Dear all, I refine a structure of a protein to 1.4 A and found a few SO4-Ions. I tried to refine this sulfurs and some of these seems to be not fully occupied, as the negative difference density suggest. I tried to refine the occupancy of the sulfate ions to get an idea how strong the different binding sites might be occupied. All sulfate ions are in Chain C of my pdb. I tried to refine the occupancy individually using refine.occupancy.individual SO4 but this lead to different occupnacies for every atom for every atom and theix cant be the case for sure. Then I tried and group occupancy with resname=SO4 but now every sulfate ion has the same occupancy, which is indicated from my previous refinements also not the case, because two ions have no negative difference density. At the momentI can not figure out how I should combine the keywords for the individual occupancy refinement of the different sulfate ions. In my structure. Should I define for every ion a different chain or how I could overcome this problem? I would be very happy if anyone has a idea to sove this problem or tell me what keyword I misunderstood in the documentation. Best regards Christian
Hi Christian, all you have to do is to define each sulfate as a constrained group for occupancy refinement, like this: constrained_group { selection = "chain C and resid x" } constrained_group { selection = "chain C and resid y" } where resid is simply the residue number. The occupancy of all atoms that belong to the same constrained group will be refined to the same value. Best wishes, Marco Christian Roth wrote:
Dear all,
I refine a structure of a protein to 1.4 A and found a few SO4-Ions. I tried to refine this sulfurs and some of these seems to be not fully occupied, as the negative difference density suggest. I tried to refine the occupancy of the sulfate ions to get an idea how strong the different binding sites might be occupied. All sulfate ions are in Chain C of my pdb. I tried to refine the occupancy individually using refine.occupancy.individual SO4 but this lead to different occupnacies for every atom for every atom and theix cant be the case for sure. Then I tried and group occupancy with resname=SO4 but now every sulfate ion has the same occupancy, which is indicated from my previous refinements also not the case, because two ions have no negative difference density. At the momentI can not figure out how I should combine the keywords for the individual occupancy refinement of the different sulfate ions. In my structure. Should I define for every ion a different chain or how I could overcome this problem? I would be very happy if anyone has a idea to sove this problem or tell me what keyword I misunderstood in the documentation.
Best regards
Christian _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- ================================ Marco Bellinzoni Unité de Biochimie Structurale Institut Pasteur 25, rue du Dr. Roux 75724 Paris Cedex 15 France Tel. +33 (0)1 45688608 Fax. +33 (0)1 45688604 ================================
Hi Marco and Christian, another trick that I think will work is to assign a non-blanc altloc identifier to each SO4 ion. For example: HETATM 5269 S ASO4 601 88.394 7.885 58.375 1.00 26.69 S HETATM 5270 O1 ASO4 601 88.709 6.482 58.612 1.00 26.69 O HETATM 5271 O2 ASO4 601 88.383 8.143 56.832 1.00 26.69 O HETATM 5272 O3 ASO4 601 89.311 8.886 58.913 1.00 26.69 O HETATM 5273 O4 ASO4 601 87.037 8.083 58.916 1.00 26.69 O HETATM 5274 S ASO4 602 123.263 -1.833 44.610 1.00 41.54 S HETATM 5275 O1 ASO4 602 123.408 -1.546 46.092 1.00 41.54 O HETATM 5276 O2 ASO4 602 124.616 -2.116 44.068 1.00 41.54 O HETATM 5277 O3 ASO4 602 122.687 -0.633 43.944 1.00 41.54 O HETATM 5278 O4 ASO4 602 122.349 -3.008 44.466 1.00 41.54 O so one occupancy factor will be refined per each ion, and it will be constrained between 0 and 1.0. Pavel. On 1/27/10 1:14 AM, Marco Bellinzoni wrote:
Hi Christian,
all you have to do is to define each sulfate as a constrained group for occupancy refinement, like this:
constrained_group { selection = "chain C and resid x" } constrained_group { selection = "chain C and resid y" }
where resid is simply the residue number. The occupancy of all atoms that belong to the same constrained group will be refined to the same value.
