Re: [ccp4bb] sfall bug?
Eleanor, Thanks for the suggestion. I changed atom numbers to 1 and 2 and residue numbers to 1 and 2. The behavior is identical. Thanks! Jens On Tue, 2015-07-07 at 06:48 +0100, Eleanor Dodson wrote: I wonder if this is due to the late residue number. Could you try again reducing that to something smaller. I seem to remember SFALL stores a flag to recall which residue contributed to which density and there could be a limit on its size. Will test when I get near a working system Eleanor On 6 July 2015 at 22:53, Jens Kaiser kai...@caltech.edu wrote: All, We seem to have stumbled upon a problem in sfall. The two attached pdb files are nearly identical, except the coordinates and b-factors for the two atoms are swapped. When calculating Fs with sfall, we get drastically different mtz files. Upon calculating the corresponding Fcalc maps, it seems that the second atom in a.pdb gets ignored, whereas both atoms in b.pdb are included. There is nothing obvious in the log files to hint to what is happening (i.e. both files state Number of atoms input= 2 Number of atoms in sort = 2 Number in density generation = 2 Number completely within fft box = 2 Minimum B = 5.91 Maximum B = 5.97 Average B = 5.94 We observed this behavior on mac and on Linux. Cheers, Jens
[ccp4bb] sfall bug?
All, We seem to have stumbled upon a problem in sfall. The two attached pdb files are nearly identical, except the coordinates and b-factors for the two atoms are swapped. When calculating Fs with sfall, we get drastically different mtz files. Upon calculating the corresponding Fcalc maps, it seems that the second atom in a.pdb gets ignored, whereas both atoms in b.pdb are included. There is nothing obvious in the log files to hint to what is happening (i.e. both files state Number of atoms input= 2 Number of atoms in sort = 2 Number in density generation = 2 Number completely within fft box = 2 Minimum B = 5.91 Maximum B = 5.97 Average B = 5.94 We observed this behavior on mac and on Linux. Cheers, Jens a.pdb Description: application/aportisdoc b.pdb Description: application/aportisdoc
Re: [ccp4bb] PAD images
SSRL Bluice opens the image in adxv upon double click in the diffraction window. HTH, Jens On Mon, 2015-04-27 at 16:57 -0700, Bernhard Rupp (Hofkristallrat a.D.) wrote: Thanks - particularly great if we had these images/option available to look at in real time during data collection, w/o first having to download the raw data (not really feasible during remote data collection). I don't think the ESRF online data base has the option, but other beam lines may? Thx, BR -Original Message- From: James Holton [mailto:jmhol...@lbl.gov] Sent: Monday, April 27, 2015 4:05 PM To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PAD images In the ADXV viewer: http://www.scripps.edu/tainer/arvai/adxv.html Go to Edit:Settings and click on the Small Spots radio button. This solves most of the I can't interpret the spots problems you describe. -James Holton MAD Scientist On 4/27/2015 3:31 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote: Hi Fellows, I wonder whether it's just me and my eyesight failing (or excessive internal lubrication) It seems that the art of looking at diffraction patterns and being able to tell a lot about modulation, superstructures, extinctions, etc. becomes kind of useless old fart stuff when dealing with PAD images. I can't for my life see interpretable patterns on frames where the beamline autoprocessing delivers actual data sets. The absence of a point spread function etc that gave interpretable film-like images on IPs or CCDs, seems to be the reason. A PAD pixel with 100 counts looks like one with 100 when viewed with the low dynamic range of the displays compared to the huge dynamic range of the detector. Is there somewhere in the process a humanly unusable composite image with a point spread that allows visual pre-processing, inspection, and interpretation despite a low dynamic display range? Looking at the hklview or similar after processing is pointless (no pun intended), because the stuff I might be interested in is already processed away. Some humanly interpretable raw data images would be quite useful... Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org http://www.ruppweb.org/ - The man who follows the crowd will get no further than the crowd. The man who walks alone will find himself in places where no one has been before. -
Re: [ccp4bb] Strange Ancient Diffraction Pattern...
Gloria, I think this one might be modulated, you can clearly distinguish Bragg and satellite reflections. -j. On Wed, 2015-04-01 at 07:06 -0500, Gloria Borgstahl wrote: Ah Ha! drum roll A quasicrystal ! On Wed, Apr 1, 2015 at 7:00 AM, Julia Griese gri...@dbb.su.se wrote: This one appears to be of a similar age. It has a most puzzling, but pretty pentagonal pattern (and a backstop). Unfortunately Mosflm doesn't appear to support the image format. /Julia On 01/04/15 13:08, Harry Powell wrote: Hi Jacob I noticed that there's no backstop shadow that might give a clue as to the direct beam position. Do you know what wavelength radiation was used to bake this? On 1 Apr 2015, at 12:03, Keller, Jacob wrote: Can anyone index this? It's got mostly split spots and a strange diffuse scattering background JPK *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org *** roundmatzah.jpg Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) -- Dr. Julia Griese Postdoctoral Researcher Stockholm Center for Biomembrane Research Department of Biochemistry and Biophysics Stockholm University 106 91 Stockholm Sweden phone: +46-(0)8-162 778 email: gri...@dbb.su.se
Re: [ccp4bb] active 3D monitors: successor of Asus VG278HR?
