Re: [ccp4bb] ligand bonds (AlF3) breaking up after refinement in refmac
Hi Ansuman, I think that the refinement is putting the atoms in the right place so there is no 'exploding', 1.8 to 1.9A is the ideal length for Mg-F. Even though you did not add Mg, if it is required for catalysis there must be some around and this would then recruited into the MgF3-. As there is not very much, it looks to me like the occupancy is low - reflected both in the negative peak and the way the density looks. Unfortunately, it is very hard to distinguish between Al and Mg but it looks very much to me like you have MgF3- bound here. Best wishes, Matt. On 17/01/2015 19:41, ansuman biswas wrote: Dear Matthew, I did not add Mg to the crystallization condition. Although, Mg is required for the catalysis. But I added MgF3 and carried out the refinement only to find out a negative density around Mg and again it was exploded (fig). The ideal Al-F bond length is around 1.65A in AlF3. I downloaded several AlF3 bound structures and found that the bond length varies from 1.65A to 1.8A. And when I measured the broken bond distance between Al and F, it came out around 1.8A. I did prepare a cif file using that AlF3 and refined, only to find out an exploded AlF3. Also, no such warning, mentioning the actual bond length, is there in the log file of Refmac. regards, Ansuman On Saturday, 17 January 2015 8:51 PM, Matthew BOWLER mbow...@embl.fr wrote: Dear Ansuman, I agree with Matthew that the refinement seems to be OK - the reason the bonds are longer is because what you actually have bound is MgF3- and not AlF3. MgF3- is a much better transition state analogue as it is isosteric and isoelectronic with a transferring phosphoryl group. At pH values above ~7.5 Al precipitates out as AlOH and this leaves Mg to fill the gap. AlF3 does exist as a species but it is octahedral and not trigonal bipyramidal and has a water molecule occupying the missing F. There are plenty of MgF structures in the PDB and the MgF bond length is around 1.9A so I am pretty sure this is the species that you have bound. Hope this helps, best wishes, Matt. On 2015-01-16 20:07, ansuman biswas wrote: Dear users, I have a data at 2.2 A resolution. I am able to model AlF3 into the electron density (fig attached). However after one cycle of refinement the AlF3 molecule is exploding and the atoms move apart (fig2). AlF3 is already present in refmac library. First, I used that. But it broke up after refinement. Then, I extracted AlF3 coordinate from already published PDB and prepared the cif file. But, it also failed. I modified the cif file by changing the bond lengths according to the broken AlF3 structure but it was of no help. Kindly suggest how to carry out the refinement. regards, Ansuman -- Matthew Bowler Synchrotron Crystallography Group European Molecular Biology Laboratory 71 avenue des Martyrs CS 90181 F-38042 Grenoble France === Tel: +33 (0) 4.76.20.76.37 Fax: +33 (0) 4.76.20.71.99 http://www.embl.fr/ ===
Re: [ccp4bb] Redundancy vs no of frames
Dear Rohit Kumar, I prefer the term multiplicity instead of redundancy because the latter has a connotation of not really needed any more. The relation then is multiplicity = c * number_of_frames * oscillation_range where the constant c depends mainly on the space group. HTH, Kay On Sun, 18 Jan 2015 02:35:46 +0530, rohit kumar rohit...@gmail.com wrote: Dear all, Can anyone tell me how to calculate number of frames from redundancy or vica versa Thank you
Re: [ccp4bb] Redundancy vs no of frames
Dear Bernhard, You are being charmingly modest and self-critical: your philosophical discourse has always contributed to broadening an initially narrow question in an enlightening way :-) . In this case, it seems to me that Rohit's narrow question itself has only been touched upon. Clearly, we know what is meant by the redundancy he mentions in his question, independently of the extent to which it can or not help reduce errors in the final merged data: it is the number of times that unique reflections are measured through symmetry equivalence, and perhaps Friedel equivalence if no anomalous differences are to be ignored. Kay's gives an outline of a formula, but I would say that it is a very noisy outline, in the sense that it suggests a linearity that applies only in the limit of very high multiplicity. The main thing is that when one is far from that limit, redundancy can be very uneven across the set of unique reflections (it can even be zero for a subset of them if the available frames do not achieve completeness) and that this pattern depends not only on the space