Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
I thought about this and I think the only workable solution that will keep everyone happy and maintain the status quo as far as possible is to get an extra data item added to mmCIF for the parameter combination multiplicity*occupancy (I believe this parameter is called the 'site population' in Shel-X). So in addition to '_atom_site.occupancy' (which is in the core CIF dictionary) we would have (say) '_atom_site.population' specifically for mmCIF. That way programs that created mmCIF files for deposition could use either parameter without ambiguity, and we don't need to change any existing programs, except for those few that do CIF - PDB conversion. Existing macromolecular CIF files would have to be updated to show the new data item, that's all. This assumes of course that that really is the data they actually contain, maybe some don't, that would need to be checked: I suspect the PDB doesn't verify which parameter is actually deposited. Uncertainty about what the 'occupancy' column actually contains in the case of special positions is what we want to resolve. A bit untidy I know, but I can't see any other way that doesn't involve major upheavals. We would also need to get the PDB Contents Guide changed so that it refers to 'site population' instead of occupancy. That way no programs reading/writing PDB files (except mine!) would need to be changed. Does anyone have a better suggestion? -- Ian On Thu, Dec 16, 2010 at 9:10 PM, Dale Tronrud det...@uoxray.uoregon.edu wrote: On 12/16/10 06:47, Ian Tickle wrote: For the sake of argument let's say that 0.02 Ang is too big to be rounding error. So if you see that big a shift then the intention of the refinement program (or rather the programmer) which allowed such a value to be appear in the output should be that it's real. If the intention of the user was that the atom is actually on axis then the program should not have allowed such a large shift, since it will be interpreted as 'much bigger than rounding error' and therefore 'significantly off-axis'. I would certainly hope that no one believes that the precision of the parameters in a PDB file are significant to the level of round-off error! It's bad enough that a small number of people take the three decimal points of precision in the PDB file seriously. When a person places an atom in a model they aren't stating a believe that that is the EXACT location of the atom, only that they believe the center of the locus of all equivalent atoms in the crystal falls near that spot. If it's 0.02 A from a special position (and the SU of the position is larger than that) then it might be on the special position and it might not. If I come across one of your models and you have an atom exactly on a special position (assuming you're able to do that with three decimal points in a PDB file) I'd still assume that you only intend that there is an atom in the vicinity of that point and it might be exactly on the axis but it might be a little off. All structural models are fuzzy. Dale Tronrud
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Dale The reward of the full calculation is that all the complications you describe disappear. An atom that sits 0.001 A from a special position is not unstable in the least. That's indeed a very interesting observation, I have to admit that I didn't think that would be achievable. But there must still be some threshold of distance at which even that fails? Presumably within rounding error? Or are you saying (I assume you aren't!) that you can even refine all co-ordinates of an atom exactly on a special position? Say the x and z co-ordinates of an atom at (0,y,0) in monoclinic? Presumably the atom would have to be given a random push one way or the other (random number generators are generally not a feature of crystallographic refinement programs, with the obvious exception of simulated annealing!)? ? I always avoid programing tests of a == b for real numbers because the round-off errors will always bite you at some point. This means that a test of an atom exactly on a special position can't be done reliably in floating point math. Obviously common sense has to be applied here and tests for strict floating-point equality studiously avoided. But this is very easily remedied, my optimisation programs are full of tests like IF(ABS(X-Y).LT.1E-6) THEN ... and I'm certain so are yours (assuming of course you still program in Fortran!). This implies that in the case that an atom is off-axis and disordered you have to take care not to place it within say a few multiples of rounding error of the axis, since then it might be indeed be confused with one 'on' the special position. However if someone claims that an atom sits within say 10*rounding error of an axis as distinct from being on the axis, then a) there's no way that can be proved, and b) it would be indistinguishable from being on the s.p. and the difference in terms of structure factors and maps would be insignificant anyway, so it may as well be on-axis. I think this is how the Oxford CRYSTALS software ( http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at least 30 years, deals with this issue, so I can't accept that it can't be made to work, even if I haven't got all the precise details straight of how it's done in practice. Your preferred assumption is that any atom near enough to a special position is really on the special position and should have an occupancy of one. My assumption is that no atom is every EXACTLY on the special position and if they are close enough to their symmetry image to forbid coexistence the occupancy should be 1/n. I think either assumption is reasonable but, of course, prefer mine for what I consider practical reasons. It helps that I have to code to make mine work. Whichever way it's done is only a matter of convention (clearly both ways work just as well), however I would reiterate that my main concern here is that convention and practice appear to have parted company in this particular instance! Cheers -- IAn
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
I think this is how the Oxford CRYSTALS software ( http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at least 30 years, deals with this issue, so I can't accept that it can't be made to work, even if I haven't got all the precise details straight of how it's done in practice. PS just to point out that CRYSTALS is now (since 2009) open source, so anyone can download it and find out for themselves how it's done! Cheers -- Ian
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Or you could write and ask the author, who is always willing to help (sorry, David!)... On 16 Dec 2010, at 11:24, Ian Tickle wrote: I think this is how the Oxford CRYSTALS software ( http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at least 30 years, deals with this issue, so I can't accept that it can't be made to work, even if I haven't got all the precise details straight of how it's done in practice. PS just to point out that CRYSTALS is now (since 2009) open source, so anyone can download it and find out for themselves how it's done! Cheers -- Ian Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Dear Ian, You still have an arbitrary threshold: at high resolution you see two disordered atoms off-axis and at low resolution you see one ordered atom on-axis. However, somewhere in between you or the program has to decide whether you still see two atoms or if the data (resolution) does not warrant such a statement and you switch to the one-atom model. As George Sheldrick confirmed, there is a discontinuous transition between the two, which does not correspond to the physical reality. There is no quantum transition or something when the atom get closer than a certain limit to a crystallographic symmetry element. The atom does not care, its position is just determined by the local force fields and if those force fields have two local minima close together, the atom will be disordered. The decision to switch from a model where the atom is added once with full occupancy to the fourier transform calculation, or whether the atom is added twice with half occupancy is an arbitrary decision, made by the programmer or the user of the program. Cheers, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle Sent: Wednesday, December 15, 2010 6:57 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms That's my whole point, it's not an arbitrary threshold, it's determined completely by what the data are capable of telling you about the structure, depending on the resolution. Either you have sufficient resolution to be able to say that the atom is disordered off the s.p. or you don't and you have no choice but to constrain it to the s.p., whether it's actually disordered or not. In any case there is no discontinuous change in occupancy at all, I never suggested that there should be. Say at high resolution you see 2 disordered atoms off-axis each with 1/2 occupancy, so total occupancy = 1. At lower resolution you see 1 ordered atom on-axis with occupancy 1 - so no change in total occupancy. It makes absolutely no difference if instead if you store multiplicity*occupancy in the file, the total occupancy is still 1. However multiplicity*occupancy is not conserved so will change discontinuously (off-axis total = 1, on-axis total = 1/2); occupancy is conserved (it represents real atoms after all!). I have no issue with Shel-X if it's writing out the occupancy for deposition (or at least making best efforts to do so). What it does for intermediate files is the user's own data conversion problem if s/he decides to switch between different programs. Cheers -- Ian On Wed, Dec 15, 2010 at 5:20 PM, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: I agree with Herman. It is simply not acceptable to have a sudden discontinuous change in effective occupancy at some arbitrary point as a disordered atom approaches a special position. Anyway, whatever the CIF people decide, I will not introduce an incompatibility between different versions of SHELX. When SHELXL produces a small molecule CIF for depostion, it of course attempts to generate the occupancy according to the CIF definition. Not too surprisingly, there are a few complicated cases of 'nearly special positions' where the program gets this wrong. This is probably the most serious known 'bug' in SHELXL, but is proving rather difficult to eliminate completely. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 15 Dec 2010, Ian Tickle wrote: Hi Herman What makes an atom on a special position is that it is literally ON the s.p.: it can't be 'almost on' the s.p. because then if you tried to refine the co-ordinates perpendicular to the axis you would find that the matrix would be singular or at least so badly conditioned that the solution would be poorly defined. The only solution to that problem is to constrain (i.e. fix) these co-ordinates to be exactly on the axis and not attempt to refine them. The data are telling you that you have insufficient resolution so you are not justified in placing the atom very close to the axis; the best you can do is place the atom with unit occupancy exactly _on_ the axis. It's only once the atom is a 'significant' distance (i.e. relative to the resolution) away from the axis that these co-ordinates can be independently refined. Then the data are telling you that the atom is disordered. If you collected higher resolution data you might well be able to detect successfully refine disordered atoms closer to the axis than with low resolution data. So it has nothing to do with the programmer setting an arbitrary threshold. This would have to be some complicated function of atom type, occupancy, B factor, resolution, data quality etc to work properly anyway so I doubt
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
You still have an arbitrary threshold: at high resolution you see two disordered atoms off-axis and at low resolution you see one ordered atom on-axis. However, somewhere in between you or the program has to decide whether you still see two atoms or if the data (resolution) does not warrant such a statement and you switch to the one-atom model. Switching between interpretations happens all the time as higher resolution data is obtained! Let's say at low resolution you see density apparently for one copy of a side-chain (i.e. the density is not of sufficient resolution to warrant interpreting it as disordered two half side-chains) and you fit that. To keep it simple I'm assuming it's on a general, not a special position. Then you collect high-resolution data and now you see that the same side-chain is disordered. Rephrasing your statement: somewhere in between you or the program has to decide whether you still see one (ordered, with occupancy=1) side-chain or if the data (resolution) warrants such a statement and you switch to the two side-chain (disordered, now with sum occupancy=1) model. As George Sheldrick confirmed, there is a discontinuous transition between the two, which does not correspond to the physical reality. There is no quantum transition or something when the atom get closer than a certain limit to a crystallographic symmetry element. The atom does not care, its position is just determined by the local force fields and if those force fields have two local minima close together, the atom will be disordered. I'm sorry I don't see this discontinuity that you are referring to at all (I think you have forgotten to include the symmetry copy), and I'm certainly not claiming there is any quantum transition. Let's start with a disordered (1/2 occupancy) atom off a 2-fold axis and see what happens to the electron density as it approaches and finally sits on the 2-fold. Here are the electron densities (this would obviously look at lot better graphed - my apologies!): 1 6 10 6 1 * 1 6 10 6 1 Now move the atom closer in steps to the axis so it overlaps more and more with its symmetry copy: * 1 6 10 6 2 6 10 6 1 1 6 10 7 7 10 6 1 1 6 11 12 11 6 1 1 7 16 16 7 1 2 12 20 12 2 * On the final step the fully overlapped atom has twice the occupancy (i.e. 1 instead of 1/2) as the original as evidenced by a peak height of 20 units, compared with 10. In which step did the discontinuity occur? Clearly we could make the steps as small as we like, and you would see a smooth transition from 2 1/2 atoms to 1 whole one. The decision to switch from a model where the atom is added once with full occupancy to the fourier transform calculation, or whether the atom is added twice with half occupancy is an arbitrary decision, made by the programmer or the user of the program. I completely agree, both ways of doing it work equally well and it's all down to convention. As I pointed out to Dale, the way I'm describing does work in practice, as evidenced by the fact that CRYSTALS which does it the way I describe, has been doing it this way for the last 40 years. So I can't accept that it can't work in practice when plainly it does! This issue here is purely one of divergence of agreed convention (CIF, mmCIF PDB) and practice. Cheers -- Ian
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
On 16/12/2010 12:24, Ian Tickle wrote: I think this is how the Oxford CRYSTALS software ( http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at least 30 years, deals with this issue, so I can't accept that it can't be made to work, even if I haven't got all the precise details straight of how it's done in practice. PS just to point out that CRYSTALS is now (since 2009) open source, so anyone can download it and find out for themselves how it's done! Do you have a link? I was looking and didn't find it Thanks Jon
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Hi Jon, try this: http://www.xtl.ox.ac.uk/download.html -- Ian On Thu, Dec 16, 2010 at 1:14 PM, Jon Wright wri...@esrf.fr wrote: On 16/12/2010 12:24, Ian Tickle wrote: I think this is how the Oxford CRYSTALS software ( http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at least 30 years, deals with this issue, so I can't accept that it can't be made to work, even if I haven't got all the precise details straight of how it's done in practice. PS just to point out that CRYSTALS is now (since 2009) open source, so anyone can download it and find out for themselves how it's done! Do you have a link? I was looking and didn't find it Thanks Jon