In addition to what others have -- correctly -- stated I want to add one more thing: Yes, you are right, if you do not get your hands on a monitor with built-in emitter, you'll need ad least a K4000 and in many cases the VESA din bracket (~$50). You do not have to buy the expensive ($800+) 3D Vision pro emitter, though, for about $150 you can get the 3D Vision 2 (the 2 is important!) kit, that includes the DIN-to-Phone jack cable (officially for connection to DLP) you'll need to connect the graphics card to the emitter. Don't use the DP-DVI adapter, there's not enough bandwidth - go straight out of the DVI and you'll be fine (this realization cost me a day). HTH, Jens On Thu, 2015-01-08 at 15:08 +0100, Tobias Beck wrote: Dear all, I am looking again at 3D monitors. Last year I bought for my old lab the VG278HR and the PNY K600, as advised by the CCP4BB. (The 3D test images from Nvidia were running fine under Windows, but I did not get around to finish the set up with pymol and coot under linux.) Now at a new place, I looked at available monitors again (that have the built-in emitter since I want to use the K600 graphics card) and noticed that the VG278HR is out of stock. The VG278H, which seems to be a very similar model, is also out of stock. This page http://www.nvidia.com/object/3d-vision-displays.html also lists the Acer HN274H as a 27'' monitor with built-in emitter, but that seems to be out of stock as well (I would prefer not to buy a refurbished or used one). The monitors mentioned above are also listed here: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo (The smaller BenQ XL2420TX listed there is also out of stock). Has anybody ordered a 3D monitor with built-in emitter recently or could provide me with a current list of 27'' monitors with built-in emitters? I checked with Nvidia via their chat support, but they did not have an updated list, just provided links to the manufacturers' homepages. If monitors with built-in emitters are not available anymore, I need to buy a different graphics card in order for the setup to work with linux, right? Thank you and best wishes, Tobias. -- ___ Dr. Tobias Beck - group leader - RWTH Aachen University Institute of Inorganic Chemistry Landoltweg 1, office: 304N 52056 Aachen, Germany phone: +49-241-80-90057 fax: +49-241-80-99003 ___
Re: [ccp4bb] map manipulation questions
I found the most versatile program to manipulate maps is MAIN (http://www-bmb.ijs.si). You can copy and move maps from any cell to any other cell and get immediate visual feedback to see if things went the way you expected it. Cheers, Jens On Mon, 2014-05-19 at 17:25 -0400, Niu Tou wrote: Dear All, I have a ccp4 format map file in P1 spacegroup, I would like to manipulate it in several ways: 1. enlarge the cell dimension . When I tried CELL keyword in MAPMAN, the density scaled up together with the cell dimension. Does anybody know how to do it without changing the density? 2. Change the space group to P2. 3. Move the density away from its original place, i.e. apply a translocation vector to it. Does anybody know the answers? Thanks in advance! Regards, Niu
Re: [ccp4bb] Confusion about space group nomenclature
Bernhard et al, @ Jens: I think the precise and correct term applicable to the 65 should be pro-chiral spacegroups. They are not chiral by themselves, but addition of something /allows/ for the creation of a chiral object (i.e. the crystal). For a moment I though we have it…. but then the rest would be anti-chiral? I never thought about it that way but actually, yes! You put something chiral into their AU and those little buggers go on and invert it. They are really anti-chiral. So we have the three groups chiral, prochiral and antichiral. I like the suggestion of calling the chiral and prochiral groups the Sohncke groups (beware everybody misspelled that poor guy, he has a ck in his last name). That keeps the history of our field in the expressions we use and might even inspire people to look up who the people were on whose shoulders we stand. Jens PS: I had to laugh when I looked him up on Wikipedia: Leonhard Sohncke (22 February 1842 Halle – 1 November 1897 München) was a German mathematician who classified the 65 chiral space groups, sometimes called Sohncke groups. The German Wikipedia entry is much more complete. Also, I guess inspired by this thread, anonymous created an entry in Wikipedia L.A. Sonke - about 3h ago...