group but on the orientation of the symmetry axes with respect to the rotation axis. Of course, as you add frames, you add more reflections and something is bound to increase; but the way in which that increase is distributed between completeness and redundancy can be quite capricious. This was the motivation for Raimond Ravelli's beautiful work on his STRATEGY program (http://www.crystal.chem.uu.nl/distr/strategy.html). In the days when people alway tried to collect a complete dataset in a minimum number of frames, one moment of inattention caused by synchrotron fatigue could easily lead to collecting half the data with a multiplicity of 2 instead of complete data with a redundancy of 1, e.g. if one forgot about a 2-fold axis perpendicular to the rotation axis that perversely related the second half of the dataset to the first. Raimond told me that he was once bitten in this way, and promised to himself that he would never be again - so he wrote his program! I am digressing (into history rather than philosophy) myself ... . The short answer to your question, Rohit, is ... that there is no short answer to it in the guise of a simple formula, unless you have a very large redundancy. Talking about redundancy as a single number is also misleading: it is a distribution, whose magnitude can vary a lot across the set of unique reflections - unless, again, it is very large everywhere. All data processing programs will give you an idea of that distribution, at least as a function of resolution (although it would often be useful to be able to examine it in 3D). With best wishes, Gerard. -- On Sun, Jan 18, 2015 at 02:12:51PM +0100, Bernhard Rupp wrote: In defense of redundancy: While the IUCr online dictionary is notably silent about multiplicity, the term itself seems already oversubscribed and used differently in various crystallographic contexts. (i) Each general or special position in a crystal structure has a certain multiplicity, defined by symmetry. (ii) General reflection multiplicity M is usually is defined by reflection symmetry, and when reflections are affected by special operations, the resulting corresponding lower multiplicity because they map onto themselves is accounted for in the epsilon factor e. Btw a useful table of M and e is Iwasaki Ito Acta Cryst. (1977). A33, 227-229 (iii) In case of Laue patterns, overlap of higher order reflections is also called Multiplicity afaik (various Helliwell/Moffat et al papers explain this). So expanding the term multiplicity to include multiple instances of measurements of the same reflections - while admittedly avoiding the connotation of obsolescence - adds to its promiscuous meaning, where context becomes part of the definition I abstain from making any suggestions because in the past this has led to interesting but time-consuming philosophical discourse, proving in general the multiplicity of my reflections and positions redundant if not obsolete. Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kay Diederichs Sent: Sonntag, 18. Januar 2015 09:28 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Redundancy vs no of frames Dear Rohit Kumar, I prefer the term multiplicity instead of redundancy because the latter has a connotation of not really needed any more. The relation then is multiplicity = c * number_of_frames * oscillation_range where the constant c depends mainly on the space group. HTH, Kay On Sun, 18 Jan 2015 02:35:46 +0530, rohit kumar rohit...@gmail.com wrote: Dear all, Can anyone tell me how to calculate number of frames from redundancy or vica versa Thank you -- === *
Re: [ccp4bb] Redundancy vs no of frames
At the risk of further extending this philosophical (if not etymological) discussion: in further defence of 'redundancy' I would point out that 'no longer needed' is not the only meaning of 'redundant', though admittedly it is the one that most often grabs the headlines! The meaning of 'redundant' in the context of employment is actually a relatively recent one and somewhat changed from the original meaning. In a scientific context there's a second meaning of 'redundant', and in fact this one is much closer to the original one. In information theory the term 'redundant' applies to extra information added to a message being passed down a transmission line, in order to reduce corruption and loss of information, i.e. redundancy is absolutely needed to reduce the error rate. In a crystallographic context the purpose of redundancy, i.e. measurements over and above those strictly required to obtain a structure, is also obviously to reduce errors. 