Re: [ccp4bb] cmakereference : reading reflections
Bryan Lepore wrote: does cmakereference v0.2 in ccp4 6.1.13 require 'project', 'dataset' or 'crystal' to be in the .mtz? because i thought by default, these were eponymous I'm pretty sure it doesn't. e.g my .mtz - that has labels F and sigF - : * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength: 1 project crystal dataset ... because i am stuck this error : CCP4MTZfile: import_hkl_data - Missing column, crystal or dataset: NONE.F_sigF.F terminate called after throwing an instance of 'clipper::Message_fatal' ... if the labels are not F or sigF the same error occurs. Looks like you're missing -colin-fo '/*/*/[F,SIGF]' from your command line. If you're using stdin or a command script that would be: colin-fo /*/*/[F,SIGF] Kevin -- EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm
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] cns .map in coot
On 14/12/10 20:01, Julian Nomme wrote: I can easily convert my composite omit map from cns to ccp4 format and open it into coot. Very good, but no need to do that. However, how can I make coot use this map to fit density to my structure ? I can only use this map for visual support and for example, coot doesn't assign any density on the bar graph generated by using the Density fit analysis option to check the geometry. Does anyone have any idea how to fix this problem? It is not clear to me if the density is displayed in the wrong place (which might well be our problem) or that it's simply a matter of scale of the density fit graph begin wrong (which is your problem). If the latter, use Extensions - Refine - Set Density Fit Graph Weight... Paul
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
[ccp4bb] problem with PyMol on Ubuntu
I running Ubuntu on a laptop (Toshiba Satellite L505 ATI/AMD FGLRX graphics driver). I downloaded and installed PyMol but it runs poorly. For some reason, it runs fine the very first time I use it after I login, but every time I launch it after that all of the buttons and text of the the PyMol Viewer appear as nonsensical characters and the molecule is very distorted. Is there any way that I can fix this so that I do not have to log out and login every time I want to use it?
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] off topic: advice for crystallography workstation/server
Ronnie, The main rub is that any of the graphical software will have to be run on the local CPU to take advantage of accelerated video graphics. The approach I've taken is to have a central server (which is actually my office workstation) that serves up a home and software directories to satellite workstations that then run software on their own CPUs. Users get a portable desktop this way. The data traffic to my server is actually quite low. I'm running Linux, though. My central server (which is really nothing special in terms of hardware) has extra disk storage and a quad-core CPU, and handles the nightly backups. The clients all have dual core CPUs and their own accelerated graphics cards. Cheers. On 12/15/2010 11:26 AM, Ronnie Berntsson wrote: Dear all, We are currently considering buying a computer which can be used by multiple people, via our existing network, as a workstation for crystallography purposes. My thoughts are currently going towards a 8-core Apple Pro (or 12-core) with a lot of RAM, with OS X Server, which in theory should be able to handle multiple (up to 4) users simultaneously running crystallography software. The idea would be to have the users access this computer using their own laptops (starting their own virtual sessions?) connected to the same network. Does this sound like a viable strategy, or should it be setup in a different way? In that case how? Would it need advanced setup and maintenance, or would it be possible to jsut set up a number of user accounts in OS X Server, and let it run? I'm reasonably computer savvy, but haven't really done something like this before, so I would very much appreciate your advice or personal experiences regarding this matter. I know that I could probably get a cheaper computer if I went for a pc with linux, but I have more experience with OS X, and would therefore want to stay with it. Thank you in advance, Ronnie Berntsson -- Ronnie Berntsson, PhD PostDoctoral Fellow Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology Institute Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4, 9747 AG Groningen, The Netherlands -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu
Re: [ccp4bb] problem with PyMol on Ubuntu