Best wishes, Marco
Christian Roth wrote:
Dear all, I refine a structure of a protein to 1.4 A and found a few SO4-Ions. I tried to refine this sulfurs and some of these seems to be not fully occupied, as the negative difference density suggest. I tried to refine the occupancy of the sulfate ions to get an idea how strong the different binding sites might be occupied. All sulfate ions are in Chain C of my pdb. I tried to refine the occupancy individually using refine.occupancy.individual SO4 but this lead to different occupnacies for every atom for every atom and theix cant be the case for sure. Then I tried and group occupancy with resname=SO4 but now every sulfate ion has the same occupancy, which is indicated from my previous refinements also not the case, because two ions have no negative difference density. At the momentI can not figure out how I should combine the keywords for the individual occupancy refinement of the different sulfate ions. In my structure. Should I define for every ion a different chain or how I could overcome this problem? I would be very happy if anyone has a idea to sove this problem or tell me what keyword I misunderstood in the documentation.
Best regards Christian _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Dear Pavel, your trick seems to me potentially 'dangerous', though: if you assign an altloc identifier to a whole residue, its atoms won't 'see' any other atom that does have a different altloc identifier because it is like they don't exist at the same time - is this right? If so, in principle, a sulfate labelled with an altloc identifier 'A' should not see neighbouring atoms which are labelled as altloc 'B', which may well be the whole side chain of a residue in close contact, modelled in double conformation. That way, no restraints will be applied on close non bonded atoms, etc... Or am I missing something? Thanks, Marco Pavel Afonine wrote:
Hi Marco and Christian,
another trick that I think will work is to assign a non-blanc altloc identifier to each SO4 ion. For example:
HETATM 5269 S ASO4 601 88.394 7.885 58.375 1.00 26.69 S HETATM 5270 O1 ASO4 601 88.709 6.482 58.612 1.00 26.69 O HETATM 5271 O2 ASO4 601 88.383 8.143 56.832 1.00 26.69 O HETATM 5272 O3 ASO4 601 89.311 8.886 58.913 1.00 26.69 O HETATM 5273 O4 ASO4 601 87.037 8.083 58.916 1.00 26.69 O HETATM 5274 S ASO4 602 123.263 -1.833 44.610 1.00 41.54 S HETATM 5275 O1 ASO4 602 123.408 -1.546 46.092 1.00 41.54 O HETATM 5276 O2 ASO4 602 124.616 -2.116 44.068 1.00 41.54 O HETATM 5277 O3 ASO4 602 122.687 -0.633 43.944 1.00 41.54 O HETATM 5278 O4 ASO4 602 122.349 -3.008 44.466 1.00 41.54 O
so one occupancy factor will be refined per each ion, and it will be constrained between 0 and 1.0.
Pavel.
On 1/27/10 1:14 AM, Marco Bellinzoni wrote:
Hi Christian,
all you have to do is to define each sulfate as a constrained group for occupancy refinement, like this:
constrained_group { selection = "chain C and resid x" } constrained_group { selection = "chain C and resid y" }
where resid is simply the residue number. The occupancy of all atoms that belong to the same constrained group will be refined to the same value.
Best wishes, Marco
Christian Roth wrote:
Dear all, I refine a structure of a protein to 1.4 A and found a few SO4-Ions. I tried to refine this sulfurs and some of these seems to be not fully occupied, as the negative difference density suggest. I tried to refine the occupancy of the sulfate ions to get an idea how strong the different binding sites might be occupied. All sulfate ions are in Chain C of my pdb. I tried to refine the occupancy individually using refine.occupancy.individual SO4 but this lead to different occupnacies for every atom for every atom and theix cant be the case for sure. Then I tried and group occupancy with resname=SO4 but now every sulfate ion has the same occupancy, which is indicated from my previous refinements also not the case, because two ions have no negative difference density. At the momentI can not figure out how I should combine the keywords for the individual occupancy refinement of the different sulfate ions. In my structure. Should I define for every ion a different chain or how I could overcome this problem? I would be very happy if anyone has a idea to sove this problem or tell me what keyword I misunderstood in the documentation.