'Additional' here clearly does not necessarily imply 'not needed'. 'Redundant' comes from the Latin 're', meaning 'again', and 'unda', meaning 'wave', from which of course we get 'inundated' and 'undulator', so 'redundant' means literally 'coming in waves' or 'overflowing'. So we could say that redundancy is the process of being inundated by data from an undulator! As BR points out 'multiplicity' has long been used to indicate the number of equivalent reflexions generated by the point-group symmetry (so in PG222 h00, hk0 and hkl have respectively multiplicites of 1, 2 and 4 for non-zero hkl). I googled 'reflection multiplicity' and the top hit was http://pd.chem.ucl.ac.uk/pdnn/symm2/multj.htm . Suppose I want to express the following idea: Redundancy is likely to be correlated with multiplicity. How do I express that unambiguously if 'redundancy' is redefined as 'multiplicity'? Cheers -- Ian On 18 January 2015 at 13:12, Bernhard Rupp b...@ruppweb.org wrote: In defense of redundancy: While the IUCr online dictionary is notably silent about multiplicity, the term itself seems already oversubscribed and used differently in various crystallographic contexts. (i) Each general or special position in a crystal structure has a certain multiplicity, defined by symmetry. (ii) General reflection multiplicity M is usually is defined by reflection symmetry, and when reflections are affected by special operations, the resulting corresponding lower multiplicity because they map onto themselves is accounted for in the epsilon factor e. Btw a useful table of M and e is Iwasaki Ito Acta Cryst. (1977). A33, 227-229 (iii) In case of Laue patterns, overlap of higher order reflections is also called Multiplicity afaik (various Helliwell/Moffat et al papers explain this). So expanding the term multiplicity to include multiple instances of measurements of the same reflections - while admittedly avoiding the connotation of obsolescence - adds to its promiscuous meaning, where context becomes part of the definition I abstain from making any suggestions because in the past this has led to interesting but time-consuming philosophical discourse, proving in general the multiplicity of my reflections and positions redundant if not obsolete. Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kay Diederichs Sent: Sonntag, 18. Januar 2015 09:28 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Redundancy vs no of frames Dear Rohit Kumar, I prefer the term multiplicity instead of redundancy because the latter has a connotation of not really needed any more. The relation then is multiplicity = c * number_of_frames * oscillation_range where the constant c depends mainly on the space group. HTH, Kay On Sun, 18 Jan 2015 02:35:46 +0530, rohit kumar rohit...@gmail.com wrote: Dear all, Can anyone tell me how to calculate number of frames from redundancy or vica versa Thank you
Re: [ccp4bb] Redundancy vs no of frames
PS see http://en.wikipedia.org/wiki/Cyclic_redundancy_check . I. On 18 January 2015 at 13:54, Ian Tickle ianj...@gmail.com wrote: At the risk of further extending this philosophical (if not etymological) discussion: in further defence of 'redundancy' I would point out that 'no longer needed' is not the only meaning of 'redundant', though admittedly it is the one that most often grabs the headlines! The meaning of 'redundant' in the context of employment is actually a relatively recent one and somewhat changed from the original meaning. In a scientific context there's a second meaning of 'redundant', and in fact this one is much closer to the original one. In information theory the term 'redundant' applies to extra information added to a message being passed down a transmission line, in order to reduce corruption and loss of information, i.e. redundancy is absolutely needed to reduce the error rate. In a crystallographic context the purpose of redundancy, i.e. measurements over and above those strictly required to obtain a structure, is also obviously to reduce errors. 'Additional' here clearly does not necessarily imply 'not needed'. 'Redundant' comes from the Latin 're', meaning 'again', and 'unda', meaning 'wave', from which of course we get 'inundated' and 'undulator', so 'redundant' means literally 'coming in waves' or 'overflowing'. So we could say that redundancy is the process of being inundated by data from an undulator! As BR points out 'multiplicity' has long been used to indicate the number of equivalent reflexions generated by the point-group symmetry (so in PG222 h00, hk0 and hkl have respectively multiplicites of 1, 2 and 4 for non-zero hkl). I googled 'reflection multiplicity' and the top hit was http://pd.chem.ucl.ac.uk/pdnn/symm2/multj.htm . Suppose I want to express the following idea: Redundancy is likely to be correlated with multiplicity. How do I express that unambiguously if 'redundancy' is redefined as 'multiplicity'? Cheers -- Ian On 18 January 2015 at 13:12, Bernhard Rupp b...