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Dear Ian, Of course there is no dicontinuity, but you create one the moment you decide that certain symmetry operators no longer apply to certain atoms. Confusion arises e.g. when you download a pdb file of fairly high resolution and find a water molecule with an occupancy of e.g. 0.45 at 0.02 Å from a symmetry axis. Is it a special water suffering from some rounding errors with a total occupancy of 0.45, or a rotationally disordered water (perhaps refined by an overzealous crystallographer) with a combined occupancy of 0.90? This in my eyes unneccessary distinction between special and non-special positions does create confusion and unnecessarily complicates the programming of programs working with coordinates files. If certain refinement program have difficulties with atoms close to symmetry axes, one could always add the approprioate constraints of restraints. Cheers, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle Sent: Thursday, December 16, 2010 1:31 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms You still have an arbitrary threshold: at high resolution you see two disordered atoms off-axis and at low resolution you see one ordered atom on-axis. However, somewhere in between you or the program has to decide whether you still see two atoms or if the data (resolution) does not warrant such a statement and you switch to the one-atom model. Switching between interpretations happens all the time as higher resolution data is obtained! Let's say at low resolution you see density apparently for one copy of a side-chain (i.e. the density is not of sufficient resolution to warrant interpreting it as disordered two half side-chains) and you fit that. To keep it simple I'm assuming it's on a general, not a special position. Then you collect high-resolution data and now you see that the same side-chain is disordered. Rephrasing your statement: somewhere in between you or the program has to decide whether you still see one (ordered, with occupancy=1) side-chain or if the data (resolution) warrants such a statement and you switch to the two side-chain (disordered, now with sum occupancy=1) model. As George Sheldrick confirmed, there is a discontinuous transition between the two, which does not correspond to the physical reality. There is no quantum transition or something when the atom get closer than a certain limit to a crystallographic symmetry element. The atom does not care, its position is just determined by the local force fields and if those force fields have two local minima close together, the atom will be disordered. I'm sorry I don't see this discontinuity that you are referring to at all (I think you have forgotten to include the symmetry copy), and I'm certainly not claiming there is any quantum transition. Let's start with a disordered (1/2 occupancy) atom off a 2-fold axis and see what happens to the electron density as it approaches and finally sits on the 2-fold. Here are the electron densities (this would obviously look at lot better graphed - my apologies!): 1 6 10 6 1 * 1 6 10 6 1 Now move the atom closer in steps to the axis so it overlaps more and more with its symmetry copy: * 1 6 10 6 2 6 10 6 1 1 6 10 7 7 10 6 1 1 6 11 12 11 6 1 1 7 16 16 7 1 2 12 20 12 2 * On the final step the fully overlapped atom has twice the occupancy (i.e. 1 instead of 1/2) as the original as evidenced by a peak height of 20 units, compared with 10. In which step did the discontinuity occur? Clearly we could make the steps as small as we like, and you would see a smooth transition from 2 1/2 atoms to 1 whole one. The decision to switch from a model where the atom is added once with full occupancy to the fourier transform calculation, or whether the atom is added twice with half occupancy is an arbitrary decision, made by the programmer or the user of the program. I completely agree, both ways of doing it work equally well and it's all down to convention. As I pointed out to Dale, the way I'm describing does work in practice, as evidenced by the fact that CRYSTALS which does it the way I describe, has been doing it this way for the last 40 years. So I can't accept that it can't work in practice when plainly it does! This issue here is purely one of divergence of agreed convention (CIF, mmCIF PDB) and practice. Cheers -- Ian
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Ooops sorry that's only the executable, I guess to have to contact David for the source. -- Ian On Thu, Dec 16, 2010 at 1:14 PM, Jon Wright wri...@esrf.fr wrote: On 16/12/2010 12:24, Ian Tickle wrote: I think this is how the Oxford CRYSTALS software ( http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at least 30 years, deals with this issue, so I can't accept that it can't be made to work, even if I haven't got all the precise details straight of how it's done in practice. PS just to point out that CRYSTALS is now (since 2009) open source, so anyone can download it and find out for themselves how it's done! Do you have a link? I was looking and didn't find it Thanks Jon
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
On Thu, Dec 16, 2010 at 1:18 PM, herman.schreu...@sanofi-aventis.com wrote: Of course there is no dicontinuity, but you create one the moment you decide that certain symmetry operators no longer apply to certain atoms. Change 'atoms' in that statement to 'reflections', or to 'map grid points', then read it again. Does the (-h,k,-l) operator apply to the (0,k,0) reflections or the (-x,y,-z) operator to the grid points (0,y,0)? Do you multiply the intensities of the (0,k,0) reflections or the electron densities of the (0,y,0) points by 0.5 because they are on the axis in order to make it easier to program, or do you decide that will confuse the user, and instead deal with the multiplicity factor internally in the program? Confusion arises e.g. when you download a pdb file of fairly high resolution and find a water molecule with an occupancy of e.g. 0.45 at 0.02 Å from a symmetry axis. Is it a special water suffering from some rounding errors with a total occupancy of 0.45, or a rotationally disordered water (perhaps refined by an overzealous crystallographer) with a combined occupancy of 0.90? For the sake of argument let's say that 0.02 Ang is too big to be rounding error. So if you see that big a shift then the intention of the refinement program (or rather the programmer) which allowed such a value to be appear in the output should be that it's real. If the intention of the user was that the atom is actually on axis then the program should not have allowed such a large shift, since it will be interpreted as 'much bigger than rounding error' and therefore 'significantly off-axis'. Of course even if the intention of the user was that splitting the atom across the 2-fold is meaningful, the user may still have got it wrong if the data doesn't justify splitting the atom like that. The important point is how the program's actions are interpreted by other programs and users - that's why we have conventions. Single precision floating point rounding error is ~ 1 in 10^7, so even if we allow 100 times that with a 100 Ang axis it's still only 0.001 Ang. Despite Dale being able to successful refine a 1/2 atom 0.001 Ang from an axis I don't think he can claim that moving an atom by 0.001 Ang makes any difference above rounding error to the structure factors. If the data can't detect the difference, then the user should not be claiming that there is one, and programs should not allow atoms to be set as close as 0.001 Ang, (or whatever the consensus is a suitable multiple of the rounding error) from an axis: it just makes no sense. You just have to decide what is the smallest realistic shift that the best data could possibly detect under optimal conditions, agree that programs can't set an off-axis shift below that, and set the rounding error test lower than that (say by an order of magnitude for safety). As I said CRYSTALS must do something like this and it has worked fine for the last 40 years on small molecules where clearly the resolution is going to allow you to detect much smaller off-axis shifts than for macromolecules, so the choice of rounding threshold will be even more critical. This in my eyes unneccessary distinction between special and non-special positions does create confusion and unnecessarily complicates the programming of programs working with coordinates files. I suspect the reason that the CIF committee decided that it was necessary to adopt this convention is that it makes transparent the connection between occupancy, the chemical formula and static disorder, i.e. if you see partial occupancy then you know its disordered; occupancy=1 simply and clearly signifies that a whole atom is present. This connection is obfuscated by multiplying by the point multiplicity, which is really just an algorithmic issue for the programmer to deal with internally (exactly as for reflections and map grid points), and shouldn't 'leak out' into the user's domain. It's a very minor complication compared with everything else that goes on in a refinement program. If you're dealing with reflections or maps you still have to program the point multiplicity, you can't avoid it. So it's not as though you have to write additional subroutines specifically for atoms. Cheers -- Ian
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
On 12/16/10 03:06, Ian Tickle wrote: Dale The reward of the full calculation is that all the complications you describe disappear. An atom that sits 0.001 A from a special position is not unstable in the least. That's indeed a very interesting observation, I have to admit that I didn't think that would be achievable. But there must still be some threshold of distance at which even that fails? Presumably within rounding error? Or are you saying (I assume you aren't!) that you can even refine all co-ordinates of an atom exactly on a special position? Say the x and z co-ordinates of an atom at (0,y,0) in monoclinic? Presumably the atom would have to be given a random push one way or the other (random number generators are generally not a feature of crystallographic refinement programs, with the obvious exception of simulated annealing!)? To be frank, I wrote this code about 15 years ago, it works, and I've not given any thought to atoms on special positions since. I'll have to go back to my notes and code to dig up the exact method. Anyone with a copy of TNT can look up the code. I am, however, not in the least concerned about what happens when an atom falls exactly on a special position because I just don't think that any part of a protein model can be considered exact. If I have a model with two atoms, of occ=1/2 each, sitting 0.0001 A apart - it fits the density and I think everyone knows what that model means, or at least they should. If you decide to shove them each 0.5 A and call them a single atom with occ=1, your model will fit the density just as well and I have no problem with that either. By the way, the refinement issue has nothing to do with special positions. The instability you observe occurs any time you build two atoms into the same bit of density. If your model has two atoms, at a general position, with exactly the same coordinates the Normal matrix will have a singularity. The problem doesn't come up much because we normally choose not to build such models. It can be an issue in models with disorder where different conformations interpenetrate each other but the stereochemical restraints usually come to the rescue then. ? I always avoid programing tests of a == b for real numbers because the round-off errors will always bite you at some point. This means that a test of an atom exactly on a special position can't be done reliably in floating point math. Obviously common sense has to be applied here and tests for strict floating-point equality studiously avoided. But this is very easily remedied, my optimisation programs are full of tests like IF(ABS(X-Y).LT.1E-6) THEN ... and I'm certain so are yours (assuming of course you still program in Fortran!). This implies that in the case that an atom is off-axis and disordered you have to take care not to place it within say a few multiples of rounding error of the axis, since then it might be indeed be confused with one 'on' the special position. However if someone claims that an atom sits within say 10*rounding error of an axis as distinct from being on the axis, then a) there's no way that can be proved, and b) it would be indistinguishable from being on the s.p. and the difference in terms of structure factors and maps would be insignificant anyway, so it may as well be on-axis. If the difference is insignificant, it may as well be off-axis. I guess if the difference is insignificant it just comes down to personal preferences. Dale Tronrud I think this is how the Oxford CRYSTALS software ( http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at least 30 years, deals with this issue, so I can't accept that it can't be made to work, even if I haven't got all the precise details straight of how it's done in practice. Your preferred assumption is that any atom near enough to a special position is really on the special position and should have an occupancy of one. My assumption is that no atom is every EXACTLY on the special position and if they are close enough to their symmetry image to forbid coexistence the occupancy should be 1/n. I think either assumption is reasonable but, of course, prefer mine for what I consider practical reasons. It helps that I have to code to make mine work. Whichever way it's done is only a matter of convention (clearly both ways work just as well), however I would reiterate that my main concern here is that convention and practice appear to have parted company in this particular instance! Cheers -- IAn
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
On 12/16/10 06:47, Ian Tickle wrote: For the sake of argument let's say that 0.02 Ang is too big to be rounding error. So if you see that big a shift then the intention of the refinement program (or rather the programmer) which allowed such a value to be appear in the output should be that it's real. If the intention of the user was that the atom is actually on axis then the program should not have allowed such a large shift, since it will be interpreted as 'much bigger than rounding error' and therefore 'significantly off-axis'. I would certainly hope that no one believes that the precision of the parameters in a PDB file are significant to the level of round-off error! It's bad enough that a small number of people take the three decimal points of precision in the PDB file seriously. When a person places an atom in a model they aren't stating a believe that that is the EXACT location of the atom, only that they believe the center of the locus of all equivalent atoms in the crystal falls near that spot. If it's 0.02 A from a special position (and the SU of the position is larger than that) then it might be on the special position and it might not. If I come across one of your models and you have an atom exactly on a special position (assuming you're able to do that with three decimal points in a PDB file) I'd still assume that you only intend that there is an atom in the vicinity of that point and it might be exactly on the axis but it might be a little off. All structural models are fuzzy. Dale Tronrud