Dear Michael, we are running pymol on several ubuntu machines including laptops. I simply installed the package pymol from synaptic. If you cannot find the pymol package you might have to activate all software sources / channels. There is no need to download any files from the pymol website. Best regards, Claudio Shah Am Mittwoch, den 15.12.2010, 10:50 -0500 schrieb Michael Murphy: I running Ubuntu on a laptop (Toshiba Satellite L505 ATI/AMD FGLRX graphics driver). I downloaded and installed PyMol but it runs poorly. For some reason, it runs fine the very first time I use it after I login, but every time I launch it after that all of the buttons and text of the the PyMol Viewer appear as nonsensical characters and the molecule is very distorted. Is there any way that I can fix this so that I do not have to log out and login every time I want to use it? -- Claudio Shah, PhD student Max-Delbrück-Centrum für Molekulare Medizin (MDC) AG Daumke | House 31.2 Room 0228 Robert-Rössle-Str. 10 13125 Berlin - Germany phone: +49 30 9406 3275 fax: +49 30 9406 3814 email: claudio.s...@mdc-berlin.de
Re: [ccp4bb] problem with PyMol on Ubuntu
Thanks Claudio, I have two versions of PyMol currently installed. One came with Phenix when I installed it, that is version 1.3. The other PyMol installation was found and installed by the Ubuntu update manager. Both of them have this same problem. MikeM On Wed, Dec 15, 2010 at 11:21 AM, Claudio Shah claudio.s...@mdc-berlin.dewrote: Dear Michael, we are running pymol on several ubuntu machines including laptops. I simply installed the package pymol from synaptic. If you cannot find the pymol package you might have to activate all software sources / channels. There is no need to download any files from the pymol website. Best regards, Claudio Shah Am Mittwoch, den 15.12.2010, 10:50 -0500 schrieb Michael Murphy: I running Ubuntu on a laptop (Toshiba Satellite L505 ATI/AMD FGLRX graphics driver). I downloaded and installed PyMol but it runs poorly. For some reason, it runs fine the very first time I use it after I login, but every time I launch it after that all of the buttons and text of the the PyMol Viewer appear as nonsensical characters and the molecule is very distorted. Is there any way that I can fix this so that I do not have to log out and login every time I want to use it? -- Claudio Shah, PhD student Max-Delbrück-Centrum für Molekulare Medizin (MDC) AG Daumke | House 31.2 Room 0228 Robert-Rössle-Str. 10 13125 Berlin - Germany phone: +49 30 9406 3275 fax: +49 30 9406 3814 email: claudio.s...@mdc-berlin.de
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
[ccp4bb] off topic: advice for crystallography workstation/server
Dear all, We are currently considering buying a computer which can be used by multiple people, via our existing network, as a workstation for crystallography purposes. My thoughts are currently going towards a 8-core Apple Pro (or 12-core) with a lot of RAM, with OS X Server, which in theory should be able to handle multiple (up to 4) users simultaneously running crystallography software. The idea would be to have the users access this computer using their own laptops (starting their own virtual sessions?) connected to the same network. Does this sound like a viable strategy, or should it be setup in a different way? In that case how? Would it need advanced setup and maintenance, or would it be possible to jsut set up a number of user accounts in OS X Server, and let it run? I'm reasonably computer savvy, but haven't really done something like this before, so I would very much appreciate your advice or personal experiences regarding this matter. I know that I could probably get a cheaper computer if I went for a pc with linux, but I have more experience with OS X, and would therefore want to stay with it. Thank you in advance, Ronnie Berntsson -- Ronnie Berntsson, PhD PostDoctoral Fellow Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology Institute Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4, 9747 AG Groningen, The Netherlands
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
Dear Ian, I think you are putting too much importance on the numerical instability of an atom's position when refining with full matrix refinement. When developing TNT's code for calculating second derivatives I found that building into the calculation the effects of such an atom overlapping its own, symmetry related, electron density eliminated the instability and no constraints to special positions were required. I was only working with block diagonal second derivatives with one block per atom but I don't see any reason the proper calculation would not work with the full matrix. The electron density of an atom near a special position is nearly that of one far away. It is not reasonable that a proper calculation would blow up for one and not the other. The key is doing the proper calculation. It's true that the proper calculation of the atomic block for an atom near a special position took more time than the calculation for all the other atoms in the model. You can't just calculate generic look-up tables that apply to all atoms. 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. It does, of course, have to have an occupancy of 1/n. 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. 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. Dale Tronrud On 12/15/10 08:54, 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