@ruppweb.org wrote: In defense of redundancy: While the IUCr online dictionary is notably silent about multiplicity, the term itself seems already oversubscribed and used differently in various crystallographic contexts. (i) Each general or special position in a crystal structure has a certain multiplicity, defined by symmetry. (ii) General reflection multiplicity M is usually is defined by reflection symmetry, and when reflections are affected by special operations, the resulting corresponding lower multiplicity because they map onto themselves is accounted for in the epsilon factor e. Btw a useful table of M and e is Iwasaki Ito Acta Cryst. (1977). A33, 227-229 (iii) In case of Laue patterns, overlap of higher order reflections is also called Multiplicity afaik (various Helliwell/Moffat et al papers explain this). So expanding the term multiplicity to include multiple instances of measurements of the same reflections - while admittedly avoiding the connotation of obsolescence - adds to its promiscuous meaning, where context becomes part of the definition I abstain from making any suggestions because in the past this has led to interesting but time-consuming philosophical discourse, proving in general the multiplicity of my reflections and positions redundant if not obsolete. Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kay Diederichs Sent: Sonntag, 18. Januar 2015 09:28 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Redundancy vs no of frames Dear Rohit Kumar, I prefer the term multiplicity instead of redundancy because the latter has a connotation of not really needed any more. The relation then is multiplicity = c * number_of_frames * oscillation_range where the constant c depends mainly on the space group. HTH, Kay On Sun, 18 Jan 2015 02:35:46 +0530, rohit kumar rohit...@gmail.com wrote: Dear all, Can anyone tell me how to calculate number of frames from redundancy or vica versa Thank you
Re: [ccp4bb] Redundancy vs no of frames
In defense of redundancy: While the IUCr online dictionary is notably silent about multiplicity, the term itself seems already oversubscribed and used differently in various crystallographic contexts. (i) Each general or special position in a crystal structure has a certain multiplicity, defined by symmetry. (ii) General reflection multiplicity M is usually is defined by reflection symmetry, and when reflections are affected by special operations, the resulting corresponding lower multiplicity because they map onto themselves is accounted for in the epsilon factor e. Btw a useful table of M and e is Iwasaki Ito Acta Cryst. (1977). A33, 227-229 (iii) In case of Laue patterns, overlap of higher order reflections is also called Multiplicity afaik (various Helliwell/Moffat et al papers explain this). So expanding the term multiplicity to include multiple instances of measurements of the same reflections - while admittedly avoiding the connotation of obsolescence - adds to its promiscuous meaning, where context becomes part of the definition I abstain from making any suggestions because in the past this has led to interesting but time-consuming philosophical discourse, proving in general the multiplicity of my reflections and positions redundant if not obsolete. Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kay Diederichs Sent: Sonntag, 18. Januar 2015 09:28 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Redundancy vs no of frames Dear Rohit Kumar, I prefer the term multiplicity instead of redundancy because the latter has a connotation of not really needed any more. The relation then is multiplicity = c * number_of_frames * oscillation_range where the constant c depends mainly on the space group. HTH, Kay On Sun, 18 Jan 2015 02:35:46 +0530, rohit kumar rohit...@gmail.com wrote: Dear all, Can anyone tell me how to calculate number of frames from redundancy or vica versa Thank you
Re: [ccp4bb] Visualizing Stereo view