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Dear George Is applying the multiplicity factor to the occupancy internally in the program such a issue anyway? It need only be done once per atom on input (i.e. you multiply each input occupancy by the multiplicity to get the combined multiplicity*occupancy value that you would have reading in directly in the current version), and then once per atom again on output, reversing the process. There shouldn't be any need to change anything in the inner atom/reflection loop where obviously it would indeed have slowed things down. I can see though that the backwards-compatibility issue is more serious. However I suspect it will affect only a small proportion of cases (though I accept that the fact that it may affect any at all may be sufficient grounds for you to reject it!). If the input value exceeds the multiplicity we can say that it's definitely an occupancy (otherwise clearly the occupancy would be 1). If it's less there's an ambiguity for sure; however then it's more likely to be the multiplicity*occupancy (so the occupancy is nearer to 1), on the grounds that small occupancies are less likely to be observed, because the effect on diffraction will be less significant. I accept that second-guessing the user's intentions in this way is not ideal! I wonder how often fractional occupancies are observed at special positions anyway? Regards -- Ian On Fri, Dec 10, 2010 at 11:28 PM, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: SHELXL also expects that the occupancy of a fully occupied atom on a threefold axis should be set at 1/3, and will generate this automatically if necessary. It will also generate automatically the necessary constraints for the x, y and z parameters (and for the Uij if the atom is anisotropic). It is essential that this is done correctly if a full-matrix refinement is being performed (e.g. to get esd estimates), otherwise the refinement can explode. The user may change or switch off the tolerance for detecting whether an atom is on a special position (with the SPEC instruction). Setting the occupancy to a fraction avoided a complicated IF construction inside a loop and 35 years ago computers were so slow! I can't change it now because I have to preserve upwards compatibility. Unfortunately the CIF committee decided to use the other definition (i.e. the Zn on the threefold axis has an occupancy of 1.0) and this has caused considerable confusion in the small molecule world ever since; atoms are frequently encountered on special positions in inorganic and mineral structures. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Fri, 10 Dec 2010, Ed Pozharski wrote: On Fri, 2010-12-10 at 21:53 +, Ian Tickle wrote: Hmmm - but shouldn't the occupancy of the Zn be 1.00 if it's on the special position Shouldn't 1/3 be better for programming purposes? If you set occupancy to 1.0, then you should specify that symmetry operators do not apply for these atoms, making Fc calculation a bit more cumbersome. If definition of the asu content is you get full content of the unit cell after applying symmetry operators, then occupancy *must* be 1/3, right? The first zinc and the water are on special position, but because they are not excluded from positional refinement (perhaps they should be), they will drift a bit. CNS has distance cutoff for treating atoms as special positions, if it jumps over the limit during, say, simulated annealing, it will cause problems. Perhaps PROLSQ did something similar. It is a good question if it's better to fix these in place or let them wobble a bit to account for some potential disorder. While I see the formal argument that it should be nailed to three-fold axes, it is also true that this is a mathematical compromise to simplify modeling that does not reflect physical reality (i.e. you don't have three partially occupied zinc ions, it's just one). In any event, given that this is a 1.5A structure, (-0.002 0.004) is statistically speaking the same as (0 0). Cheers, Ed. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Dear Ian, Of course I could convert the occupancy on reading the atom in and convert it back agains on reading it out. This is not quite so trivial as it sounds because I need to set a threshold as to how close the atom has to be to a special position to be treated as special, and take care that rounding errors have the same effect on input and output and that the coordinates have not moved in or out of the special zone in the meantime. As it stands in SHELX, an atom that is near to a twofold will have an occupancy of 0.5 whether it is disordered close to a special position or whether it is really special, so this is never a problem. SHELXL is mainly used for small molecules that frequently have atoms on speical positions, and disordered solvent molecules approximately on sppecial positions are also very common (for example in centrosymmetric space groups toluene usually lies on the center of symmetry). Occupancies are often tied to free variables which would also complicate any changes to the code. And in any case, SHELX has been upwards compatible for the last 35 years and I wish it to remain that way. Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 15 Dec 2010, Ian Tickle wrote: Dear George Is applying the multiplicity factor to the occupancy internally in the program such a issue anyway? It need only be done once per atom on input (i.e. you multiply each input occupancy by the multiplicity to get the combined multiplicity*occupancy value that you would have reading in directly in the current version), and then once per atom again on output, reversing the process. There shouldn't be any need to change anything in the inner atom/reflection loop where obviously it would indeed have slowed things down. I can see though that the backwards-compatibility issue is more serious. However I suspect it will affect only a small proportion of cases (though I accept that the fact that it may affect any at all may be sufficient grounds for you to reject it!). If the input value exceeds the multiplicity we can say that it's definitely an occupancy (otherwise clearly the occupancy would be 1). If it's less there's an ambiguity for sure; however then it's more likely to be the multiplicity*occupancy (so the occupancy is nearer to 1), on the grounds that small occupancies are less likely to be observed, because the effect on diffraction will be less significant. I accept that second-guessing the user's intentions in this way is not ideal! I wonder how often fractional occupancies are observed at special positions anyway? Regards -- Ian On Fri, Dec 10, 2010 at 11:28 PM, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: SHELXL also expects that the occupancy of a fully occupied atom on a threefold axis should be set at 1/3, and will generate this automatically if necessary. It will also generate automatically the necessary constraints for the x, y and z parameters (and for the Uij if the atom is anisotropic). It is essential that this is done correctly if a full-matrix refinement is being performed (e.g. to get esd estimates), otherwise the refinement can explode. The user may change or switch off the tolerance for detecting whether an atom is on a special position (with the SPEC instruction). Setting the occupancy to a fraction avoided a complicated IF construction inside a loop and 35 years ago computers were so slow! I can't change it now because I have to preserve upwards compatibility. Unfortunately the CIF committee decided to use the other definition (i.e. the Zn on the threefold axis has an occupancy of 1.0) and this has caused considerable confusion in the small molecule world ever since; atoms are frequently encountered on special positions in inorganic and mineral structures. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Fri, 10 Dec 2010, Ed Pozharski wrote: On Fri, 2010-12-10 at 21:53 +, Ian Tickle wrote: Hmmm - but shouldn't the occupancy of the Zn be 1.00 if it's on the special position Shouldn't 1/3 be better for programming purposes? If you set occupancy to 1.0, then you should specify that symmetry operators do not apply for these atoms, making Fc calculation a bit more cumbersome. If definition of the asu content is you get full content of the unit cell after applying symmetry operators, then occupancy *must* be 1/3, right? The first zinc and the water are on special position, but because they are not excluded from positional refinement (perhaps they should be), they will drift a bit. CNS has distance cutoff for treating atoms as special
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Dear George I would say that an atom has fractional occupancy (but unit multiplicity) unless it's exactly on the special position (though I can foresee problems with rounding of decimal places for an atom say at x=1/3), so that effectively once the atom is fixed exactly on the s.p. the symmetry copies coalesce into a single atom with unit occupancy (but fractional multiplicity). This is at least one advantage of having co-ordinates stored as fractional - it would probably be more tricky with orthogonalised co-ordinates. Presumably once an input atom has satisfied the condition of being 'sufficiently close' to a s.p. to be considered as 'on' the s.p. then the constraints fix the co-ordinates exactly on the special position and henceforth it's forcibly prevented from moving off it? In any case if an atom is very close to its symmetry copy you are going to have matrix conditioning problems for the co-ordinates perpendicular to the axis of symmetry (or mirror plane), so then you have no choice but to disallow co-ordinate shifts of the atom which would take it off the special position? Cheers -- Ian On Wed, Dec 15, 2010 at 11:42 AM, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: Dear Ian, Of course I could convert the occupancy on reading the atom in and convert it back agains on reading it out. This is not quite so trivial as it sounds because I need to set a threshold as to how close the atom has to be to a special position to be treated as special, and take care that rounding errors have the same effect on input and output and that the coordinates have not moved in or out of the special zone in the meantime. As it stands in SHELX, an atom that is near to a twofold will have an occupancy of 0.5 whether it is disordered close to a special position or whether it is really special, so this is never a problem. SHELXL is mainly used for small molecules that frequently have atoms on speical positions, and disordered solvent molecules approximately on sppecial positions are also very common (for example in centrosymmetric space groups toluene usually lies on the center of symmetry). Occupancies are often tied to free variables which would also complicate any changes to the code. And in any case, SHELX has been upwards compatible for the last 35 years and I wish it to remain that way. Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 15 Dec 2010, Ian Tickle wrote: Dear George Is applying the multiplicity factor to the occupancy internally in the program such a issue anyway? It need only be done once per atom on input (i.e. you multiply each input occupancy by the multiplicity to get the combined multiplicity*occupancy value that you would have reading in directly in the current version), and then once per atom again on output, reversing the process. There shouldn't be any need to change anything in the inner atom/reflection loop where obviously it would indeed have slowed things down. I can see though that the backwards-compatibility issue is more serious. However I suspect it will affect only a small proportion of cases (though I accept that the fact that it may affect any at all may be sufficient grounds for you to reject it!). If the input value exceeds the multiplicity we can say that it's definitely an occupancy (otherwise clearly the occupancy would be 1). If it's less there's an ambiguity for sure; however then it's more likely to be the multiplicity*occupancy (so the occupancy is nearer to 1), on the grounds that small occupancies are less likely to be observed, because the effect on diffraction will be less significant. I accept that second-guessing the user's intentions in this way is not ideal! I wonder how often fractional occupancies are observed at special positions anyway? Regards -- Ian On Fri, Dec 10, 2010 at 11:28 PM, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: SHELXL also expects that the occupancy of a fully occupied atom on a threefold axis should be set at 1/3, and will generate this automatically if necessary. It will also generate automatically the necessary constraints for the x, y and z parameters (and for the Uij if the atom is anisotropic). It is essential that this is done correctly if a full-matrix refinement is being performed (e.g. to get esd estimates), otherwise the refinement can explode. The user may change or switch off the tolerance for detecting whether an atom is on a special position (with the SPEC instruction). Setting the occupancy to a fraction avoided a complicated IF construction inside a loop and 35 years ago computers were so slow! I can't change it now because I have to preserve upwards compatibility. Unfortunately the CIF committee decided to use the other definition (i.e. the Zn on the
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Dear Ian, Yes. Once an atom has been identified as on a special position because it is within a specied tolerance, SHELXL applies the appropriate contraints to both the coordinates and the Uij so there is no danger of the atom wandering off the special position. Usually, when an atom it very close to a special position but not actually on it, it is part of a disordered solvent molecule and will be prevented from misbehaving by distance and Uij restraints imposed by the user; in such a case the user usually also switches off the special position check for that disordered molecule (SPEC -1) to avoid atoms being idealized onto the special position by the program. For solvent molecules disordered on special positions it is also necessary to ignore symmetry equivalent atoms when generating idealized hydrogen atoms etc. (PART -N in SHELXL). This is all routine practice in small molecule crystallography. I agree that the use of orthogonal rather than crystal coordinates can obscur the situation, e.g. for an atom on a threefold axis. Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 15 Dec 2010, Ian Tickle wrote: Dear George I would say that an atom has fractional occupancy (but unit multiplicity) unless it's exactly on the special position (though I can foresee problems with rounding of decimal places for an atom say at x=1/3), so that effectively once the atom is fixed exactly on the s.p. the symmetry copies coalesce into a single atom with unit occupancy (but fractional multiplicity). This is at least one advantage of having co-ordinates stored as fractional - it would probably be more tricky with orthogonalised co-ordinates. Presumably once an input atom has satisfied the condition of being 'sufficiently close' to a s.p. to be considered as 'on' the s.p. then the constraints fix the co-ordinates exactly on the special position and henceforth it's forcibly prevented from moving off it? In any case if an atom is very close to its symmetry copy you are going to have matrix conditioning problems for the co-ordinates perpendicular to the axis of symmetry (or mirror plane), so then you have no choice but to disallow co-ordinate shifts of the atom which would take it off the special position? Cheers -- Ian On Wed, Dec 15, 2010 at 11:42 AM, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: Dear Ian, Of course I could convert the occupancy on reading the atom in and convert it back agains on reading it out. This is not quite so trivial as it sounds because I need to set a threshold as to how close the atom has to be to a special position to be treated as special, and take care that rounding errors have the same effect on input and output and that the coordinates have not moved in or out of the special zone in the meantime. As it stands in SHELX, an atom that is near to a twofold will have an occupancy of 0.5 whether it is disordered close to a special position or whether it is really special, so this is never a problem. SHELXL is mainly used for small molecules that frequently have atoms on speical positions, and disordered solvent molecules approximately on sppecial positions are also very common (for example in centrosymmetric space groups toluene usually lies on the center of symmetry). Occupancies are often tied to free variables which would also complicate any changes to the code. And in any case, SHELX has been upwards compatible for the last 35 years and I wish it to remain that way. Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 15 Dec 2010, Ian Tickle wrote: Dear George Is applying the multiplicity factor to the occupancy internally in the program such a issue anyway? It need only be done once per atom on input (i.e. you multiply each input occupancy by the multiplicity to get the combined multiplicity*occupancy value that you would have reading in directly in the current version), and then once per atom again on output, reversing the process. There shouldn't be any need to change anything in the inner atom/reflection loop where obviously it would indeed have slowed things down. I can see though that the backwards-compatibility issue is more serious. However I suspect it will affect only a small proportion of cases (though I accept that the fact that it may affect any at all may be sufficient grounds for you to reject it!). If the input value exceeds the multiplicity we can say that it's definitely an occupancy (otherwise clearly the occupancy would be 1). If it's less there's an ambiguity for sure; however then it's more likely to