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 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
Re: [ccp4bb] off topic: advice for crystallography workstation/server
Ronnie Just a few comments.. There are no 'true' virtual sessions for OS X Server. (Well there is, but it's developed by a separate company and they charge per seat == expensive). What I define as a 'virtual session' is that you get a login window and your own desktop all running over VNC. (and you can do this for multiple users). The Apple Remote Desktop software only shares one screen/one user. Just as the other commenter said, multiple users on a crystallographic workstation is moot if you need 3d or even graphics intensive visualization (as each computer would benefit from having coot/pymol run locally). The number of programs taking advantage of multiple processors is growing, but far from mainstream (support, software usability, benefits etc). Much of crystallography remains to be a 'serial' rather than a 'parallel' experience. That being said, each your money may be better spent giving each user a Mac Mini (the price for 3-4 Minis == 1 Lowest end Mac Pro) .. and if you truly want multiple user management get a Mini Server that does manages user accounts/policies with local home directories. You could even keep the software on the main server and map it to the clients so you have version control over the xtal packages. F On Dec 15, 2010, at 9:26 AM, Ronnie Berntsson wrote: Dear all, We are currently considering buying a computer which can be used by multiple people, via our existing network, as a workstation for crystallography purposes. My thoughts are currently going towards a 8-core Apple Pro (or 12-core) with a lot of RAM, with OS X Server, which in theory should be able to handle multiple (up to 4) users simultaneously running crystallography software. The idea would be to have the users access this computer using their own laptops (starting their own virtual sessions?) connected to the same network. Does this sound like a viable strategy, or should it be setup in a different way? In that case how? Would it need advanced setup and maintenance, or would it be possible to jsut set up a number of user accounts in OS X Server, and let it run? I'm reasonably computer savvy, but haven't really done something like this before, so I would very much appreciate your advice or personal experiences regarding this matter. I know that I could probably get a cheaper computer if I went for a pc with linux, but I have more experience with OS X, and would therefore want to stay with it. Thank you in advance, Ronnie Berntsson -- Ronnie Berntsson, PhD PostDoctoral Fellow Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology Institute Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4, 9747 AG Groningen, The Netherlands - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
[ccp4bb] could you kindly give me the suggestion
Actually i have sioved my structure of the protein but the B factor (temperature) overall is very high . it sis more than 50 so how can i reduce this or what is the acceptable B factor for the submission Best Regards AFSHAN
Re: [ccp4bb] could you kindly give me the suggestion
By all means 50 is OK. The low end B in the PDB is probably ~10, whereas the high end is ~100 On Wed, 2010-12-15 at 10:24 -0800, Afshan Fayazi wrote: Actually i have sioved my structure of the protein but the B factor (temperature) overall is very high . it sis more than 50 so how can i reduce this or what is the acceptable B factor for the submission Best Regards AFSHAN -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] off topic: advice for crystallography workstation/server
We have a slightly different approach to this. Local machines are laptops if you want to do model building you can do it locally either 2d or connected to a Zalman in 3D. I have one Mac mini hooked up to a Zalman as permanent 3D station. The dual HexaCore MacPro (16 GB RAM) is connected also to a Zalman but is mostly used remotely via ssh in X11. Since you most likely want to use the MacPro for number crunching the ssh connection is fast enough, also for bringing up the ccp4I interface it still works fine even from home. I have a second 8core MacPro in my office used the same way, although right now I only have a 2D display connected to it, but the cores are accessible for number crunching. We are not using OSX Server, multiple users can have simultaneous ssh sessions. I link to a central .bashrc script so that every user has access to all software as soon as they log in. This requires me when setting up a new user to change the local .bashrc file to instead read the /etc/.bashrc that's all. So not sure if you really need OSX Server for your purposes. Maybe if you could specify what types of things you want to run on those machines it would be easier to make suggestions. I would not built in Coot over the network, that's just frustratingly slow and you don't