You can create stereo images for publications in pymol: http://www.pymolwiki.org/index.php/Stereo_ray Adding labels and getting them to float at the correct depth within the image can be tricky. As for visualizing the stereo images, you can either practice alot and get good at cross eyed stereo viewing, or you can buy a pair of glasses to assist you in seeing the 3d effect. If you google cross eyed stereo glasses, you will get many options to purchase. Old chemistry texts used to come with a pair, but I'm not sure that students actually purchase textbooks anymore. On Sat, Jan 17, 2015 at 23:50 PM, jeorgemarley thomas kirtswab...@gmail.com wrote: Dear all, First of all sorry to put this off topic and silly question on bb. Can anybody suggest me, how to create a stereo image and how it is different from the normal. How can I visualize it, if anybody has answer for this please suggest me its significance in analysis. Thank you very much in advance. Thanks Jeorge -- Sent from MetroMail
Re: [ccp4bb] additional density on cysteine residue
Don't forget to check the anomalous difference Fourier - this may fix any S atoms - the resolution is god enough Eleanor On 18 January 2015 at 01:12, Robert Stroud str...@msg.ucsf.edu wrote: I suspect it may be a reaction with your reducing agent. What did you use either in the preparation, or in the crystallization. If you didn’t have reducing agent it probably oxidized to sulfuric acid. You should figure it out with difference maps and maybe mass spec also. bob On Jan 17, 2015, at 4:10 PM, sreetama das somon_...@yahoo.co.in wrote: Hi, Thanks for the quick replies. I modelled in CME and refined. However, I get a blob of negative density around the S-S bond, which is retained up to 5 sigma. Does it mean it is not CME ? Thanks regards, sreetama On Sunday, 18 January 2015 12:41 AM, Roger Rowlett rrowl...@colgate.edu wrote: If CSO does not account for the density -- the SO bond should be about 1.8 A IIRC -- a possibility is an adventitious metal ion. Roger Rowlett On Jan 17, 2015 1:25 PM, sreetama das somon_...@yahoo.co.in wrote: Dear Users, I am solving a structure from x-ray diffraction data (1.62A resolution). The protein has a single cysteine residue (which is also the catalytic residue), and it has a positive density on it (fig 1; R/Rfree = 16.88/19.94). The positive density is retained upto 11.5 sigma level. Modelling with water retains the positive density (fig 2; R/Rfree = 16.85/19.94) upto 5.2 sigma level. Modelling with CSO (S-hydroxycysteine, fig 3, R/Rfree = 16.82/ 19.81) produces partial positive and negative densities, which are retained upto 5 sigma. Moreover, after real-space refinement in coot followed by refinement in refmac, the N-terminus of CSO is not bonded to the preceding residue, nor is its C-terminus bonded to the succedding residue. All maps are contoured at 1sigma (2Fo-Fc map) and 3sigma (fo-fc map). The protein preparation contained Tris buffer at pH 7.2, NaCl, glycerol and beta-mercaptoethanol (2mM), while the crystallization condition contained citric acid (pH 3.5) and ammonium sulfate. Please suggest how to interpret the data. thanking in advance, sreetama coot_CME.png all the best! Bob
Re: [ccp4bb] Visualizing Stereo view
Are most stereo images now for cross-eyed viewing? I thought they were for wall-eyed viewing. Perhaps a warning would be helpful for people starting out at looking at published stereoviews. If you look at a stereoview constructed for wall-eyed viewing but look at it with crossed eyes, you'll change the handedness of the object. And if you're showing surfaces, they get turned inside-out (or something like it). I usually get a headache soon after mixing modes like this and only know that the surfaces are messed up. Also, in answer to one of Jeorge's questions, the two images in stereoviews differ by a small rotation about a vertical axis. The two images are what each of your eyes would see if looking at a single object. Because your eyes are separated by about 2.25 inches (I'm a stubborn non-metrical American...), the left- and right-eye views differ slightly. The amount also depends on how close your eyes are supposed to be from the object. I think long ago things were worked out so the rotation is 6 degrees and that corresponds to the viewer-object distance being about 30 inches. If you place the left eye view on the left, you need to look at the two images in wall-eyed mode. If you place the left eye view on the right, you need to cross your eyes to generate the stereo image. For those of us who can view stereoimages without the assistance of glasses or computers, life is good. I recommend developing the ability to do that. Ron On Sun, 18 Jan 2015, Jim Fairman wrote: You can create stereo images for publications in pymol: http://www.pymolwiki.org/index.php/Stereo_ray Adding labels and getting them to float at the correct depth within the image can be tricky. As for visualizing the stereo images, you can either practice alot and get good at cross eyed stereo viewing, or you can buy a pair of glasses to assist you in seeing the 3d effect. If you google cross eyed stereo glasses, you will get many options to purchase. Old chemistry texts used to come with a pair, but I'm not sure that students actually purchase textbooks anymore. On Sat, Jan 17, 2015 at 23:50 PM, jeorgemarley thomas kirtswab...