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Dear George I notice that the Oxford CRYSTALS program, which is what I used when I did small-molecule crystallography and which is still quite popular among the small-molecule people (maybe not as much as Shel-X!), uses the CIF convention: OCC= This parameter defines the site occupancy EXCLUDING special position effects (i.e. is the 'chemical occupancy'). The default is 1.0. Special position effects are computed by CRYSTALS and multiplied onto this parameter. (from http://www.xtl.ox.ac.uk/crystalsmanual-atomic.html ) Also the mmCIF specification on this is the same CIF one (hardly surprising I guess since it's derived from it): _atom_site.occupancy The fraction of the atom type present at this site. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site. (from http://mmcif.pdb.org/dictionaries/mmcif_std.dic/Items/_atom_site.occupancy.html ) which doesn't say so specifically, but it's implied since if the multiplicity is included then the maximum value of the sum is the multiplicity, not 1.0. So there's a real possibility of user - and programmer - confusion here! I must say that until I looked at the 4INS file I had assumed that the PDB occupancy was what it claimed to be, i.e. the real 'chemical' occupancy not the multiplicity-fudged one. Cheers -- Ian On Wed, Dec 15, 2010 at 1:53 PM, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: Dear Ian, Yes. Once an atom has been identified as on a special position because it is within a specied tolerance, SHELXL applies the appropriate contraints to both the coordinates and the Uij so there is no danger of the atom wandering off the special position. Usually, when an atom it very close to a special position but not actually on it, it is part of a disordered solvent molecule and will be prevented from misbehaving by distance and Uij restraints imposed by the user; in such a case the user usually also switches off the special position check for that disordered molecule (SPEC -1) to avoid atoms being idealized onto the special position by the program. For solvent molecules disordered on special positions it is also necessary to ignore symmetry equivalent atoms when generating idealized hydrogen atoms etc. (PART -N in SHELXL). This is all routine practice in small molecule crystallography. I agree that the use of orthogonal rather than crystal coordinates can obscur the situation, e.g. for an atom on a threefold axis. Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 15 Dec 2010, Ian Tickle wrote: Dear George I would say that an atom has fractional occupancy (but unit multiplicity) unless it's exactly on the special position (though I can foresee problems with rounding of decimal places for an atom say at x=1/3), so that effectively once the atom is fixed exactly on the s.p. the symmetry copies coalesce into a single atom with unit occupancy (but fractional multiplicity). This is at least one advantage of having co-ordinates stored as fractional - it would probably be more tricky with orthogonalised co-ordinates. Presumably once an input atom has satisfied the condition of being 'sufficiently close' to a s.p. to be considered as 'on' the s.p. then the constraints fix the co-ordinates exactly on the special position and henceforth it's forcibly prevented from moving off it? In any case if an atom is very close to its symmetry copy you are going to have matrix conditioning problems for the co-ordinates perpendicular to the axis of symmetry (or mirror plane), so then you have no choice but to disallow co-ordinate shifts of the atom which would take it off the special position? Cheers -- Ian On Wed, Dec 15, 2010 at 11:42 AM, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: Dear Ian, Of course I could convert the occupancy on reading the atom in and convert it back agains on reading it out. This is not quite so trivial as it sounds because I need to set a threshold as to how close the atom has to be to a special position to be treated as special, and take care that rounding errors have the same effect on input and output and that the coordinates have not moved in or out of the special zone in the meantime. As it stands in SHELX, an atom that is near to a twofold will have an occupancy of 0.5 whether it is disordered close to a special position or whether it is really special, so this is never a problem. SHELXL is mainly used for small molecules that frequently have atoms on speical positions, and disordered solvent molecules approximately on sppecial positions are also very common (for example in centrosymmetric space groups toluene usually lies on the center of symmetry). Occupancies are often tied to free variables which
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Dear Ian, In my view, the confusion arises by NOT including the multiplicity into the occupancy. If we make the gedanken experiment and look at a range of crystal structures with a rotationally disordered water molecule near a symmetry axis (they do exist!) then as long as the water molecule is sufficiently far from the axis, it is clear that the occupancy should be 1/2 or 1/3 or whatever is the multiplicity. However, as the molecule approaches the axis at a certain moment at a certain treshold set by the programmer of the refinement program, the molecule suddenly becomes special and the occupancy is set to 1.0. So depending on rounding errors, different thresholds etc. different programs may make different decisions on whether a water is special or not. For me, this is confusing. Best regards, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle Sent: Wednesday, December 15, 2010 3:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms Dear George I notice that the Oxford CRYSTALS program, which is what I used when I did small-molecule crystallography and which is still quite popular among the small-molecule people (maybe not as much as Shel-X!), uses the CIF convention: OCC= This parameter defines the site occupancy EXCLUDING special position effects (i.e. is the 'chemical occupancy'). The default is 1.0. Special position effects are computed by CRYSTALS and multiplied onto this parameter. (from http://www.xtl.ox.ac.uk/crystalsmanual-atomic.html ) Also the mmCIF specification on this is the same CIF one (hardly surprising I guess since it's derived from it): _atom_site.occupancy The fraction of the atom type present at this site. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site. (from http://mmcif.pdb.org/dictionaries/mmcif_std.dic/Items/_atom_site.occupancy.html ) which doesn't say so specifically, but it's implied since if the multiplicity is included then the maximum value of the sum is the multiplicity, not 1.0. So there's a real possibility of user - and programmer - confusion here! I must say that until I looked at the 4INS file I had assumed that the PDB occupancy was what it claimed to be, i.e. the real 'chemical' occupancy not the multiplicity-fudged one. Cheers -- Ian On Wed, Dec 15, 2010 at 1:53 PM, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: Dear Ian, Yes. Once an atom has been identified as on a special position because it is within a specied tolerance, SHELXL applies the appropriate contraints to both the coordinates and the Uij so there is no danger of the atom wandering off the special position. Usually, when an atom it very close to a special position but not actually on it, it is part of a disordered solvent molecule and will be prevented from misbehaving by distance and Uij restraints imposed by the user; in such a case the user usually also switches off the special position check for that disordered molecule (SPEC -1) to avoid atoms being idealized onto the special position by the program. For solvent molecules disordered on special positions it is also necessary to ignore symmetry equivalent atoms when generating idealized hydrogen atoms etc. (PART -N in SHELXL). This is all routine practice in small molecule crystallography. I agree that the use of orthogonal rather than crystal coordinates can obscur the situation, e.g. for an atom on a threefold axis. Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 15 Dec 2010, Ian Tickle wrote: Dear George I would say that an atom has fractional occupancy (but unit multiplicity) unless it's exactly on the special position (though I can foresee problems with rounding of decimal places for an atom say at x=1/3), so that effectively once the atom is fixed exactly on the s.p. the symmetry copies coalesce into a single atom with unit occupancy (but fractional multiplicity). This is at least one advantage of having co-ordinates stored as fractional - it would probably be more tricky with orthogonalised co-ordinates. Presumably once an input atom has satisfied the condition of being 'sufficiently close' to a s.p. to be considered as 'on' the s.p. then the constraints fix the co-ordinates exactly on the special position and henceforth it's forcibly prevented from moving off it? In any case if an atom is very close to its symmetry copy you are going to have matrix conditioning problems for the co-ordinates perpendicular to the axis of symmetry (or mirror plane), so then you have no choice but to disallow co-ordinate shifts of the atom which would take it off the special position
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Hi Herman What makes an atom on a special position is that it is literally ON the s.p.: it can't be 'almost on' the s.p. because then if you tried to refine the co-ordinates perpendicular to the axis you would find that the matrix would be singular or at least so badly conditioned that the solution would be poorly defined. The only solution to that problem is to constrain (i.e. fix) these co-ordinates to be exactly on the axis and not attempt to refine them. The data are telling you that you have insufficient resolution so you are not justified in placing the atom very close to the axis; the best you can do is place the atom with unit occupancy exactly _on_ the axis. It's only once the atom is a 'significant' distance (i.e. relative to the resolution) away from the axis that these co-ordinates can be independently refined. Then the data are telling you that the atom is disordered. If you collected higher resolution data you might well be able to detect successfully refine disordered atoms closer to the axis than with low resolution data. So it has nothing to do with the programmer setting an arbitrary threshold. This would have to be some complicated function of atom type, occupancy, B factor, resolution, data quality etc to work properly anyway so I doubt that it would be feasible. Instead it's determined completely by what the data are capable of telling you about the structure, as indeed it should be. My main concern was the conflict between some program implementations and the PDB and mmCIF format descriptions on this issue. For example the PDB documentation says that the ATOM record contains the occupancy (where this is defined in the CIF/mmCIF documentation). If it had intended that it should contain multiplicity*occupancy instead then presumably it would have said so. Cheers -- Ian On Wed, Dec 15, 2010 at 4:01 PM, herman.schreu...@sanofi-aventis.com wrote: Dear Ian, In my view, the confusion arises by NOT including the multiplicity into the occupancy. If we make the gedanken experiment and look at a range of crystal structures with a rotationally disordered water molecule near a symmetry axis (they do exist!) then as long as the water molecule is sufficiently far from the axis, it is clear that the occupancy should be 1/2 or 1/3 or whatever is the multiplicity. However, as the molecule approaches the axis at a certain moment at a certain treshold set by the programmer of the refinement program, the molecule suddenly becomes special and the occupancy is set to 1.0. So depending on rounding errors, different thresholds etc. different programs may make different decisions on whether a water is special or not. For me, this is confusing. Best regards, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle Sent: Wednesday, December 15, 2010 3:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms Dear George I notice that the Oxford CRYSTALS program, which is what I used when I did small-molecule crystallography and which is still quite popular among the small-molecule people (maybe not as much as Shel-X!), uses the CIF convention: OCC= This parameter defines the site occupancy EXCLUDING special position effects (i.e. is the 'chemical occupancy'). The default is 1.0. Special position effects are computed by CRYSTALS and multiplied onto this parameter. (from http://www.xtl.ox.ac.uk/crystalsmanual-atomic.html ) Also the mmCIF specification on this is the same CIF one (hardly surprising I guess since it's derived from it): _atom_site.occupancy The fraction of the atom type present at this site. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site. (from http://mmcif.pdb.org/dictionaries/mmcif_std.dic/Items/_atom_site.occupancy.html ) which doesn't say so specifically, but it's implied since if the multiplicity is included then the maximum value of the sum is the multiplicity, not 1.0. So there's a real possibility of user - and programmer - confusion here! I must say that until I looked at the 4INS file I had assumed that the PDB occupancy was what it claimed to be, i.e. the real 'chemical' occupancy not the multiplicity-fudged one. Cheers -- Ian On Wed, Dec 15, 2010 at 1:53 PM, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: Dear Ian, Yes. Once an atom has been identified as on a special position because it is within a specied tolerance, SHELXL applies the appropriate contraints to both the coordinates and the Uij so there is no danger of the atom wandering off the special position. Usually, when an atom it very close to a special position but not actually on it, it is part of a disordered solvent molecule and will be prevented from misbehaving by distance and Uij restraints imposed by the user; in such a case
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
I agree with Herman. It is simply not acceptable to have a sudden discontinuous change in effective occupancy at some arbitrary point as a disordered atom approaches a special position. Anyway, whatever the CIF people decide, I will not introduce an incompatibility between different versions of SHELX. When SHELXL produces a small molecule CIF for depostion, it of course attempts to generate the occupancy according to the CIF definition. Not too surprisingly, there are a few complicated cases of 'nearly special positions' where the program gets this wrong. This is probably the most serious known 'bug' in SHELXL, but is proving rather difficult to eliminate completely. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 15 Dec 2010, Ian Tickle wrote: Hi Herman What makes an atom on a special position is that it is literally ON the s.p.: it can't be 'almost on' the s.p. because then if you tried to refine the co-ordinates perpendicular to the axis you would find that the matrix would be singular or at least so badly conditioned that the solution would be poorly defined. The only solution to that problem is to constrain (i.e. fix) these co-ordinates to be exactly on the axis and not attempt to refine them. The data are telling you that you have insufficient resolution so you are not justified in placing the atom very close to the axis; the best you can do is place the atom with unit occupancy exactly _on_ the axis. It's only once the atom is a 'significant' distance (i.e. relative to the resolution) away from the axis that these co-ordinates can be independently refined. Then the data are telling you that the atom is disordered. If you collected higher resolution data you might well be able to detect successfully refine disordered atoms closer to the axis than with low resolution data. So it has nothing to do with the programmer setting an arbitrary threshold. This would have to be some complicated function of atom type, occupancy, B factor, resolution, data quality etc to work properly anyway so I doubt that it would be feasible. Instead it's determined completely by what the data are capable of telling you about the structure, as indeed it should be. My main concern was the conflict between some program implementations and the PDB and mmCIF format descriptions on this issue. For example the PDB documentation says that the ATOM record contains the occupancy (where this is defined in the CIF/mmCIF documentation). If it had intended that it should contain multiplicity*occupancy instead then presumably it would have said so. Cheers -- Ian On Wed, Dec 15, 2010 at 4:01 PM, herman.schreu...@sanofi-aventis.com wrote: Dear Ian, In my view, the confusion arises by NOT including the multiplicity into the occupancy. If we make the gedanken experiment and look at a range of crystal structures with a rotationally disordered water molecule near a symmetry axis (they do exist!) then as long as the water molecule is sufficiently far from the axis, it is clear that the occupancy should be 1/2 or 1/3 or whatever is the multiplicity. However, as the molecule approaches the axis at a certain moment at a certain treshold set by the programmer of the refinement program, the molecule suddenly becomes special and the occupancy is set to 1.0. So depending on rounding errors, different thresholds etc. different programs may make different decisions on whether a water is special or not. For me, this is confusing. Best regards, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle Sent: Wednesday, December 15, 2010 3:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms Dear George I notice that the Oxford CRYSTALS program, which is what I used when I did small-molecule crystallography and which is still quite popular among the small-molecule people (maybe not as much as Shel-X!), uses the CIF convention: OCC= This parameter defines the site occupancy EXCLUDING special position effects (i.e. is the 'chemical occupancy'). The default is 1.0. Special position effects are computed by CRYSTALS and multiplied onto this parameter. (from http://www.xtl.ox.ac.uk/crystalsmanual-atomic.html ) Also the mmCIF specification on this is the same CIF one (hardly surprising I guess since it's derived from it): _atom_site.occupancy The fraction of the atom type present at this site. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site. (from http://mmcif.pdb.org/dictionaries/mmcif_std.dic/Items/_atom_site.occupancy.html ) which doesn't say so