get the benefit of graphics acceleration. Here's an incomplete list of stuff on those MacPros: USF stuff e.g Moleman etc. Coot, Pymol Docking software CCP4 package Phenix XDS Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/http://web.me.com/bosch_lab/ On Dec 15, 2010, at 12:51 PM, Francis E Reyes wrote: Dear all, We are currently considering buying a computer which can be used by multiple people, via our existing network, as a workstation for crystallography purposes. My thoughts are currently going towards a 8-core Apple Pro (or 12-core) with a lot of RAM, with OS X Server, which in theory should be able to handle multiple (up to 4) users simultaneously running crystallography software. The idea would be to have the users access this computer using their own laptops (starting their own virtual sessions?) connected to the same network. Does this sound like a viable strategy, or should it be setup in a different way? In that case how? Would it need advanced setup and maintenance, or would it be possible to jsut set up a number of user accounts in OS X Server, and let it run? I'm reasonably computer savvy, but haven't really done something like this before, so I would very much appreciate your advice or personal experiences regarding this matter. I know that I could probably get a cheaper computer if I went for a pc with linux, but I have more experience with OS X, and would therefore want to stay with it. Thank you in advance, Ronnie Berntsson -- Ronnie Berntsson, PhD PostDoctoral Fellow Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology Institute Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4, 9747 AG Groningen, The Netherlands - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.eduhttp://pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Re: [ccp4bb] cmakereference : reading reflections
On Wed, Dec 15, 2010 at 6:10 AM, Kevin Cowtan cow...@ysbl.york.ac.uk wrote: Looks like you're missing -colin-fo '/*/*/[F,SIGF]' that did it. i gather the input is much like buccaneer then. also - is 0.2 the latest version - and the only command line options in v0.2 (15/04/05) that i see listed are: Usage: cmakereference -pdbid accession-code COMPULSORY -pdbin .ent.Z-file -cifin .ent.Z-file -mtzout filename -pdbout filename -resolution reso -Bryan
Re: [ccp4bb] cryoprotectant for protein crystal grown from Di-sodium hydrogen phosphate
Mother liquor plus 30% glycerol or 30% glucose will cryoprotect pretty much anything, if it does not cause crystal cracking. We have had very good general luck with 25-30% glucose, and it's easy to prepare from your well solution or crystallization master mix. Add 150 mg of glucose to a microcentrifuge tube, make up to the 0.5 mL mark with your crystallization well solution, sonicate or otherwise mix thoroughly until dissolved. You can either transfer and swish crystals in the cryo solution, or gradually dilute your drop to 10X volume of the cryo-solution. Cheers. On 12/15/2010 4:13 PM, Jerry McCully wrote: Dear All; Recently we got some crystals from the condition #51 in the SaltRx crystallization kit from Hampton research. It contains 1.5M Na2HPO4 and 0.1M Tris(pH8.5). We am going to do a test diffraction ASAP. What cryoprotectant did you use for this condition? Thanks a lot and have a nice holiday season! Jinghua -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu
Re: [ccp4bb] Refmac twin refinement and the output map
Dear Yu I cannot say about other programs. refmac uses equation in slides No 13-14 of the presentation: http://www.ysbl.york.ac.uk/refmac/Presentations/ Refmac_Erice_workshop.ppt If your crystal is a perfect twin and you have processed data in true space group then refmac will give map for a single crystal. However accuracy of results have never been analysed. Moreover I would be very careful in the beginning of refinement (i.e. immediately after molecular replacement with high R factors). In these cases twin fraction refinement and map coefficients may not be as reliable as they should be. regards Garib On 15 Dec 2010, at 17:25, zhang yu wrote: Dear all, I have a question about twin refinement of Refmac in CPP4. I was told that the refmac (Phenix also?) will generate the detwined map after the refinement with twin. My question is that If my crystal is a perfect hemihedral twin, how can the refmac make a detwined map after the refinement? Thanks -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
Re: [ccp4bb] cryoprotectant for protein crystal grown from Di-sodium hydrogen phosphate
I've had good luck cryoprotecting high salt crystal conditions with sodium malonate (2.0-2.5M). Start with a 5M sodium malonate solution and dilute to 40-50% with mother liquor. good luck, Rob From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Jerry McCully [for-crystallizai...@hotmail.com] Sent: Wednesday, December 15, 2010 1:13 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] cryoprotectant for protein crystal grown from Di-sodium hydrogen phosphate Dear All; Recently we got some crystals from the condition #51 in the SaltRx crystallization kit from Hampton research. It contains 1.5M Na2HPO4 and 0.1M Tris(pH8.5). We am going to do a test diffraction ASAP. What cryoprotectant did you use for this condition? Thanks a lot and have a nice holiday season! Jinghua