@gmail.com wrote: Dear all, First of all sorry to put this off topic and silly question on bb. Can anybody suggest me, how to create a stereo image and how it is different from the normal. How can I visualize it, if anybody has answer for this please suggest me its significance in analysis. Thank you very much in advance. Thanks Jeorge -- Sent from MetroMail
Re: [ccp4bb] coot 0.8.1 freezes my graphics
Wrong board, try sending it to the cootbb Jūrgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Streetx-apple-data-detectors://4, W8708 Baltimore, MD 21205x-apple-data-detectors://5/0 Office: +1-410-614-4742tel:%2B1-410-614-4742 Lab: +1-410-614-4894tel:%2B1-410-614-4894 Fax: +1-410-955-2926tel:%2B1-410-955-2926 http://lupo.jhsph.eduhttp://lupo.jhsph.edu/ On Jan 18, 2015, at 13:32, Kenneth A. Satyshur satys...@wisc.edumailto:satys...@wisc.edu wrote: Coot is our best program there ever was for fitting electron density. It is very simple to use and easy to teach. But sometimes improvements are made that seem to just slow things down. Having used 0.7.1 for a long time, i noticed that rotation and scaling of density is very quick, but translations are much slower (cntrl left mouse). Now in 0.8.1, translations have become impossibly slow. They freeze the whole graphics system for as long as 10 seconds. It is recalculating a map, and this can be seen using top to display the cpu usage. Also, we are now given a spherical density, which is annoying, really, since cell edges are not spherical and its hard to examine 3D space in a bubble. But there must be a way of speeding up the recalculation of the map during translation. I have a dual quad core with 15 idle cores while coot recalculates its new map in one core. Maybe multi core is the way to go. I hope this can be fixed. Otherwise I will stick with the 0.7 version that makes a cuboid map. I really enjoy the rapid examination of density that coot provides especially in 3D. thanks to the Coot team. Linux paprika 2.6.32-504.3.3.el6.x86_64 #1 SMP Fri Dec 12 16:05:43 EST 2014 x86_64 x86_64 x86_64 GNU/Linux 24 Gb memory, Nvidia Quadro FX 4800 Stereo graphics with Nvidia drives installed and the kernal recompiled. -- Kenneth A. Satyshur, M.S.,Ph.D. Senior Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207 satyshur.vcf
Re: [ccp4bb] Redundancy vs no of frames
Also RAID (REDUNDANT array of inexpensive disks). To me redundancy implies robustness, overdetermination, like when I measure absorbance at 1500 wavelengths to calculate the concentration of five absorbing species with a 2-parameter baseline offset. Exactly the connotation we want for our more-than-complete datasets. eab On 01/18/2015 09:29 AM, Ian Tickle wrote: PS see http://en.wikipedia.org/wiki/Cyclic_redundancy_check . I. On 18 January 2015 at 13:54, Ian Tickle ianj...@gmail.com mailto:ianj...@gmail.com wrote: At the risk of further extending this philosophical (if not etymological) discussion: in further defence of 'redundancy' I would point out that 'no longer needed' is not the only meaning of 'redundant', though admittedly it is the one that most often grabs the headlines! The meaning of 'redundant' in the context of employment is actually a relatively recent one and somewhat changed from the original meaning. In a scientific context there's a second meaning of 'redundant', and in fact this one is much closer to the original one. In information theory the term 'redundant' applies to extra information added to a message being passed down a transmission line, in order to reduce corruption and loss of information, i.e. redundancy is absolutely needed to reduce the error rate. In a crystallographic context the purpose of redundancy, i.e. measurements over and above those strictly required to obtain a structure, is also obviously to reduce errors. 'Additional' here clearly does not necessarily imply 'not needed'. 