Best regards Christian _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- ================================ Marco Bellinzoni Unité de Biochimie Structurale Institut Pasteur 25, rue du Dr. Roux 75724 Paris Cedex 15 France Tel. +33 (0)1 45688608 Fax. +33 (0)1 45688604 ================================
Hi Marco,
your trick seems to me potentially 'dangerous', though: if you assign an altloc identifier to a whole residue, its atoms won't 'see' any other atom that does have a different altloc identifier because it is like they don't exist at the same time - is this right?
that's true. Although, I don't know what is actually correct... If the occupancy of the whole ion is less than 1.0 that means there are situations (unit cells) where this ion is simply absent at that particular location and therefore there is nothing to "see" for the surrounding atoms.
If so, in principle, a sulfate labelled with an altloc identifier 'A' should not see neighbouring atoms which are labelled as altloc 'B', which may well be the whole side chain of a residue in close contact, modelled in double conformation. That way, no restraints will be applied on close non bonded atoms, etc...
Correct. Anyway, I was just pointing out an alternative option for group occupancy refinement, and thanks for emphasizing the implications for geometry restraints. Pavel.
But if you want to refine occupancies of SO4 group only then other atoms, i.e. protein atoms, will not have any altloc. So, no danger and Pavel's trick will work. Vaheh -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Pavel Afonine Sent: Wednesday, January 27, 2010 12:33 PM To: PHENIX user mailing list Subject: Re: [phenixbb] occupancy refinement Hi Marco,
your trick seems to me potentially 'dangerous', though: if you assign an altloc identifier to a whole residue, its atoms won't 'see' any other atom that does have a different altloc identifier because it is like they don't exist at the same time - is this right?
that's true. Although, I don't know what is actually correct... If the occupancy of the whole ion is less than 1.0 that means there are situations (unit cells) where this ion is simply absent at that particular location and therefore there is nothing to "see" for the surrounding atoms.
If so, in principle, a sulfate labelled with an altloc identifier 'A' should not see neighbouring atoms which are labelled as altloc 'B', which may well be the whole side chain of a residue in close contact, modelled in double conformation. That way, no restraints will be applied on close non bonded atoms, etc...
Correct. Anyway, I was just pointing out an alternative option for group occupancy refinement, and thanks for emphasizing the implications for geometry restraints. Pavel. _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
It did work for me earlier this month http://phenix-online.org/pipermail/phenixbb/2010-January/003180.html As for potential pitfalls of this approach mentioned by Marco, Vaheh is absolutely right that only *other* alternate conformers pose danger here. But even if there are alternate conformers nearby, couldn't some of them clash with the ligands because, you know, ligand is not always there? In any event, simple visual inspection should resolve any specific case. Assigned altLoc is a workaround though and it is my understanding that default phenix.refine behavior with respect to partial occupancy ligands will change in the future to more expected single occupancy per residue default: http://phenix-online.org/pipermail/phenixbb/2010-January/003183.html Ed. On Wed, 2010-01-27 at 12:38 -0500, Oganesyan, Vaheh wrote:
But if you want to refine occupancies of SO4 group only then other atoms, i.e. protein atoms, will not have any altloc. So, no danger and Pavel's trick will work.
Vaheh
-----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Pavel Afonine Sent: Wednesday, January 27, 2010 12:33 PM To: PHENIX user mailing list Subject: Re: [phenixbb] occupancy refinement
Hi Marco,
your trick seems to me potentially 'dangerous', though: if you assign an altloc identifier to a whole residue, its atoms won't 'see' any other atom that does have a different altloc identifier because it is like they don't exist at the same time - is this right?
that's true. Although, I don't know what is actually correct... If the occupancy of the whole ion is less than 1.0 that means there are situations (unit cells) where this ion is simply absent at that particular location and therefore there is nothing to "see" for the surrounding atoms.
If so, in principle, a sulfate labelled with an altloc identifier 'A' should not see neighbouring atoms which are labelled as altloc 'B', which may well be the whole side chain of a residue in close contact, modelled in double conformation. That way, no restraints will be applied on close non bonded atoms, etc...
Correct.
Anyway, I was just pointing out an alternative option for group occupancy refinement, and thanks for emphasizing the implications for geometry restraints.
Pavel.
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore ---------------------------------------------- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. ------------------------------ / Lao Tse /
participants (5)
-
Christian Roth -
Ed Pozharski -
Marco Bellinzoni -
Oganesyan, Vaheh -
Pavel Afonine