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms Dear George I notice that the Oxford CRYSTALS program, which is what I used when I did small-molecule crystallography and which is still quite popular among the small-molecule people (maybe not as much as Shel-X!), uses the CIF convention: OCC= This parameter defines the site occupancy EXCLUDING special position effects (i.e. is the 'chemical occupancy'). The default is 1.0. Special position effects are computed by CRYSTALS and multiplied onto this parameter. (from http://www.xtl.ox.ac.uk/crystalsmanual-atomic.html ) Also the mmCIF specification on this is the same CIF one (hardly surprising I guess since it's derived from it): _atom_site.occupancy The fraction of the atom type present at this site. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site. (from http://mmcif.pdb.org/dictionaries/mmcif_std.dic/Items/_atom_site.occupancy.html ) which doesn't say so specifically, but it's implied since if the multiplicity is included then the maximum value of the sum is the multiplicity, not 1.0. So there's a real possibility of user - and programmer - confusion here! I must say that until I looked at the 4INS file I had assumed that the PDB occupancy was what it claimed to be, i.e. the real 'chemical' occupancy not the multiplicity-fudged one. Cheers -- Ian On Wed, Dec 15, 2010 at 1:53 PM, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: Dear Ian, Yes. Once an atom has been identified as on a special position because it is within a specied tolerance, SHELXL applies the appropriate contraints to both the coordinates and the Uij so there is no danger of the atom wandering off the special position. Usually, when an atom it very close to a special position but not actually on it, it is part of a disordered solvent molecule and will be prevented from misbehaving by distance and Uij restraints imposed by the user; in such a case the user usually also switches off the special position check for that disordered molecule (SPEC -1) to avoid atoms being idealized onto the special position by the program. For solvent molecules disordered on special positions it is also necessary to ignore symmetry equivalent atoms when generating idealized hydrogen atoms etc. (PART -N in SHELXL). This is all routine practice in small molecule crystallography. I agree that the use of orthogonal rather than crystal coordinates can obscur the situation, e.g. for an atom on a threefold axis. Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 15 Dec 2010, Ian Tickle wrote: Dear George I would say that an atom has fractional occupancy (but unit multiplicity) unless it's exactly on the special position (though I can foresee problems with rounding of decimal places for an atom say at x=1/3), so that effectively once the atom is fixed exactly on the s.p. the symmetry copies coalesce into a single atom with unit occupancy (but fractional multiplicity). This is at least one advantage of having co-ordinates stored as fractional - it would probably be more tricky with orthogonalised co-ordinates. Presumably once an input atom has satisfied the condition of being 'sufficiently close' to a s.p. to be considered as 'on' the s.p. then the constraints fix the co-ordinates exactly on the special position and henceforth it's forcibly prevented from moving off it? In any case if an atom is very close to its symmetry copy you are going to have matrix conditioning problems for the co-ordinates perpendicular to the axis of symmetry (or mirror plane), so then you have no choice but to disallow co-ordinate shifts of the atom which would take it off the special position? Cheers -- Ian On Wed, Dec 15, 2010 at 11:42 AM, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: Dear Ian, Of course I could convert the occupancy on reading the atom in and convert it back agains on reading it out. This is not quite so trivial as it sounds because I need to set a threshold as to how close the atom has to be to a special position to be treated as special, and take care that rounding errors have the same effect on input and output and that the coordinates have not moved in or out of the special zone in the meantime. As it stands in SHELX, an atom that is near to a twofold will have an occupancy of 0.5 whether it is disordered close to a special position or whether it is really special, so this is never a problem. SHELXL is mainly used for small molecules that frequently have atoms on speical positions, and disordered solvent molecules approximately on sppecial positions are also very common (for example
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
decisions on whether a water is special or not. For me, this is confusing. Best regards, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle Sent: Wednesday, December 15, 2010 3:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms Dear George I notice that the Oxford CRYSTALS program, which is what I used when I did small-molecule crystallography and which is still quite popular among the small-molecule people (maybe not as much as Shel-X!), uses the CIF convention: OCC= This parameter defines the site occupancy EXCLUDING special position effects (i.e. is the 'chemical occupancy'). The default is 1.0. Special position effects are computed by CRYSTALS and multiplied onto this parameter. (from http://www.xtl.ox.ac.uk/crystalsmanual-atomic.html ) Also the mmCIF specification on this is the same CIF one (hardly surprising I guess since it's derived from it): _atom_site.occupancy The fraction of the atom type present at this site. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site. (from http://mmcif.pdb.org/dictionaries/mmcif_std.dic/Items/_atom_site.occupancy.html ) which doesn't say so specifically, but it's implied since if the multiplicity is included then the maximum value of the sum is the multiplicity, not 1.0. So there's a real possibility of user - and programmer - confusion here! I must say that until I looked at the 4INS file I had assumed that the PDB occupancy was what it claimed to be, i.e. the real 'chemical' occupancy not the multiplicity-fudged one. Cheers -- Ian On Wed, Dec 15, 2010 at 1:53 PM, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: Dear Ian, Yes. Once an atom has been identified as on a special position because it is within a specied tolerance, SHELXL applies the appropriate contraints to both the coordinates and the Uij so there is no danger of the atom wandering off the special position. Usually, when an atom it very close to a special position but not actually on it, it is part of a disordered solvent molecule and will be prevented from misbehaving by distance and Uij restraints imposed by the user; in such a case the user usually also switches off the special position check for that disordered molecule (SPEC -1) to avoid atoms being idealized onto the special position by the program. For solvent molecules disordered on special positions it is also necessary to ignore symmetry equivalent atoms when generating idealized hydrogen atoms etc. (PART -N in SHELXL). This is all routine practice in small molecule crystallography. I agree that the use of orthogonal rather than crystal coordinates can obscur the situation, e.g. for an atom on a threefold axis. Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 15 Dec 2010, Ian Tickle wrote: Dear George I would say that an atom has fractional occupancy (but unit multiplicity) unless it's exactly on the special position (though I can foresee problems with rounding of decimal places for an atom say at x=1/3), so that effectively once the atom is fixed exactly on the s.p. the symmetry copies coalesce into a single atom with unit occupancy (but fractional multiplicity). This is at least one advantage of having co-ordinates stored as fractional - it would probably be more tricky with orthogonalised co-ordinates. Presumably once an input atom has satisfied the condition of being 'sufficiently close' to a s.p. to be considered as 'on' the s.p. then the constraints fix the co-ordinates exactly on the special position and henceforth it's forcibly prevented from moving off it? In any case if an atom is very close to its symmetry copy you are going to have matrix conditioning problems for the co-ordinates perpendicular to the axis of symmetry (or mirror plane), so then you have no choice but to disallow co-ordinate shifts of the atom which would take it off the special position? Cheers -- Ian On Wed, Dec 15, 2010 at 11:42 AM, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: Dear Ian, Of course I could convert the occupancy on reading the atom in and convert it back agains on reading it out. This is not quite so trivial as it sounds because I need to set a threshold as to how close the atom has to be to a special position to be treated as special, and take care that rounding errors have the same effect on input and output and that the coordinates have not moved in or out of the special zone in the meantime. As it stands
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Personally I find it disturbing to have the occupancy of B 31 set to 0.33 and that of D 31 set to 1.00 simply because of an insignificant shift in the position of the atom. Dale Tronrud H2O on or near a 3-fold must be disordered because obviously H2O only has 2-fold symmetry. It could of course be H3O+ which does have 3-fold symmetry and which therefore could be ordered. We can therefore choose between 2 possibilities: either it's ordered _on_ the 3-fold with site occupancy=1 (site multiplicity=1/3), or it's disordered _off_ the 3-fold with occupancy=1/3 (site multiplicity=1). I completely agree with you that the deviation of 'B 31' from the special position is plainly not significant: certainly there is no way such a small shift could be detected (or indeed refined!), so we may as well assume that its symmetry does allow it to sit on the s.p.. So like 'D 31' it should be set exactly on the s.p. and its occupancy set to 1. Disorder should be indicated by fractional occupancy only if the molecular symmetry clearly demands it (and in this case it's not clear), or the disorder is observable in the map and it's possible to sensibly refine it as disordered. The difficulty comes if a refinement program refines an atom near the 3-fold exactly onto the 3-fold, and this atom either must be disordered because of molecular symmetry as in the H2O case, or the disorder is observable in the map. An atom which is just off a 3-fold would be likely to generate singularities in the matrix if you tried to refine its x y co-ordinates anyway (you could of course fix them manually and not refine them, but then how do you decide what values to fix them at?). In that case it would be better to fix the atom exactly on the 3-fold and set the occupancy to 1, since then it can still be considered in reality to be the sum of 3 exactly superposed disordered atoms each with occupancy 1/3, which must however be treated in the refinement as a single atom with occupancy=1. Cheers -- Ian
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Of course metal ions, So4 etc often lie on special positions - the insulin hexamer is generated around Zn atoms on the 3-fold axis. Eleanor On 12/09/2010 01:29 PM, Ian Tickle wrote: Of course it's always possible for an asymmetric molecule (or part of a molecule, such as a side-chain) to lie on or near a symmetry axis, provided it's rotationally disordered with occupancy 0.5 (assuming a 2-fold). In other words half the molecules are randomly distributed over half of the asymmetric units in one orientation and the other half are in the other a.u.s in the symmetry-related orientation, so the copies never clash. The occupancy must be near 0.5 because if it deviated much from that you would start to see breakdown of the symmetry of the diffraction pattern (with higher Rmerge etc), and you would likely conclude that the space group is actually a sub-group of the original one without the symmetry axis. Obviously it will depend on the quality of the data, the resolution and the scattering power of the disorder part whether you are able in practice to detect such a breakdown of symmetry. The question here though is whether an atom (say the CG of the ASP) of the rotationally disordered molecule/part-molecule in such a situation necessarily lies _on_ a special position. It would be pure coincidence if it did, for the simple reason that there's absolutely no reason why it should do so. In other words, because it has occupancy 0.5 (obviously it must have the same occupancy as the atoms that it's covalently bonded to, assuming there's no other disorder present), it must be disordered and so doesn't have to obey the bulk symmetry. In fact, it would be equally 'happy' slightly displaced from the special position. There will be no significant minimum in the internal energy of the system for a disordered atom on a special position, because the reason it's disordered is that there are no strong interactions with the surrounding atoms, which would favour one possible orientation over the other. This is quite different from the original question posed by Gloria where (I assume) we have a molecule on a special position where there is no rotational disorder (it may still have occupancy disorder, i.e. it may only be present in a fraction of the a.u.s). Here clearly the occupancy may be 0.5 for a 2-fold and so no clashes with the symmetry mate(s) are permitted (assuming of course that the space group is correct!). In this case the molecule itself must therefore possess at least the symmetry of the special position, e.g. H2O or SO4 for a 2-fold, as Ralf says. Being ordered (or at least not as disordered) such a molecule must have strong interactions with its neighbours, so any shift off the special position would likely result in an increase in internal energy. Cheers -- Ian On Thu, Dec 9, 2010 at 11:26 AM,herman.schreu...@sanofi-aventis.com wrote: Hi Ralf Gloria, It is of course all a matter of definition, but it happens now and again that an asymmetric ligand is lying on top of a twofold axis. This is usually modeled by fitting the ligand in two orientations at half occupancy. In one of the proteins I am working on there is the carboxylic acid group of an Asp sitting on a 2-fold axis. I have modeled the Asp with 2 alternative conformations: in conformation A, the Asp side chain would clash with itself over the 2-fold axis, thus if one protein molecule has the Asp in conformation A, the twofold related protein molecule must have the Asp in conformation B (or some other conformation). I do not know whether you would call this a Wyckoff position, but side chains of proteins do sit on top of crystallographic symmetry axes. Best, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ralf W. Grosse-Kunstleve Sent: Thursday, December 09, 2010 3:47 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms Hi Gloria, My hobby is space group symmetry. My interest phenix development. so I can't imagine a protein crystallographer would ever need to apply the modulation function to a protein atom that happened to be on one. That's true. Protein residues don't have internal symmetry, therefore they are not compatible with crystallographic special positions. (Wyckoff positions are enumerations of classes of special positions.) In the PDB molecules with internal symmetry are really rare, except for H2O and SO4. But these contribute so little to the total scattering that it isn't important to handle them in a special way. So Wyckoff positions remain foreign in the macromolecular context. Ralf - Original Message From: Gloria Borgstahlgborgst...@gmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Wed, December 8, 2010 12:16:54 PM Subject: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms I've gotten some interesting responses, that I will summarize for the group later, but I thought I should clarify why