'Redundant' comes from the Latin 're', meaning 'again', and 'unda', meaning 'wave', from which of course we get 'inundated' and 'undulator', so 'redundant' means literally 'coming in waves' or 'overflowing'. So we could say that redundancy is the process of being inundated by data from an undulator! As BR points out 'multiplicity' has long been used to indicate the number of equivalent reflexions generated by the point-group symmetry (so in PG222 h00, hk0 and hkl have respectively multiplicites of 1, 2 and 4 for non-zero hkl). I googled 'reflection multiplicity' and the top hit was http://pd.chem.ucl.ac.uk/pdnn/symm2/multj.htm . Suppose I want to express the following idea: Redundancy is likely to be correlated with multiplicity. How do I express that unambiguously if 'redundancy' is redefined as 'multiplicity'? Cheers -- Ian On 18 January 2015 at 13:12, Bernhard Rupp b...@ruppweb.org mailto:b...@ruppweb.org wrote: In defense of redundancy: While the IUCr online dictionary is notably silent about multiplicity, the term itself seems already oversubscribed and used differently in various crystallographic contexts. (i) Each general or special position in a crystal structure has a certain multiplicity, defined by symmetry. (ii) General reflection multiplicity M is usually is defined by reflection symmetry, and when reflections are affected by special operations, the resulting corresponding lower multiplicity because they map onto themselves is accounted for in the epsilon factor e. Btw a useful table of M and e is Iwasaki Ito Acta Cryst. (1977). A33, 227-229 (iii) In case of Laue patterns, overlap of higher order reflections is also called Multiplicity afaik (various Helliwell/Moffat et al papers explain this). So expanding the term multiplicity to include multiple instances of measurements of the same reflections - while admittedly avoiding the connotation of obsolescence - adds to its promiscuous meaning, where context becomes part of the definition I abstain from making any suggestions because in the past this has led to interesting but time-consuming philosophical discourse, proving in general the multiplicity of my reflections and positions redundant if not obsolete. Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kay Diederichs Sent: Sonntag, 18. Januar 2015 09:28 To: CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Redundancy vs no of frames Dear Rohit Kumar, I prefer the term multiplicity instead of redundancy because the latter has a connotation of not really needed any more. The relation then is multiplicity = c * number_of_frames * oscillation_range where the constant c depends mainly on the space group. HTH, Kay On Sun, 18 Jan 2015 02:35:46 +0530, rohit kumar rohit...@gmail.com mailto:rohit...@gmail.com wrote: Dear all, Can anyone tell me how to calculate number of frames from redundancy or vica versa Thank you
[ccp4bb] coot 0.8.1 freezes my graphics
Coot is our best program there ever was for fitting electron density. It is very simple to use and easy to teach. But sometimes improvements are made that seem to just slow things down. Having used 0.7.1 for a long time, i noticed that rotation and scaling of density is very quick, but translations are much slower (cntrl left mouse). Now in 0.8.1, translations have become impossibly slow. They freeze the whole graphics system for as long as 10 seconds. It is recalculating a map, and this can be seen using top to display the cpu usage. Also, we are now given a spherical density, which is annoying, really, since cell edges are not spherical and its hard to examine 3D space in a bubble. But there must be a way of speeding up the recalculation of the map during translation. I have a dual quad core with 15 idle cores while coot recalculates its new map in one core. Maybe multi core is the way to go. I hope this can be fixed. Otherwise I will stick with the 0.7 version that makes a cuboid map. I really enjoy the rapid examination of density that coot provides especially in 3D. thanks to the Coot team. Linux paprika 2.6.32-504.3.3.el6.x86_64 #1 SMP Fri Dec 12 16:05:43 EST 2014 x86_64 x86_64 x86_64 GNU/Linux 24 Gb memory, Nvidia Quadro FX 4800 Stereo graphics with Nvidia drives installed and the kernal recompiled. -- Kenneth A. Satyshur, M.S.,Ph.D. Senior Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207 attachment: satyshur.vcf
Re: [ccp4bb] Visualizing Stereo view
