phenix.refine change: support for residues on symmetry elements
The current development version of phenix.refine (dev-268 or later) supports residues located on symmetry elements, e.g. SO4 on a three-fold axis. phenix.refine now computes structure factors slightly differently compared to older versions. The new rules are: - Atoms with occupancy == 1 are subject to automatic handling of the symmetry. Example: An atom near a three-fold axis (distance to symmetry copy <= 0.5 A) is moved onto the axis and constrained in refinement to stay on the axis. The "special position factor" (1/3 is this case) is taken into account internally. The factor does not appear in the occupancy. - Atoms with occupancy != 1 are assumed to take the special position factor into account in the occupancy. Automatic handling of the symmetry is turned off. Example: A disordered SO4 molecule near a three-fold axis should have occupancies of 0.33 for all atoms. - If all atoms in a residue have occupancies != 1, all nonbonded symmetry interactions between the atoms in the residue are disabled. These three rules are meant - to bring phenix.refine in line with other programs and the PDB. - "to do the right thing" in most cases without manual intervention. Please let me know if you see problems with the new way phenix.refine uses occupancies to determine special position constraints and exclusions for nonbonded symmetry interactions. Does anyone need atoms with partial occupancies but constrained to stay on a symmetry axis during refinement? Ralf
Ralf ----- GREAT However I do not get what it is ==1 and !=1 Are they have meaning or it is encoding striking back? And to the last question: yes, it is good to keep coordinates constrained to stay on the symmetry element. It should be a default. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica D, co-editor e-mail: [email protected] Tel: ++972 3640 8723 Fax: ++972 3640 9407 Cellular: ++972 547 459 608 On Dec 27, 2009, at 20:24 , Ralf W. Grosse-Kunstleve wrote:
The current development version of phenix.refine (dev-268 or later) supports residues located on symmetry elements, e.g. SO4 on a three-fold axis. phenix.refine now computes structure factors slightly differently compared to older versions. The new rules are:
- Atoms with occupancy == 1 are subject to automatic handling of the symmetry. Example: An atom near a three-fold axis (distance to symmetry copy <= 0.5 A) is moved onto the axis and constrained in refinement to stay on the axis. The "special position factor" (1/3 is this case) is taken into account internally. The factor does not appear in the occupancy.
- Atoms with occupancy != 1 are assumed to take the special position factor into account in the occupancy. Automatic handling of the symmetry is turned off. Example: A disordered SO4 molecule near a three-fold axis should have occupancies of 0.33 for all atoms.
- If all atoms in a residue have occupancies != 1, all nonbonded symmetry interactions between the atoms in the residue are disabled.
These three rules are meant - to bring phenix.refine in line with other programs and the PDB. - "to do the right thing" in most cases without manual intervention.
Please let me know if you see problems with the new way phenix.refine uses occupancies to determine special position constraints and exclusions for nonbonded symmetry interactions.
Does anyone need atoms with partial occupancies but constrained to stay on a symmetry axis during refinement?
Ralf _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Felix,
However I do not get what it is ==1
That's short for "is equal to". -- Use in many programming languages to distinguish assignment and test for equality.
and !=1
"is not equal to"
or it is encoding striking back?
Yes, sorry, that's the world I live in ...
And to the last question: yes, it is good to keep coordinates constrained to stay on the symmetry element. It should be a default.
It was the default in the past. I could make it the default again as a special case for single-atom residues, but I found quite a few HOH in the PDB where the water was near the symmetry axis but clearly not on the symmetry axis. If I change phenix.refine back for single-atom residues it will again not be compatible with other programs and many entries in the PDB. Ideas: - Using atom selections to tell phenix.refine which atoms with partial occupancy to constrain to a symmetry axis, e.g. symmetry_constraints = chain S and resid 101 - Using negative occupancy as a flag to request symmetry constraints. The first alternative would mean work for the user and open the door to oversights, the second would confuse other programs (although they could easily be adjusted). Ralf
== : equal
!= : not equal
2009/12/27 Felix Frolow
Ralf ----- GREAT However I do not get what it is ==1 and !=1 Are they have meaning or it is encoding striking back? And to the last question: yes, it is good to keep coordinates constrained to stay on the symmetry element. It should be a default. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel
Acta Crystallographica D, co-editor
e-mail: [email protected] Tel: ++972 3640 8723 Fax: ++972 3640 9407 Cellular: ++972 547 459 608
On Dec 27, 2009, at 20:24 , Ralf W. Grosse-Kunstleve wrote:
The current development version of phenix.refine (dev-268 or later) supports residues located on symmetry elements, e.g. SO4 on a three-fold axis. phenix.refine now computes structure factors slightly differently compared to older versions. The new rules are:
- Atoms with occupancy == 1 are subject to automatic handling of the symmetry. Example: An atom near a three-fold axis (distance to symmetry copy <= 0.5 A) is moved onto the axis and constrained in refinement to stay on the axis. The "special position factor" (1/3 is this case) is taken into account internally. The factor does not appear in the occupancy.
- Atoms with occupancy != 1 are assumed to take the special position factor into account in the occupancy. Automatic handling of the symmetry is turned off. Example: A disordered SO4 molecule near a three-fold axis should have occupancies of 0.33 for all atoms.