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Dear Ian, what I see are two minima, symmetrically aranged around the special position. One minimum is closer the molecule A, the other closer to the symmetry-related molecule B and waters will randomly be either in minimum A, or in minimum B. Crystal packing prevents the water from moving the protein molecules such that it can make perfect hydrogen bonds with both protein at the same time. Cheers, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle Sent: Thursday, December 09, 2010 6:36 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms The forces acting on an atom at a special position must have the same symmetry on average as the special position, so the atom will be in equilibrium, and there will at first sight be no net force (i.e. zero energy gradient) to push the atom away from the special position. However there are 2 solutions to this: metastable equilibrium where the energy is a maximum, and stable equilibrium where it's a minimum. In the metastable case it will be like a pencil balanced on its point where a small disturbance, such as from random thermal motion, will be sufficient to move it off the special position to an asymmetric position of lower energy thus breaking the symmetry, and of course the initial displacement will be completely random leading to the disorder you observe. In the case of stable equilibrium the atom will simply respond to the disturbance by executing random thermal motion centred on the special position. Which case you see in practice will obviously depend on the precise arrangement of forces acting on the atom. Cheers -- Ian On Thu, Dec 9, 2010 at 4:12 PM, herman.schreu...@sanofi-aventis.com wrote: Even with the famous waters on true Wyckoff positions, I usually observe an elongated or even partly split density, suggesting that the water is disordered, being sometimes closer to one monomer, sometimes closer to the symmetry-related monomer. Since the position of proteins in a crystal is in general not determined by a single water-mediated hydrogen bond, the water will in general not be able to make perfect hydrogen bonds to both symmetry-related monomers at the same time. I think therefore that even waters should generally be considered to be disordered and only in exceptional cases will occupy true Wyckoff positions. Best, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle Sent: Thursday, December 09, 2010 3:35 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms cases out there (and so far I have heard of a disulfide bond on a 2-fold connecting two homodimers). I'm slightly puzzled by this example. If the S-S bond is on the special position, then the rest of the molecule can't have 2-fold symmetry, so would have to be rotationally disordered with occupancy = 0.5 to avoid clashing with its symmetry mate: * X -- C * \ * S | S * \ * C -- X * where the *'s indicate the 2-fold axis (i.e. vertically in the plane of the page). In this case, for the reasons I gave in my previous post there's no reason for the disordered S atoms to be exactly on the 2-fold; it would be pure coincidence if they were. If you mean instead that the 2-fold is _perpendicular_ to the S-S bond (i.e. coming straight out of the page in the diagram), the molecule does indeed have 2-fold symmetry and can be ordered with occupancy = 1, but then the S atoms are not on special positions, so this would not be an example of protein atoms _on_ a special position. One could imagine an example, say where the same side-chain on each monomer is cross-linked (e.g. LYS with glutaraldehyde), forming the homodimer: X -- C -- N = C -- C -- C -- C -- C = N -- C -- X Here the central C atom could be on a 2-fold (i.e. axis perpendicular to the page) special position without rotational disorder. I've no idea whether such a structure actually exists! Cheers -- Ian
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Does one regard the metal atom in a metalloprotein as being part of the protein? If so, a shared metal could occupy a special position in a dimer for example. In Acta Cryst. (2008). D64, 257-263 Metals in proteins: correlation between the metal-ion type, coordination number and the amino-acid residues involved in the coordination I. Dokmanic, M. Sikic and S. Tomic ( http://scripts.iucr.org/cgi-bin/paper?S090744490706595X ) it says there are 25 cases of metal atoms in special positions. Also Acta Cryst. (2002). D58, 29-38 The 2.6 Å resolution structure of Rhodobacter capsulatus bacterioferritin with metal-free dinuclear site and heme iron in a crystallographic `special position' D. Cobessi, L.-S. Huang, M. Ban, N. G. Pon, F. Daldal and E. A. Berry ( http://scripts.iucr.org/cgi-bin/paper?S0907444901017267 ) though the 'special position' is justifiably in quotation marks in this example as disorder is present. Colin
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Colin Nave wrote: .. Also Acta Cryst. (2002). D58, 29-38 The 2.6 Å resolution structure of Rhodobacter capsulatus bacterioferritin with metal-free dinuclear site and heme iron in a crystallographic `special position' D. Cobessi, L.-S. Huang, M. Ban, N. G. Pon, F. Daldal and E. A. Berry ( http://scripts.iucr.org/cgi-bin/paper?S0907444901017267 ) though the 'special position' is justifiably in quotation marks in this example as disorder is present. Colin Yes, this was an example of Ian's rotationally disordered with occupancy 0.5 possibility. Heme has a pseudo-two-fold axis passing through the plane of the ring, which is violated only by the position of the methyl and vinyl substituents on either side: rotating through the pseudo-2-fold superimposes methyl on vinyl and vice versa on either side. This axis was sitting on a crystallographic 2-fold. We did trial refinements in a lower symmetry space group so the axis became NCS, and we refined with the heme in one orientation or the other. In either case, difference maps showed positive density for another atom beyond the methyl, and negative density on CB of the vinyl. So we concluded the heme was oriented both ways, and in the average satisfied the symmetry of the higher space group. Putting it with half occupancy in the asymmetric unit allowed crystallographic symmetry to generate the rotated half. Looking at it from the heme's point of view, this makes sense. Its environment is perfectly symmetrical, so there is no way for it to choose one orientation over the other and both are adopted equally. (The two-fold is intrinsic to the biological unit, not generated by crystal packing). I think the heme iron was right on the crystallographic axis. When refining in the lower space-group with two .5 occupancy non-interacting hemes, the propionates (which actually satisfy the covalent symmetry) in the two hemes took on different conformations, not sure if this was significant or just taking liberties where freedom is given. eab
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Good point Colin! 2-Zn insulin is of course a classic example of this, where the two independent Zn2+ ions both sit on the crystallographic 3-fold in R3. It doesn't matter whether you count the metal ion as part of the protein or not: if I understand Gloria's original question correctly, all that matters is that the atom/ion is present in the crystal structure. In fact here are some extracts from the PDB entry (4INS): REMARK 375 ZNZN B 31 LIES ON A SPECIAL POSITION. REMARK 375 ZNZN D 31 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 251 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 44 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 134 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 215 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 269 LIES ON A SPECIAL POSITION. HETATM 835 ZNZN B 31 -0.002 -0.004 7.891 0.33 10.40 ZN HETATM 836 ZNZN D 31 0.000 0.000 -8.039 0.33 11.00 ZN HETATM 885 O HOH B 251 -0.023 -0.033 11.206 0.33 21.05 O etc Hmmm - but shouldn't the occupancy of the Zn be 1.00 if it's on the special position (assuming it's not disordered), though the first Zn above and the water do appear to be disordered since they're not actually on the special position. Fractional occupancy always implies some kind of disorder: occupancy = 1/3 of an atom on a special position would imply occupancy disorder, i.e. it's randomly present in only 1/3 of the unit cells. -- Ian On Fri, Dec 10, 2010 at 1:11 PM, Colin Nave colin.n...@diamond.ac.uk wrote: Does one regard the metal atom in a metalloprotein as being part of the protein? If so, a shared metal could occupy a special position in a dimer for example. In Acta Cryst. (2008). D64, 257-263 Metals in proteins: correlation between the metal-ion type, coordination number and the amino-acid residues involved in the coordination I. Dokmanic, M. Sikic and S. Tomic ( http://scripts.iucr.org/cgi-bin/paper?S090744490706595X ) it says there are 25 cases of metal atoms in special positions. Also Acta Cryst. (2002). D58, 29-38 The 2.6 Å resolution structure of Rhodobacter capsulatus bacterioferritin with metal-free dinuclear site and heme iron in a crystallographic `special position' D. Cobessi, L.-S. Huang, M. Ban, N. G. Pon, F. Daldal and E. A. Berry ( http://scripts.iucr.org/cgi-bin/paper?S0907444901017267 ) though the 'special position' is justifiably in quotation marks in this example as disorder is present. Colin
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
The proper occupancy for an atom on a special position depends on how one defines the meaning of the number in that column. In the past, refinement programs, at least I know mine did, simply expanded all atoms in the coordinate file by the symmetry operators to determine the contents of the unit cell. With that operation the occupancy of the atoms on special positions had to be reduced. It is certainly true that there are 1/3 the number of atoms in the unit cell represented by ZN D 31 than, for example, the CA of residue 50. Most modern refinement programs try to handle this automatically, since users proved unreliable at detecting this condition and modifying their coordinate files. They use the interpretation that the site is fully occupied but there are only 1/3 the number of these sites than sites at general positions. Personally I find it disturbing to have the occupancy of B 31 set to 0.33 and that of D 31 set to 1.00 simply because of an insignificant shift in the position of the atom. Dale Tronrud On 12/10/10 13:53, Ian Tickle wrote: Good point Colin! 2-Zn insulin is of course a classic example of this, where the two independent Zn2+ ions both sit on the crystallographic 3-fold in R3. It doesn't matter whether you count the metal ion as part of the protein or not: if I understand Gloria's original question correctly, all that matters is that the atom/ion is present in the crystal structure. In fact here are some extracts from the PDB entry (4INS): REMARK 375 ZNZN B 31 LIES ON A SPECIAL POSITION. REMARK 375 ZNZN D 31 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 251 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 44 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 134 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 215 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 269 LIES ON A SPECIAL POSITION. HETATM 835 ZNZN B 31 -0.002 -0.004 7.891 0.33 10.40 ZN HETATM 836 ZNZN D 31 0.000 0.000 -8.039 0.33 11.00 ZN HETATM 885 O HOH B 251 -0.023 -0.033 11.206 0.33 21.05 O etc Hmmm - but shouldn't the occupancy of the Zn be 1.00 if it's on the special position (assuming it's not disordered), though the first Zn above and the water do appear to be disordered since they're not actually on the special position. Fractional occupancy always implies some kind of disorder: occupancy = 1/3 of an atom on a special position would imply occupancy disorder, i.e. it's randomly present in only 1/3 of the unit cells. -- Ian On Fri, Dec 10, 2010 at 1:11 PM, Colin Nave colin.n...@diamond.ac.uk wrote: Does one regard the metal atom in a metalloprotein as being part of the protein? If so, a shared metal could occupy a special position in a dimer for example. In Acta Cryst. (2008). D64, 257-263 Metals in proteins: correlation between the metal-ion type, coordination number and the amino-acid residues involved in the coordination I. Dokmanic, M. Sikic and S. Tomic ( http://scripts.iucr.org/cgi-bin/paper?S090744490706595X ) it says there are 25 cases of metal atoms in special positions. Also Acta Cryst. (2002). D58, 29-38 The 2.6 Å resolution structure of Rhodobacter capsulatus bacterioferritin with metal-free dinuclear site and heme iron in a crystallographic `special position' D. Cobessi, L.-S. Huang, M. Ban, N. G. Pon, F. Daldal and E. A. Berry ( http://scripts.iucr.org/cgi-bin/paper?S0907444901017267 ) though the 'special position' is justifiably in quotation marks in this example as disorder is present. Colin
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
No that surely can't be right. Application of a symmetry operator to a point on a special position which is unchanged by the operator doesn't generate a symmetry copy of the point, because there is no symmetry copy of such a point! For general Wyckoff positions it does, for sure. If you look at the entry for R3 (hexagonal or rhombohedral setting, it doesn't matter which) on the Wyckoff position website I indicated earlier, you'll see a column labelled 'multiplicity' which is 3 for the general position and 1 for the special position. This means that the symmetry operator generates 3 symmetry copies of a general position (including the original), but only 1 copy (i.e. only the original) of the special positions on the 3-fold. That's precisely why such points are called special positions - i.e. you have to treat them specially! If what you describe is what the refinement program or whatever is doing then it would imply there's a programming error, i.e. the program is not treating special positions as special, it's treating them instead as general positions. As I said whenever you see fractional occupancy reported it should imply some kind of disorder, i.e. the atom exists on that site in only the indicated fraction of the unit cells in the lattice. -- Ian On Fri, Dec 10, 2010 at 10:02 PM, Sue Roberts s...@email.arizona.edu wrote: Hi Ian No disorder is involved. The occupancy of an (fully occupied) atom on an n-fold rotation axis is 1/n If a two-fold, 1/2 If a three-fold, 1/3 When you sum over all the atoms in the unit cell, application of the symmetry operations to atoms lying on the rotation axis generates atoms with unchanged coordinates. Hence to generate a fully occupied atom on a n-fold symmetry axis, the original occupancy has to be 1/n. Sue On Dec 10, 2010, at 2:53 PM, Ian Tickle wrote: Good point Colin! 2-Zn insulin is of course a classic example of this, where the two independent Zn2+ ions both sit on the crystallographic 3-fold in R3. It doesn't matter whether you count the metal ion as part of the protein or not: if I understand Gloria's original question correctly, all that matters is that the atom/ion is present in the crystal structure. In fact here are some extracts from the PDB entry (4INS): REMARK 375 ZN ZN B 31 LIES ON A SPECIAL POSITION. REMARK 375 ZN ZN D 31 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 251 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 44 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 134 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 215 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 269 LIES ON A SPECIAL POSITION. HETATM 835 ZN ZN B 31 -0.002 -0.004 7.891 0.33 10.40 ZN HETATM 836 ZN ZN D 31 0.000 0.000 -8.039 0.33 11.00 ZN HETATM 885 O HOH B 251 -0.023 -0.033 11.206 0.33 21.05 O etc Hmmm - but shouldn't the occupancy of the Zn be 1.00 if it's on the special position (assuming it's not disordered), though the first Zn above and the water do appear to be disordered since they're not actually on the special position. Fractional occupancy always implies some kind of disorder: occupancy = 1/3 of an atom on a special position would imply occupancy disorder, i.e. it's randomly present in only 1/3 of the unit cells. -- Ian On Fri, Dec 10, 2010 at 1:11 PM, Colin Nave colin.n...@diamond.ac.uk wrote: Does one regard the metal atom in a metalloprotein as being part of the protein? If so, a shared metal could occupy a special position in a dimer for example. In Acta Cryst. (2008). D64, 257-263 Metals in proteins: correlation between the metal-ion type, coordination number and the amino-acid residues involved in the coordination I. Dokmanic, M. Sikic and S. Tomic ( http://scripts.iucr.org/cgi-bin/paper?S090744490706595X ) it says there are 25 cases of metal atoms in special positions. Also Acta Cryst. (2002). D58, 29-38 The 2.6 Å resolution structure of Rhodobacter capsulatus bacterioferritin with metal-free dinuclear site and heme iron in a crystallographic `special position' D. Cobessi, L.-S. Huang, M. Ban, N. G. Pon, F. Daldal and E. A. Berry ( http://scripts.iucr.org/cgi-bin/paper?S0907444901017267 ) though the 'special position' is justifiably in quotation marks in this example as disorder is present. Colin Dr. Sue A. Roberts Dept. of Chemistry and Biochemistry University of Arizona 1041 E. Lowell St., Tucson, AZ 85721 Phone: 520 621 8171 s...@email.arizona.edu http://www.biochem.arizona.edu/xray
