Tracing and refining b-strands at 3.3A resolution
Hi Phenix community, I'm tracing a 3.3A averaged electron density map of a large macromolecular complex (~18,500 residues in the asymmetric unit). The map has great continuity and appears quite 'tubular'. While it is easy to interpret in a-helical regions, b-strands are more challenging, as I can't see the 'bump' corresponding to the carbonyl. If I built b-strands into the tubular density, refinement usually 'undoes' them and turns them into pseudo-loops/turns. On the positive side, a related molecule (~70% identical to mine) was solved to 1.9A resolution. So my question is, is there a way in Phenix to use a 'reference model' during refinement to force a given stretch of polypeptide chain to 'stay' b-stranded during refinement? Thanks in advance for the feedback, Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: [email protected] ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)
Hi Gino,
So my question is, is there a way in Phenix to use a 'reference model' during refinement to force a given stretch of polypeptide chain to 'stay' b-stranded during refinement?
Nope. But you could use the custom bond definitions to restrain hydrogen bonds. The syntax is explained in the phenix.refine documentation; an example is below. The main trouble is that we don't have an automatic tool to generate the bond restraints for you. Maybe others have suggestions how to use external programs? Ralf refinement.geometry_restraints.edits { bond { action = *add delete change atom_selection_1 = "chain G and resname ASP and resid 20 and name N" atom_selection_2 = "chain G and resname GLY and resid 33 and name O" symmetry_operation = None distance_ideal = 2.8 sigma = 0.1 slack = 0.3 } bond { action = *add delete change atom_selection_1 = "chain G and resname GLY and resid 33 and name N" atom_selection_2 = "chain G and resname SER and resid 21 and name O" symmetry_operation = None distance_ideal = 2.8 sigma = 0.1 slack = 0.4 } }
Ralf et al. My question with this approach is that is there any potential to have a negative effect on refining the structure, given that one is introducing a number of bonds with relatively high average deviations from the mean ? The rest of the bonded (covalent) geometry has an rms in the range 0.004 - 0.015 (-ish) but this is one to two orders of magnitude tighter than a hydrogen bond. Is the target function sophisticated enough to handle this or is there a problem with treating hbonds and covalent bonds as peers ? Phil Jeffrey Princeton Ralf W. Grosse-Kunstleve wrote:
Hi Gino,
So my question is, is there a way in Phenix to use a 'reference model' during refinement to force a given stretch of polypeptide chain to 'stay' b-stranded during refinement?
Nope. But you could use the custom bond definitions to restrain hydrogen bonds. The syntax is explained in the phenix.refine documentation; an example is below. The main trouble is that we don't have an automatic tool to generate the bond restraints for you. Maybe others have suggestions how to use external programs?
Ralf
refinement.geometry_restraints.edits { bond { action = *add delete change atom_selection_1 = "chain G and resname ASP and resid 20 and name N" atom_selection_2 = "chain G and resname GLY and resid 33 and name O" symmetry_operation = None distance_ideal = 2.8 sigma = 0.1 slack = 0.3 } bond { action = *add delete change atom_selection_1 = "chain G and resname GLY and resid 33 and name N" atom_selection_2 = "chain G and resname SER and resid 21 and name O" symmetry_operation = None distance_ideal = 2.8 sigma = 0.1 slack = 0.4 } } _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi Phil,
My question with this approach is that is there any potential to have a negative effect on refining the structure, given that one is introducing a number of bonds with relatively high average deviations from the mean ? The rest of the bonded (covalent) geometry has an rms in the range 0.004 - 0.015 (-ish) but this is one to two orders of magnitude tighter than a hydrogen bond. Is the target function sophisticated enough to handle this or is there a problem with treating hbonds and covalent bonds as peers ?
I think the L-BFGS algorithm we're using is smart enough to handle this situation, but I haven't investigated this question systematically. Note that e.g. most dihedral restraints are also much weaker than the bond restraints. Ralf
Gino, My lab recently refined a 3.4 A structure and dealt with similar problems. We found that using secondary structure restraints was the only effective way to maintain reasonable geometry during refinement. It is kind of a daunting task to input all of the definitions by hand, so we wrote a couple python scripts that are integrated with PyMol to write the appropriate restraint definition files. All you have to do is click on the atoms that you want restrained. You are welcome to the scripts if you like. Feel free to contact me if you are interested. Sean Johnson Gino Cingolani wrote:
Hi Phenix community,
I'm tracing a 3.3A averaged electron density map of a large macromolecular complex (~18,500 residues in the asymmetric unit). The map has great continuity and appears quite 'tubular'. While it is easy to interpret in a-helical regions, b-strands are more challenging, as I can't see the 'bump' corresponding to the carbonyl. If I built b-strands into the tubular density, refinement usually 'undoes' them and turns them into pseudo-loops/turns. On the positive side, a related molecule (~70% identical to mine) was solved to 1.9A resolution. So my question is, is there a way in Phenix to use a 'reference model' during refinement to force a given stretch of polypeptide chain to 'stay' b-stranded during refinement?