[ccp4bb] First Announcement - Course on Neutron Scattering Applications in Structural Biology
First Announcement: Second Course on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. May 23 - May 27, 2011 Application deadline: March 11, 2011 The Course in Neutron Scattering Applications in Structural Biology aims at educating and enabling a new generation of researcher to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in an intensive course focusing on neutron techniques used in structural biology. The course is designed for graduate students with knowledge of protein function and structure, new or with limited experience of neutron scattering. Course Objectives: 1. Educate graduate students in neutron scattering techniques, instrumentation and data collection, analysis and interpretation by offering courses taught by neutron scattering scientist. 2. Expose participants to cutting-edge research in structural biology by presenting seminars from national and international scientists to detail how neutron scattering integrate in their research program. 3. Build interactions between graduate participants and their university groups and ORNL neutron scattering experts to develop new research projects. Detailed information will be available shortly on the course web page: http://neutrons.ornl.gov/conf/gcnb2011. Information on the 2010 course can be found at: http://neutrons.ornl.gov/conf/gcnb2010. The application package consisting of 1) Information form, 2) CV, 3) Applicant motivation letter (1/2 to 1 page), 4) Principal Investigator letter of support (1/2 to 1 page), should be sent electronically to meille...@ornl.govmailto:meille...@ornl.gov before March 11, 2011. Travel and accommodation expenses are supported for selected participants from the United States. International applications are welcome. However the course organization will not be able to offer travel or accommodation support. The number of participants will be limited to 15. Attendance to the course is free of charge for all selected participants. Best Regards, Flora Flora Meilleur Assistant Professor Molecular Structural Biochemistry N C State University Neutron Scattering Sciences Division Oak Ridge National Laboratory Phone: 865-241-2897
Re: [ccp4bb] cryoprotectant for protein crystal grown from Di-sodium hydrogen phosphate
Quickly passing the crystal through Paratone N has worked well for me when I crystallize in ammonium sulfate or sodium citrate conditions. Another trick is to dissolve sucrose (table sugar) in 10uL of the reservoir solution until it is saturated. Then separate the sucrose-reservoir mix into two 5ul drops. Add 5ul of the reservoir solution to one of the drops to make a 50% solution. Pass the crystal through the 50% saturated sucrose solution, then the 100% saturated sucrose solution and freeze. Good luck with the crystal! Bryan -- Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Robert Kirchdoerfer Sent: Wednesday, December 15, 2010 4:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] cryoprotectant for protein crystal grown from Di-sodium hydrogen phosphate I've had good luck cryoprotecting high salt crystal conditions with sodium malonate (2.0-2.5M). Start with a 5M sodium malonate solution and dilute to 40-50% with mother liquor. good luck, Rob From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Jerry McCully [for-crystallizai...@hotmail.com] Sent: Wednesday, December 15, 2010 1:13 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] cryoprotectant for protein crystal grown from Di-sodium hydrogen phosphate Dear All; Recently we got some crystals from the condition #51 in the SaltRx crystallization kit from Hampton research. It contains 1.5M Na2HPO4 and 0.1M Tris(pH8.5). We am going to do a test diffraction ASAP. What cryoprotectant did you use for this condition? Thanks a lot and have a nice holiday season! Jinghua
Re: [ccp4bb] cryoprotectant for protein crystal grown from Di-sodium hydrogen phosphate
I don't know how many of these crystals you have, but if you can spare one try freezing it straight out of the drop without cryoprotection. Certain salts can act as cryoprotectants at high enough concentrations. I don't know about phosphate salts, but I've had crystals that grew in 2.5M ammonium sulfate which I froze without cryoprotection and rarely saw an ice ring in my diffraction. Good luck, Mike - Original Message - From: Jerry McCully for-crystallizai...@hotmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, December 15, 2010 1:13:09 PM GMT -08:00 US/Canada Pacific Subject: [ccp4bb] cryoprotectant for protein crystal grown from Di-sodium hydrogen phosphate Dear All; Recently we got some crystals from the condition #51 in the SaltRx crystallization kit from Hampton research. It contains 1.5M Na2HPO4 and 0.1M Tris(pH8.5). We am going to do a test diffraction ASAP. What cryoprotectant did you use for this condition? Thanks a lot and have a nice holiday season! Jinghua -- Michael C. Thompson Graduate Student Biochemistry Molecular Biology Division Department of Chemistry Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