I find that the 'rotation' method of producing the stereo views can be confusing because if you have z-clipping on, different atoms get clipped in the L R images and you see the corresponding atoms which are still visible in the other image in mono, while of course all the rest are in stereo. This gives me a headache, particularly if I have to look cross-eyed at the same time! The solution is to skew, not rotate (this brings to mind from the dim distant past Gerard Bricogne's manual on his 'skew planes' package called 'The Joy of Skewing' - which of course has nothing whatsoever to do with producing stereo images). Assuming the origin is in the centre, the rotation matrix about the vertical y axis (assuming your monitor is mounted in the conventional way) looks like this: [ cos(a) 0 sin(a) ] [ 0 1 0 ] [ -sin(a) 0 cos(a) ] where a = +- 3 deg. for the L R images (I leave it as an exercise for the reader to work out which is which!). This matrix gives for the rotated x z co-ordinates: x' = x cos(a) + z sin(a) z' = -x sin(a) + z cos(a) so z' is different for the L R images, particularly for atoms with large |x| near the L R sides of the screen (because the sine changes sign) which get clipped differently in the two images. If I recall correctly the skew matrix looks like this: [ cos(a) 0 sin(a) ] [ 0 1 0 ] [ 0 0 1 ] so: x' = x cos(a) + z sin(a) (i.e. same as above) z' = z So now whereas x' is still different for the L R images (and gives you the stereo effect), z' is the same so both eyes see exactly the same view even if z clipping is on. You may of course argue that skewing will distort the image whereas rotation won't. This is true; however the amount of distortion is tiny and not noticeable (and certainly well worth the price of making the stereo image much less confusing). Cheers -- Ian On 18 January 2015 at 19:34, Ronald E Stenkamp stenk...@u.washington.edu wrote: Are most stereo images now for cross-eyed viewing? I thought they were for wall-eyed viewing. Perhaps a warning would be helpful for people starting out at looking at published stereoviews. If you look at a stereoview constructed for wall-eyed viewing but look at it with crossed eyes, you'll change the handedness of the object. And if you're showing surfaces, they get turned inside-out (or something like it). I usually get a headache soon after mixing modes like this and only know that the surfaces are messed up. Also, in answer to one of Jeorge's questions, the two images in stereoviews differ by a small rotation about a vertical axis. The two images are what each of your eyes would see if looking at a single object. Because your eyes are separated by about 2.25 inches (I'm a stubborn non-metrical American...), the left- and right-eye views differ slightly. The amount also depends on how close your eyes are supposed to be from the object. I think long ago things were worked out so the rotation is 6 degrees and that corresponds to the viewer-object distance being about 30 inches. If you place the left eye view on the left, you need to look at the two images in wall-eyed mode. If you place the left eye view on the right, you need to cross your eyes to generate the stereo image. For those of us who can view stereoimages without the assistance of glasses or computers, life is good. I recommend developing the ability to do that. Ron On Sun, 18 Jan 2015, Jim Fairman wrote: You can create stereo images for publications in pymol: http://www.pymolwiki.org/index.php/Stereo_ray Adding labels and getting them to float at the correct depth within the image can be tricky. As for visualizing the stereo images, you can either practice alot and get good at cross eyed stereo viewing, or you can buy a pair of glasses to assist you in seeing the 3d effect. If you google cross eyed stereo glasses, you will get many options to purchase. Old chemistry texts used to come with a pair, but I'm not sure that students actually purchase textbooks anymore. On Sat, Jan 17, 2015 at 23:50 PM, jeorgemarley thomas kirtswab...@gmail.com wrote: Dear all, First of all sorry to put this off topic and silly question on bb. Can anybody suggest me, how to create a stereo image and how it is different from the normal. How can I visualize it, if anybody has answer for this please suggest me its significance in analysis. Thank you very much in advance. Thanks Jeorge -- Sent from MetroMail
Re: [ccp4bb] Visualizing Stereo view
Hi Jeorge, The easiest was of making a stereo image is with CCP4mg. You just need to tick a box when you make an image. Looking at stereo images takes practice, but it is a useful skill. It also helps with those spot-the-differences puzzles :) Cheers, Robbie -Oorspronkelijk bericht- Van: jeorgemarley thomas kirtswab...@gmail.com Verzonden: 18-1-2015 08:51 Aan: CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] Visualizing Stereo view Dear all, First of all sorry to put this off topic and silly question on bb. Can anybody suggest me, how to create a stereo image and how it is different from the normal. How can I visualize it, if anybody has answer for this please suggest me its significance in analysis. Thank you very much in advance. Thanks Jeorge