Thanks in advance for the feedback,
Gino
****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: [email protected] ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Sean Johnson, PhD R. Gaurth Hansen Assistant Professor Utah State University Department of Chemistry and Biochemistry 0300 Old Main Hill Logan, UT 84322-0300 (435) 797-2089 (435) 797-3390 (fax) [email protected]
Dear Sean, That sounds wonderful. Can I have your scripts too? many thanks waiching. Sean Johnson wrote:
Gino,
My lab recently refined a 3.4 A structure and dealt with similar problems. We found that using secondary structure restraints was the only effective way to maintain reasonable geometry during refinement. It is kind of a daunting task to input all of the definitions by hand, so we wrote a couple python scripts that are integrated with PyMol to write the appropriate restraint definition files. All you have to do is click on the atoms that you want restrained. You are welcome to the scripts if you like. Feel free to contact me if you are interested.
Sean Johnson
Gino Cingolani wrote:
Hi Phenix community,
I'm tracing a 3.3A averaged electron density map of a large macromolecular complex (~18,500 residues in the asymmetric unit). The map has great continuity and appears quite 'tubular'. While it is easy to interpret in a-helical regions, b-strands are more challenging, as I can't see the 'bump' corresponding to the carbonyl. If I built b-strands into the tubular density, refinement usually 'undoes' them and turns them into pseudo-loops/turns. On the positive side, a related molecule (~70% identical to mine) was solved to 1.9A resolution. So my question is, is there a way in Phenix to use a 'reference model' during refinement to force a given stretch of polypeptide chain to 'stay' b-stranded during refinement?
Thanks in advance for the feedback,
Gino
****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: [email protected] ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Sean, I really appreciate your offer to try out your scripts. If the offer is still good, I would love a copy. Thanks and Best Regards, -Andy Torelli =========================================== Andrew T. Torelli Ph.D. Postdoctoral Associate Department of Chemistry & Chemical Biology Baker Laboratory, Cornell University Ithaca, NY 14853 =========================================== On 8/27/2009 5:53 PM, Sean Johnson wrote:
Gino,
My lab recently refined a 3.4 A structure and dealt with similar problems. We found that using secondary structure restraints was the only effective way to maintain reasonable geometry during refinement. It is kind of a daunting task to input all of the definitions by hand, so we wrote a couple python scripts that are integrated with PyMol to write the appropriate restraint definition files. All you have to do is click on the atoms that you want restrained. You are welcome to the scripts if you like. Feel free to contact me if you are interested.
Sean Johnson
Gino Cingolani wrote:
Hi Phenix community,
I'm tracing a 3.3A averaged electron density map of a large macromolecular complex (~18,500 residues in the asymmetric unit). The map has great continuity and appears quite 'tubular'. While it is easy to interpret in a-helical regions, b-strands are more challenging, as I can't see the 'bump' corresponding to the carbonyl. If I built b-strands into the tubular density, refinement usually 'undoes' them and turns them into pseudo-loops/turns. On the positive side, a related molecule (~70% identical to mine) was solved to 1.9A resolution. So my question is, is there a way in Phenix to use a 'reference model' during refinement to force a given stretch of polypeptide chain to 'stay' b-stranded during refinement?
Thanks in advance for the feedback,
Gino
****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: [email protected] ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
To the phenix bb, I apologize for the global e-mail, I meant to reply directly to Sean Johnson. Best Regards, -Andy Torelli On 8/28/2009 10:52 AM, Andy Torelli wrote:
Sean,
I really appreciate your offer to try out your scripts. If the offer is still good, I would love a copy.
Thanks and Best Regards, -Andy Torelli
=========================================== Andrew T. Torelli Ph.D. Postdoctoral Associate Department of Chemistry & Chemical Biology Baker Laboratory, Cornell University Ithaca, NY 14853 ===========================================
participants (6)
-
Andy Torelli -
Gino Cingolani -
Phil Jeffrey -
Ralf W. Grosse-Kunstleve -
Sean Johnson -
Wai-Ching Hon