[ccp4bb] Map Sharpening
Dear all, Recently, I have solved a low resolution structure (2.85 Å) by MR; an alpha-beta mix. In this structure, one of the alpha helices (which is missing in the model) has a tube of density where I can only trace the main chain. In COOT, upon Map sharpening adjustments I could see density for few side chains. In this regard, I have some doubts about B-factors and map sharpening. To my knowledge, refinement of atomic B-factors at lower resolution is not informative and sharpening in COOT can be used only to enhance the resolution details. Is there any approach for integrating or regularizing the B-factors map sharpening in refinement for such a low resolution data? I hope, am not mixing up different things together. Correct me, if am wrong anywhere and direct me to the references on this. Thank you, Raspudin
Re: [ccp4bb] could you kindly give me the suggestion
Hi Afshan, you didn't mention the resolution, which is essential. For ultra-high resolution structures the average B may be well less than 10, and B less than ~4-5 is the condition to see the bonding density (see aldose reductase, 1uso, for instance). While a structure at 3.5A resolution may have B-factors larger than 100 or so. Pavel. On Wed, Dec 15, 2010 at 10:24 AM, Afshan Fayazi afshan...@yahoo.com wrote: **Actually i have sioved my structure of the protein but the B factor (temperature) overall is very high . it sis more than 50 so how can i reduce this or what is the acceptable B factor for the submission Best Regards AFSHAN http://de.mc517.mail.yahoo.com/mc/compose?to=bet...@unisgi1.desy.de
Re: [ccp4bb] could you kindly give me the suggestion
The average atomic B factor in the PDB at a given resolution d is roughly: B = 4*d^2+12 So, I am willing to bet your resolution is 3.1 A? If so, then you are normal (whatever that means). -James Holton MAD Scientist On Wed, Dec 15, 2010 at 8:38 PM, Pavel Afonine pafon...@gmail.com wrote: Hi Afshan, you didn't mention the resolution, which is essential. For ultra-high resolution structures the average B may be well less than 10, and B less than ~4-5 is the condition to see the bonding density (see aldose reductase, 1uso, for instance). While a structure at 3.5A resolution may have B-factors larger than 100 or so. Pavel. On Wed, Dec 15, 2010 at 10:24 AM, Afshan Fayazi afshan...@yahoo.comwrote: **Actually i have sioved my structure of the protein but the B factor (temperature) overall is very high . it sis more than 50 so how can i reduce this or what is the acceptable B factor for the submission Best Regards AFSHAN http://de.mc517.mail.yahoo.com/mc/compose?to=bet...@unisgi1.desy.de
[ccp4bb] International PhD and Postdoctoral Programmes at CNIO, Madrid
On behalf of Mar Pérez (Head of CNIO Training Office) Dear colleague, We would like to draw your attention to the calls for the International Ph.D. and Postdoctoral Programmes at the Spanish National Cancer Research Centre (CNIO) in Madrid. We would greatly appreciate if you could forward the information below to potential candidates. The *CNIO* offers excellent training and research opportunities in cutting edge basic and applied cancer research. The centre is equipped with state of the art facilities for protein expression, crystallisation, X-ray crystallography and NMR (including crystallisation robots, crystal farms, X-ray generators etc.). Several structural biology groups offer research opportunities in various areas of cancer biology. The CNIO *International Postdoctoral Programme* offers up to 4 very competitively funded two-year postdoc positions to outstanding junior scientists. Applications are considered at regular intervals; the 2010 call closes on *December 31st, 2010*. The CNIO *International Ph.D. Programme* each year supports 10 candidates for a 4-year Ph.D. We have one selection per year. The deadline for applications is *March 15th, 2011*. Our webpage provides further information on both programmes and the application procedure: - Postdoc Programme: www.cnio.es/postdoc To print a copy of the poster: http://www.cnio.es/es/cursos/descargas/postdoctorado/Poster_postdoc_2010.pdf - Ph.D. Programme: www.cnio.es/phd To print a copy of the poster: http://www.cnio.es/es/cursos/descargas/doctorado/Poster_PhD_2011.pdf Please, feel free to distribute this message on your local institute network and thank you very much in advance for advertising our programmes in your institution. Best regards, Mar Pérez, PhD Head of Training Office Fax: +34 912246980 E-mail: post...@cnio.es or p...@cnio.es Websites: www.cnio.es/postdoc and www.cnio.es/phd
