residues in a structure, you would need to give one of them a different residue name?
Thanks,
Pat
On 16 Oct 2008, at 4:52 PM, Engin Ozkan wrote:
Hi Patrick,
Let me give my best shot, I don't have my files with me. There might be some mistakes.
You can give phenix.refine the .cif file on command line for MAN-a-D.cif, which you can get from ccp4 sketcher (and I think under phenix, somewhere close to where you found mon_lib_list.cif). Then you should describe the linkage as an alpha linkage by data_link = ALPHA1-4 if you have 1-4 linkage, by something like this. In the mon_lib_list.cif, I believe they have all recognized linkage types somewhere down the file, where you can see the proper description for ALPHA1-4, ALPHA1-6, BETA1-4, and other common sugar linkages.
refinement.pdb_interpretation.apply_cif_link { data_link = ALPHA1-4 residue_selection_1 = chain X and resname MAN and resid 905 residue_selection_2 = chain X and resname MAN and resid 906 }
I also delete hydrogens and the removed O1 in coot before I do refinement in phenix, but I am not sure if this is necessary (Phenix supposedly knows the deletion, it is in the description of the bond).
Good luck,
Engin
Patrick Loll wrote:
Hi all,
I'm starting to use phenix.refine and have some questions about defining modifications during refinement:
I want to refine a structure that includes several alpha-D-mannose residues.
I see that mon_lib_list.cif contains, under the "LIST OF RECOGNIZED MODIFIED MONOMERS," the following line:
MAN-a-D MAN-b-D SUG-a-D MAN alpha_D_mannose D-pyranose
Question:
Where/how do I invoke this modification? I.e., how do I tell the refinement program that a particular sugar is an alpha, and not a beta, mannose?
Clearly I can't label the residue MAN-a-D in the PDB file, as this would step on the chain identifier.
I'm guessing that I label each sugar MAN in the PDB file, and then insert some instructions about applying the modification in the CIF file that I supply to the refinement program. However, I'm not able to find an example of the appropriate syntax.
Thanks,
Pat Loll
---------------------------------------------------------------------------------------
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA 19102-1192 USA
(215) 762-7706
[email protected] mailto:[email protected]
------------------------------------------------------------------------
_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
---------------------------------------------------------------------------------------
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA 19102-1192 USA
(215) 762-7706
[email protected] mailto:[email protected]
------------------------------------------------------------------------
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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On Thu, 16 Oct 2008, Patrick Loll wrote:
Where/how do I invoke this modification? I.e., how do I tell the refinement program that a particular sugar is an alpha, and not a beta, mannose?
take a quick look at : http://www.phenix-online.org/pipermail/phenixbb/2008-June/001080.html not sure about alpha/beta. HTH -bryan
participants (4)
-
Bryan W. Lepore -
Engin Ozkan -
Patrick Loll -
Pavel Afonine