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
On Fri, 2010-12-10 at 22:40 +, Ian Tickle wrote: Application of a symmetry operator to a point on a special position which is unchanged by the operator doesn't generate a symmetry copy of the point, because there is no symmetry copy of such a point! Why not? Symmetry-related copy may be considered just that - copy produced by a symmetry operator. What advantage do you gain by restricting it to only those that result in physically different point? There is one excellent point that you made in some past exchanges - that deposited structures are mathematical models and they do not always have to make strict physical sense. This seems to be just such case - one does not have three zincs in that spot with each being gone two thirds of the time, but making the model physically meaningful would require perhaps dropping to P1 and implementing NCS to enforce crystal symmetry. So compromising on the physical meaning of the atom record seems like a small price to pay. This feels odd - I seem to be arguing your side :) Cheers, Ed. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
An excerpt from the Shelx manual (which I think is a good reference for proper handling of atoms on special positions in refinement of small or large molecules): 4.3 Special position constraints Constraints for the coordinates and anisotropic displacement parameters for atoms on special positions are generated automatically by the program for ALL special positions in ALL space groups, in conventional settings or otherwise. For upwards compatibility with SHELX-76, free variables may still be used for this, but it is better to leave it to the program. If the occupancy is not input, the program will fix it at the appropriate value for a special position. If the user applies (correct or incorrect) special position constraints using free variables etc., the program assumes this has been done with intent and reports but does not apply the correct constraints; accidental application of wrong special position constraints is one of the easiest ways to cause a refinement to 'blow up' ! Also, please check the book of Shmueli and Weiss, Introduction to crystallographic statistics p. 5, last paragraph and the next page where a rigorous treatment of of contribution to the structure factor of atoms in general and special positions in the unit cell is given (eq. 1.2.10). Thus, occupancy of an atom on a 3-fold would be 1/3, 1/2 on a 2-fold, 1/4 on a 4-fold and so forth. Cheers, Boaz - Original Message - From: Ian Tickle ianj...@gmail.com Date: Saturday, December 11, 2010 0:41 Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms To: CCP4BB@JISCMAIL.AC.UK No that surely can't be right. Application of a symmetry operator to a point on a special position which is unchanged by the operator doesn't generate a symmetry copy of the point, because there is no symmetry copy of such a point! For general Wyckoff positions it does, for sure. If you look at the entry for R3 (hexagonal or rhombohedralsetting, it doesn't matter which) on the Wyckoff position website I indicated earlier, you'll see a column labelled 'multiplicity' which is 3 for the general position and 1 for the special position. This means that the symmetry operator generates 3 symmetry copies of a general position (including the original), but only 1 copy (i.e. only the original) of the special positions on the 3-fold. That's precisely why such points are called special positions - i.e. you have to treat them specially! If what you describe is what the refinement program or whatever is doing then it would imply there's a programming error, i.e. the program is not treating special positions as special, it's treating them instead as general positions. As I said whenever you see fractional occupancy reported it should imply some kind of disorder, i.e. the atom exists on that site in only the indicated fraction of the unit cells in the lattice. -- Ian On Fri, Dec 10, 2010 at 10:02 PM, Sue Roberts s...@email.arizona.edu wrote: Hi Ian No disorder is involved. The occupancy of an (fully occupied) atom on an n-fold rotation axis is 1/n If a two-fold, 1/2 If a three-fold, 1/3 When you sum over all the atoms in the unit cell, application of the symmetry operations to atoms lying on the rotation axis generates atoms with unchanged coordinates. Hence to generate a fully occupied atom on a n-fold symmetry axis, the original occupancy has to be 1/n. Sue On Dec 10, 2010, at 2:53 PM, Ian Tickle wrote: Good point Colin! 2-Zn insulin is of course a classic example of this, where the two independent Zn2+ ions both sit on the crystallographic 3-fold in R3. It doesn't matter whether you count the metal ion as part of the protein or not: if I understand Gloria's original question correctly, all that matters is that the atom/ion is present in the crystal structure. In fact here are some extracts from the PDB entry (4INS): REMARK 375 ZN ZN B 31 LIES ON A SPECIAL POSITION. REMARK 375 ZN ZN D 31 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 251 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 44 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 134 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 215 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 269 LIES ON A SPECIAL POSITION. HETATM 835 ZN ZN B 31 -0.002 -0.004 7.891 0.33 10.40 ZN HETATM 836 ZN ZN D 31 0.000 0.000 -8.039 0.33 11.00 ZN HETATM 885 O HOH B 251 -0.023 -0.033 11.206 0.33 21.05 O etc Hmmm - but shouldn't the occupancy of the Zn be 1.00 if it's on the special position (assuming it's not disordered), though the first Zn above and the water do appear to be disordered since they're not actually on the special position. Fractional occupancy always implies some kind of disorder: occupancy = 1/3 of an atom on a special
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
SHELXL also expects that the occupancy of a fully occupied atom on a threefold axis should be set at 1/3, and will generate this automatically if necessary. It will also generate automatically the necessary constraints for the x, y and z parameters (and for the Uij if the atom is anisotropic). It is essential that this is done correctly if a full-matrix refinement is being performed (e.g. to get esd estimates), otherwise the refinement can explode. The user may change or switch off the tolerance for detecting whether an atom is on a special position (with the SPEC instruction). Setting the occupancy to a fraction avoided a complicated IF construction inside a loop and 35 years ago computers were so slow! I can't change it now because I have to preserve upwards compatibility. Unfortunately the CIF committee decided to use the other definition (i.e. the Zn on the threefold axis has an occupancy of 1.0) and this has caused considerable confusion in the small molecule world ever since; atoms are frequently encountered on special positions in inorganic and mineral structures. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Fri, 10 Dec 2010, Ed Pozharski wrote: On Fri, 2010-12-10 at 21:53 +, Ian Tickle wrote: Hmmm - but shouldn't the occupancy of the Zn be 1.00 if it's on the special position Shouldn't 1/3 be better for programming purposes? If you set occupancy to 1.0, then you should specify that symmetry operators do not apply for these atoms, making Fc calculation a bit more cumbersome. If definition of the asu content is you get full content of the unit cell after applying symmetry operators, then occupancy *must* be 1/3, right? The first zinc and the water are on special position, but because they are not excluded from positional refinement (perhaps they should be), they will drift a bit. CNS has distance cutoff for treating atoms as special positions, if it jumps over the limit during, say, simulated annealing, it will cause problems. Perhaps PROLSQ did something similar. It is a good question if it's better to fix these in place or let them wobble a bit to account for some potential disorder. While I see the formal argument that it should be nailed to three-fold axes, it is also true that this is a mathematical compromise to simplify modeling that does not reflect physical reality (i.e. you don't have three partially occupied zinc ions, it's just one). In any event, given that this is a 1.5A structure, (-0.002 0.004) is statistically speaking the same as (0 0). Cheers, Ed. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
No disorder is involved. The occupancy of an (fully occupied) atom on an n-fold rotation axis is 1/n If a two-fold, 1/2 If a three-fold, 1/3 When you sum over all the atoms in the unit cell, application of the symmetry operations to atoms lying on the rotation axis generates atoms with unchanged coordinates. Hence to generate a fully occupied atom on a n-fold symmetry axis, the original occupancy has to be 1/n. I guess I have a few small points to add: 1) If a site on special position is not fully occupied, then the occupancy is q/n, where q is actual occupancy (for fully occupied site q=1). Since ATOM record in PDB file does not (directly) tell you whether the atom is on special position or not then it is not straightforward to know whether the occupancy of atom in question is not 1 due to disorder or due to symmetry. 2) Let's consider a hypothetical case... The maximal multiplicity of a spacial position in proteins is 24 (is that right? please correct if not), and the precision of the occupancy field in PDB file is only two digits, like: 1.00. Imagine you have a fair amount of very heavy atoms all seating at special positions with the multiplicity 24, and your structure is relatively small. Then what you will be forced to put in the PDB file is: 1/24 ~ 0.04 and not 0.042. I'm not sure if this rounding error is significant or not (and what is significant), but just to keep in mind another source of mismatch between reported and recomputed R-factors. 3) If I add an atom onto special position using Coot, will it set the occupancy as 1/n automatically or do I have to to edit the PDB file myself (and remember to do so)? (another room for an error) So, having said this, I tend to think that using occupancy 1 (and not 1/n) is a good thing. Pavel.
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Hi Ralf Gloria, It is of course all a matter of definition, but it happens now and again that an asymmetric ligand is lying on top of a twofold axis. This is usually modeled by fitting the ligand in two orientations at half occupancy. In one of the proteins I am working on there is the carboxylic acid group of an Asp sitting on a 2-fold axis. I have modeled the Asp with 2 alternative conformations: in conformation A, the Asp side chain would clash with itself over the 2-fold axis, thus if one protein molecule has the Asp in conformation A, the twofold related protein molecule must have the Asp in conformation B (or some other conformation). I do not know whether you would call this a Wyckoff position, but side chains of proteins do sit on top of crystallographic symmetry axes. Best, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ralf W. Grosse-Kunstleve Sent: Thursday, December 09, 2010 3:47 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms Hi Gloria, My hobby is space group symmetry. My interest phenix development. so I can't imagine a protein crystallographer would ever need to apply the modulation function to a protein atom that happened to be on one. That's true. Protein residues don't have internal symmetry, therefore they are not compatible with crystallographic special positions. (Wyckoff positions are enumerations of classes of special positions.) In the PDB molecules with internal symmetry are really rare, except for H2O and SO4. But these contribute so little to the total scattering that it isn't important to handle them in a special way. So Wyckoff positions remain foreign in the macromolecular context. Ralf - Original Message From: Gloria Borgstahl gborgst...@gmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Wed, December 8, 2010 12:16:54 PM Subject: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms I've gotten some interesting responses, that I will summarize for the group later, but I thought I should clarify why I asked. I was worrying about this because I have been working out the steps in how to determine the (3+1)D superspace group for a protein crystal. The last step listed in IT vol C chapter 9.8, is to consider any atoms that lie ON a Wyckoff position, and what restrictions this would apply to the modulation function that is refined for each atom. My first reaction, was Wyckoff positions? I vaguely remember those, my recollection from my experience was they were really cool, but were usually in the solvent, so I can't imagine a protein crystallographer would ever need to apply the modulation function to a protein atom that happened to be on one. But to a crystallographer working on a modulated mineral, it would happen all the time, I'll bet. So maybe this was one more thing that just didn't really apply to protein structures and lucky us we don't worry about this last step (just as I never did model that solvent water that was on one, back in the 90s). Then I thought, maybe I'm missing something, or there are special cases out there (and so far I have heard of a disulfide bond on a 2-fold connecting two homodimers). So I polled the collective knowledge of the great ccp4bb group. On Wed, Dec 8, 2010 at 10:57 AM, Gloria Borgstahl gborgst...@gmail.com wrote: My fellow crystallographers, I wanted to take a poll. How many of you have ever had a protein atom on a Wyckoff position (AKA a special position). What kind of molecules have you found at special positions (it would have to contain the symmetry of the special position, right?) I'm thinking it is impossible to have a protein atom at a special position or am I exposing my ignorance yet again... my experience is that only once I found an atom in a special position, it was a strange solvent molecule, that blew my mind for a while until I learned about special positions in crystallography. Looking forward to your responses, Gloria Gloria Borgstahl Eppley Institute for Cancer Research and Allied Diseases 987696 Nebraska Medical Center 10732A Lied Transplant Center Omaha, NE 68198-7696 http://sbl.unmc.edu Office (402) 559-8578 FAX (402) 559-3739 Professor Hobbies: Protein Crystallography, Cancer, Biochemistry, DNA Metabolism, Modulated Crystals, Crystal Perfection Interests: Manga, Led Zepplin, Cold Play, piano, BRAN, RAGBRAI, golf and lately superspace groups