- If all atoms in a residue have occupancies != 1, all nonbonded symmetry interactions between the atoms in the residue are disabled.
These three rules are meant - to bring phenix.refine in line with other programs and the PDB. - "to do the right thing" in most cases without manual intervention.
Please let me know if you see problems with the new way phenix.refine uses occupancies to determine special position constraints and exclusions for nonbonded symmetry interactions.
Does anyone need atoms with partial occupancies but constrained to stay on a symmetry axis during refinement?
Ralf _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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Hi,
when I submitted a pdb with some waters on a twofold sym. axis with
occupancies =1, the PDB wanted occupancies 0.5.
They do not want to take into account your "taken into account internally".
Maia
----- Original Message -----
From: "Ralf W. Grosse-Kunstleve"
The current development version of phenix.refine (dev-268 or later) supports residues located on symmetry elements, e.g. SO4 on a three-fold axis. phenix.refine now computes structure factors slightly differently compared to older versions. The new rules are:
- Atoms with occupancy == 1 are subject to automatic handling of the symmetry. Example: An atom near a three-fold axis (distance to symmetry copy <= 0.5 A) is moved onto the axis and constrained in refinement to stay on the axis. The "special position factor" (1/3 is this case) is taken into account internally. The factor does not appear in the occupancy.
- Atoms with occupancy != 1 are assumed to take the special position factor into account in the occupancy. Automatic handling of the symmetry is turned off. Example: A disordered SO4 molecule near a three-fold axis should have occupancies of 0.33 for all atoms.
- If all atoms in a residue have occupancies != 1, all nonbonded symmetry interactions between the atoms in the residue are disabled.
These three rules are meant - to bring phenix.refine in line with other programs and the PDB. - "to do the right thing" in most cases without manual intervention.
Please let me know if you see problems with the new way phenix.refine uses occupancies to determine special position constraints and exclusions for nonbonded symmetry interactions.
Does anyone need atoms with partial occupancies but constrained to stay on a symmetry axis during refinement?
Ralf _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Maia,
when I submitted a pdb with some waters on a twofold sym. axis with occupancies =1, the PDB wanted occupancies 0.5. They do not want to take into account your "taken into account internally".
Hopefully, time will heal it -:) More seriously (I wrote it somewhere for someone, even not once): The maximal multiplicity of a special position in proteins is 24 (or so, correct me if I'm wrong, please), and the precision of the occupancy factor field in PDB file is only two digits. Let’s imagine a relatively small structure at high resolution that contains a handful amount of heavy atoms all located at special positions with the multiplicity 24. Now, the occupancies of these heavy atoms in a PDB file all have to be set to 1./24 ~ 0.04 and not to 0.042. Depending on the number of electrons in a heavy atom, the number of heavy atoms, multiplicity of special position and overall structure size, one can easily imagine a situation when this kind of rounding error may become very significant. Therefore, I think, it is a bad idea to rely on the file format in this case, and is much better to do this trivial operation internally without any unnecessary loss of accuracy. Plus, it all happens seamlessly for the end-user, which is another step towards the automation. Pavel.
The pdb file is expected to contain the contents of the asymmetric unit. Suppose the end-user of the pdb file is a protein chemist who has just done a super-accurate atomic absorption analysis of her ultra-pure protein and determined the ratio of Cu to Fe is 0.4973. If the pdb file shows one Cu and one Fe, she probably won't realize the Cu is on a 2-fold so only half is present in each asymmetric unit. So let the crystallographers use whatever convention works for them, but in the PDB the file should contain the asymmetric unit (or some fraction of it, in the case of viruses) Pavel Afonine wrote:
Hi Maia,
when I submitted a pdb with some waters on a twofold sym. axis with occupancies =1, the PDB wanted occupancies 0.5. They do not want to take into account your "taken into account internally".
Hopefully, time will heal it -:)
More seriously (I wrote it somewhere for someone, even not once):
The maximal multiplicity of a special position in proteins is 24 (or so, correct me if I'm wrong, please), and the precision of the occupancy factor field in PDB file is only two digits. Let’s imagine a relatively small structure at high resolution that contains a handful amount of heavy atoms all located at special positions with the multiplicity 24. Now, the occupancies of these heavy atoms in a PDB file all have to be set to 1./24 ~ 0.04 and not to 0.042. Depending on the number of electrons in a heavy atom, the number of heavy atoms, multiplicity of special position and overall structure size, one can easily imagine a situation when this kind of rounding error may become very significant. Therefore, I think, it is a bad idea to rely on the file format in this case, and is much better to do this trivial operation internally without any unnecessary loss of accuracy. Plus, it all happens seamlessly for the end-user, which is another step towards the automation.
Pavel.
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Maia,
when I submitted a pdb with some waters on a twofold sym. axis with occupancies =1, the PDB wanted occupancies 0.5. They do not want to take into account your "taken into account internally".
You can just change it to 0.5 now before or during refinement. (Occupancy 1 on a two-fold doesn't make sense unless the symmetry is taken into account.) Ralf
participants (6)
-
chern -
Edward A. Berry -
Felix Frolow -
Pavel Afonine -
Peter Zwart -
Ralf W. Grosse-Kunstleve