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Of course it's always possible for an asymmetric molecule (or part of a molecule, such as a side-chain) to lie on or near a symmetry axis, provided it's rotationally disordered with occupancy 0.5 (assuming a 2-fold). In other words half the molecules are randomly distributed over half of the asymmetric units in one orientation and the other half are in the other a.u.s in the symmetry-related orientation, so the copies never clash. The occupancy must be near 0.5 because if it deviated much from that you would start to see breakdown of the symmetry of the diffraction pattern (with higher Rmerge etc), and you would likely conclude that the space group is actually a sub-group of the original one without the symmetry axis. Obviously it will depend on the quality of the data, the resolution and the scattering power of the disorder part whether you are able in practice to detect such a breakdown of symmetry. The question here though is whether an atom (say the CG of the ASP) of the rotationally disordered molecule/part-molecule in such a situation necessarily lies _on_ a special position. It would be pure coincidence if it did, for the simple reason that there's absolutely no reason why it should do so. In other words, because it has occupancy 0.5 (obviously it must have the same occupancy as the atoms that it's covalently bonded to, assuming there's no other disorder present), it must be disordered and so doesn't have to obey the bulk symmetry. In fact, it would be equally 'happy' slightly displaced from the special position. There will be no significant minimum in the internal energy of the system for a disordered atom on a special position, because the reason it's disordered is that there are no strong interactions with the surrounding atoms, which would favour one possible orientation over the other. This is quite different from the original question posed by Gloria where (I assume) we have a molecule on a special position where there is no rotational disorder (it may still have occupancy disorder, i.e. it may only be present in a fraction of the a.u.s). Here clearly the occupancy may be 0.5 for a 2-fold and so no clashes with the symmetry mate(s) are permitted (assuming of course that the space group is correct!). In this case the molecule itself must therefore possess at least the symmetry of the special position, e.g. H2O or SO4 for a 2-fold, as Ralf says. Being ordered (or at least not as disordered) such a molecule must have strong interactions with its neighbours, so any shift off the special position would likely result in an increase in internal energy. Cheers -- Ian On Thu, Dec 9, 2010 at 11:26 AM, herman.schreu...@sanofi-aventis.com wrote: Hi Ralf Gloria, It is of course all a matter of definition, but it happens now and again that an asymmetric ligand is lying on top of a twofold axis. This is usually modeled by fitting the ligand in two orientations at half occupancy. In one of the proteins I am working on there is the carboxylic acid group of an Asp sitting on a 2-fold axis. I have modeled the Asp with 2 alternative conformations: in conformation A, the Asp side chain would clash with itself over the 2-fold axis, thus if one protein molecule has the Asp in conformation A, the twofold related protein molecule must have the Asp in conformation B (or some other conformation). I do not know whether you would call this a Wyckoff position, but side chains of proteins do sit on top of crystallographic symmetry axes. Best, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ralf W. Grosse-Kunstleve Sent: Thursday, December 09, 2010 3:47 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms Hi Gloria, My hobby is space group symmetry. My interest phenix development. so I can't imagine a protein crystallographer would ever need to apply the modulation function to a protein atom that happened to be on one. That's true. Protein residues don't have internal symmetry, therefore they are not compatible with crystallographic special positions. (Wyckoff positions are enumerations of classes of special positions.) In the PDB molecules with internal symmetry are really rare, except for H2O and SO4. But these contribute so little to the total scattering that it isn't important to handle them in a special way. So Wyckoff positions remain foreign in the macromolecular context. Ralf - Original Message From: Gloria Borgstahl gborgst...@gmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Wed, December 8, 2010 12:16:54 PM Subject: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms I've gotten some interesting responses, that I will summarize for the group later, but I thought I should clarify why I asked. I was worrying about this because I have been working out the steps in how to determine the (3+1)D superspace group for a protein
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
cases out there (and so far I have heard of a disulfide bond on a 2-fold connecting two homodimers). I'm slightly puzzled by this example. If the S-S bond is on the special position, then the rest of the molecule can't have 2-fold symmetry, so would have to be rotationally disordered with occupancy = 0.5 to avoid clashing with its symmetry mate: * X -- C * \ * S | S * \ * C -- X * where the *'s indicate the 2-fold axis (i.e. vertically in the plane of the page). In this case, for the reasons I gave in my previous post there's no reason for the disordered S atoms to be exactly on the 2-fold; it would be pure coincidence if they were. If you mean instead that the 2-fold is _perpendicular_ to the S-S bond (i.e. coming straight out of the page in the diagram), the molecule does indeed have 2-fold symmetry and can be ordered with occupancy = 1, but then the S atoms are not on special positions, so this would not be an example of protein atoms _on_ a special position. One could imagine an example, say where the same side-chain on each monomer is cross-linked (e.g. LYS with glutaraldehyde), forming the homodimer: X -- C -- N = C -- C -- C -- C -- C = N -- C -- X Here the central C atom could be on a 2-fold (i.e. axis perpendicular to the page) special position without rotational disorder. I've no idea whether such a structure actually exists! Cheers -- Ian
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Even with the famous waters on true Wyckoff positions, I usually observe an elongated or even partly split density, suggesting that the water is disordered, being sometimes closer to one monomer, sometimes closer to the symmetry-related monomer. Since the position of proteins in a crystal is in general not determined by a single water-mediated hydrogen bond, the water will in general not be able to make perfect hydrogen bonds to both symmetry-related monomers at the same time. I think therefore that even waters should generally be considered to be disordered and only in exceptional cases will occupy true Wyckoff positions. Best, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle Sent: Thursday, December 09, 2010 3:35 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms cases out there (and so far I have heard of a disulfide bond on a 2-fold connecting two homodimers). I'm slightly puzzled by this example. If the S-S bond is on the special position, then the rest of the molecule can't have 2-fold symmetry, so would have to be rotationally disordered with occupancy = 0.5 to avoid clashing with its symmetry mate: * X -- C * \ * S | S * \ * C -- X * where the *'s indicate the 2-fold axis (i.e. vertically in the plane of the page). In this case, for the reasons I gave in my previous post there's no reason for the disordered S atoms to be exactly on the 2-fold; it would be pure coincidence if they were. If you mean instead that the 2-fold is _perpendicular_ to the S-S bond (i.e. coming straight out of the page in the diagram), the molecule does indeed have 2-fold symmetry and can be ordered with occupancy = 1, but then the S atoms are not on special positions, so this would not be an example of protein atoms _on_ a special position. One could imagine an example, say where the same side-chain on each monomer is cross-linked (e.g. LYS with glutaraldehyde), forming the homodimer: X -- C -- N = C -- C -- C -- C -- C = N -- C -- X Here the central C atom could be on a 2-fold (i.e. axis perpendicular to the page) special position without rotational disorder. I've no idea whether such a structure actually exists! Cheers -- Ian
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
The forces acting on an atom at a special position must have the same symmetry on average as the special position, so the atom will be in equilibrium, and there will at first sight be no net force (i.e. zero energy gradient) to push the atom away from the special position. However there are 2 solutions to this: metastable equilibrium where the energy is a maximum, and stable equilibrium where it's a minimum. In the metastable case it will be like a pencil balanced on its point where a small disturbance, such as from random thermal motion, will be sufficient to move it off the special position to an asymmetric position of lower energy thus breaking the symmetry, and of course the initial displacement will be completely random leading to the disorder you observe. In the case of stable equilibrium the atom will simply respond to the disturbance by executing random thermal motion centred on the special position. Which case you see in practice will obviously depend on the precise arrangement of forces acting on the atom. Cheers -- Ian On Thu, Dec 9, 2010 at 4:12 PM, herman.schreu...@sanofi-aventis.com wrote: Even with the famous waters on true Wyckoff positions, I usually observe an elongated or even partly split density, suggesting that the water is disordered, being sometimes closer to one monomer, sometimes closer to the symmetry-related monomer. Since the position of proteins in a crystal is in general not determined by a single water-mediated hydrogen bond, the water will in general not be able to make perfect hydrogen bonds to both symmetry-related monomers at the same time. I think therefore that even waters should generally be considered to be disordered and only in exceptional cases will occupy true Wyckoff positions. Best, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle Sent: Thursday, December 09, 2010 3:35 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms cases out there (and so far I have heard of a disulfide bond on a 2-fold connecting two homodimers). I'm slightly puzzled by this example. If the S-S bond is on the special position, then the rest of the molecule can't have 2-fold symmetry, so would have to be rotationally disordered with occupancy = 0.5 to avoid clashing with its symmetry mate: * X -- C * \ * S | S * \ * C -- X * where the *'s indicate the 2-fold axis (i.e. vertically in the plane of the page). In this case, for the reasons I gave in my previous post there's no reason for the disordered S atoms to be exactly on the 2-fold; it would be pure coincidence if they were. If you mean instead that the 2-fold is _perpendicular_ to the S-S bond (i.e. coming straight out of the page in the diagram), the molecule does indeed have 2-fold symmetry and can be ordered with occupancy = 1, but then the S atoms are not on special positions, so this would not be an example of protein atoms _on_ a special position. One could imagine an example, say where the same side-chain on each monomer is cross-linked (e.g. LYS with glutaraldehyde), forming the homodimer: X -- C -- N = C -- C -- C -- C -- C = N -- C -- X Here the central C atom could be on a 2-fold (i.e. axis perpendicular to the page) special position without rotational disorder. I've no idea whether such a structure actually exists! Cheers -- Ian
[ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
I've gotten some interesting responses, that I will summarize for the group later, but I thought I should clarify why I asked. I was worrying about this because I have been working out the steps in how to determine the (3+1)D superspace group for a protein crystal. The last step listed in IT vol C chapter 9.8, is to consider any atoms that lie ON a Wyckoff position, and what restrictions this would apply to the modulation function that is refined for each atom. My first reaction, was Wyckoff positions? I vaguely remember those, my recollection from my experience was they were really cool, but were usually in the solvent, so I can't imagine a protein crystallographer would ever need to apply the modulation function to a protein atom that happened to be on one. But to a crystallographer working on a modulated mineral, it would happen all the time, I'll bet. So maybe this was one more thing that just didn't really apply to protein structures and lucky us we don't worry about this last step (just as I never did model that solvent water that was on one, back in the 90s). Then I thought, maybe I'm missing something, or there are special cases out there (and so far I have heard of a disulfide bond on a 2-fold connecting two homodimers). So I polled the collective knowledge of the great ccp4bb group. On Wed, Dec 8, 2010 at 10:57 AM, Gloria Borgstahl gborgst...@gmail.com wrote: My fellow crystallographers, I wanted to take a poll. How many of you have ever had a protein atom on a Wyckoff position (AKA a special position). What kind of molecules have you found at special positions (it would have to contain the symmetry of the special position, right?) I'm thinking it is impossible to have a protein atom at a special position or am I exposing my ignorance yet again... my experience is that only once I found an atom in a special position, it was a strange solvent molecule, that blew my mind for a while until I learned about special positions in crystallography. Looking forward to your responses, Gloria Gloria Borgstahl Eppley Institute for Cancer Research and Allied Diseases 987696 Nebraska Medical Center 10732A Lied Transplant Center Omaha, NE 68198-7696 http://sbl.unmc.edu Office (402) 559-8578 FAX (402) 559-3739 Professor Hobbies: Protein Crystallography, Cancer, Biochemistry, DNA Metabolism, Modulated Crystals, Crystal Perfection Interests: Manga, Led Zepplin, Cold Play, piano, BRAN, RAGBRAI, golf and lately superspace groups
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Hi Gloria, My hobby is space group symmetry. My interest phenix development. so I can't imagine a protein crystallographer would ever need to apply the modulation function to a protein atom that happened to be on one. That's true. Protein residues don't have internal symmetry, therefore they are not compatible with crystallographic special positions. (Wyckoff positions are enumerations of classes of special positions.) In the PDB molecules with internal symmetry are really rare, except for H2O and SO4. But these contribute so little to the total scattering that it isn't important to handle them in a special way. So Wyckoff positions remain foreign in the macromolecular context. Ralf - Original Message From: Gloria Borgstahl gborgst...@gmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Wed, December 8, 2010 12:16:54 PM Subject: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms I've gotten some interesting responses, that I will summarize for the group later, but I thought I should clarify why I asked. I was worrying about this because I have been working out the steps in how to determine the (3+1)D superspace group for a protein crystal. The last step listed in IT vol C chapter 9.8, is to consider any atoms that lie ON a Wyckoff position, and what restrictions this would apply to the modulation function that is refined for each atom. My first reaction, was Wyckoff positions? I vaguely remember those, my recollection from my experience was they were really cool, but were usually in the solvent, so I can't imagine a protein crystallographer would ever need to apply the modulation function to a protein atom that happened to be on one. But to a crystallographer working on a modulated mineral, it would happen all the time, I'll bet. So maybe this was one more thing that just didn't really apply to protein structures and lucky us we don't worry about this last step (just as I never did model that solvent water that was on one, back in the 90s). Then I thought, maybe I'm missing something, or there are special cases out there (and so far I have heard of a disulfide bond on a 2-fold connecting two homodimers). So I polled the collective knowledge of the great ccp4bb group. On Wed, Dec 8, 2010 at 10:57 AM, Gloria Borgstahl gborgst...@gmail.com wrote: My fellow crystallographers, I wanted to take a poll. How many of you have ever had a protein atom on a Wyckoff position (AKA a special position). What kind of molecules have you found at special positions (it would have to contain the symmetry of the special position, right?) I'm thinking it is impossible to have a protein atom at a special position or am I exposing my ignorance yet again... my experience is that only once I found an atom in a special position, it was a strange solvent molecule, that blew my mind for a while until I learned about special positions in crystallography. Looking forward to your responses, Gloria Gloria Borgstahl Eppley Institute for Cancer Research and Allied Diseases 987696 Nebraska Medical Center 10732A Lied Transplant Center Omaha, NE 68198-7696 http://sbl.unmc.edu Office (402) 559-8578 FAX (402) 559-3739 Professor Hobbies: Protein Crystallography, Cancer, Biochemistry, DNA Metabolism, Modulated Crystals, Crystal Perfection Interests: Manga, Led Zepplin, Cold Play, piano, BRAN, RAGBRAI, golf and lately superspace groups