Re: [ccp4bb] Confusion about space group nomenclature
Dear Bernhard (and others), I was looking for catchy combinations of chiral or enantio and Latin or Greek words for support or allow -- until I realized there is already a name for this very concept, used widely in chemistry: I think the precise and correct term applicable to the 65 should be pro-chiral spacegroups. They are not chiral by themselves, but addition of something /allows/ for the creation of a chiral object (i.e. the crystal). Cheers, Jens On Tue, 2014-04-29 at 16:12 +0200, Bernhard Rupp wrote: Response to off-board mail: How about [calling them] non-centro-symmetric space groups, as I often tell my students? Almost, but not exact enough. The 65 are only a subset of non-centrosymmetric space groups: Not all enantiogenic (not elements of the 65-set) space groups are centrosymmetric. Simplest example Pm. According to above definition Pm (and many more lacking a center of inversion) would be a ok space group for chiral motifs. (when a space group has the 'center at ' annotation in the Tables, it has a coi and is a centrosymmetric space group). This implies that there are actually three types of crystal structures (cf. Flack): (a) chiral (non-centrosymmetric) crystal structures (b) centrosymmetric crystal structures (c) achiral non-centrosymmetric crystal structures And just as a reminder, the substructure inversion for 3 members of the 65 is not about the origin (0,0,0): I41, I4122, F4132 are their own enantiomorph, so for them there is no enantiomorphic pair (eg. I41 and I43), in fact no separate space group I43 is even necessary - look at the SG diagram #80 - both, 41 and 43 axes appear in the same SG. (2005 Erice paper of George explains more) Enough yet? Cheers, BR
Re: [ccp4bb] Confusion about space group nomenclature
actually, I'll have to amend that: Dear Bernhard (and others), I was looking for catchy combinations of chiral or enantio and Latin or Greek words for support or allow -- until I realized there is already a name for this very concept, used widely in chemistry: I think the precise and correct term applicable to the 65 should be the 22 chiral (aka 11 enantiomorphic paris) and the 43 pro-chiral spacegroups. They are not chiral by themselves, but addition of something /allows/ for the creation of a chiral object (i.e. the crystal). Cheers, Jens On Tue, 2014-04-29 at 16:12 +0200, Bernhard Rupp wrote: Response to off-board mail: How about [calling them] non-centro-symmetric space groups, as I often tell my students? Almost, but not exact enough. The 65 are only a subset of non-centrosymmetric space groups: Not all enantiogenic (not elements of the 65-set) space groups are centrosymmetric. Simplest example Pm. According to above definition Pm (and many more lacking a center of inversion) would be a ok space group for chiral motifs. (when a space group has the 'center at ' annotation in the Tables, it has a coi and is a centrosymmetric space group). This implies that there are actually three types of crystal structures (cf. Flack): (a) chiral (non-centrosymmetric) crystal structures (b) centrosymmetric crystal structures (c) achiral non-centrosymmetric crystal structures And just as a reminder, the substructure inversion for 3 members of the 65 is not about the origin (0,0,0): I41, I4122, F4132 are their own enantiomorph, so for them there is no enantiomorphic pair (eg. I41 and I43), in fact no separate space group I43 is even necessary - look at the SG diagram #80 - both, 41 and 43 axes appear in the same SG. (2005 Erice paper of George explains more) Enough yet? Cheers, BR
Re: [ccp4bb] small molecule crystallography
Andreas, What is your setup? We have a Cu Anode with an R-Axis IV, and just due to the geometry, the maximum resolution we can collect is around 1.4A. That won't do for small molecules. I think if your resolution is worse than something like 0.85A alarm bells start going off. If you can collect to higher resolution, you can process with XDS and read the XDS_ASCII.HKL (unmerged data) into xprep and run the output through shelxs/l. Olex2 is also pretty helpful for visualization and building. Cheers, Jens On Mon, 2014-03-24 at 18:04 +, Andreas Förster wrote: Dear all, I've been approached by a materials student with a petri dish full of big, sturdy, salty, yellow crystals. He claims I have the best kit for single-crystal diffraction on campus. I would very much appreciate advice on how to deal with this, anything in the range from won't work to use software X to analyze data in space group P-43N would be welcome. Thanks. Andreas
Re: [ccp4bb] High Rwork/Rfree vs. Resolution
Hi Chris, I personally would go with your thick dataset. 90% completeness is not stellar, but in my opinion not detrimental, either. I had one project that persistently yielded crystals that diffracted to rather high resolution (2.3), but in one direction no lunes were discernible and - consistent with that - the other direction's diffraction consisted of lines that had little beads on them - i.e. extremely smeary spots. XDS was the only program to integrate this data at an Rmerge better than 25% (it actually got below 10%). I was able to phase this data experimentally (Fe-MAD), use NCS and end up with amazing maps. Nevertheless, refinement was a bitch: It never went significantly below 30 for Rfree and messed up the geometry of the model, even though the electron density was clearly showing where the model should be. My explanation for this was that this was a rare case were the phases were actually determined better than the Fs. If you look back, in the days before refinement, reflection intensities were not measured, they were classified as weak, medium and strong - and that was enough to generate meaningful electron densities. In a cases like that, were the accurate determination of integrated intensities is a a problem, there should be a mechanism to submit experimental electron density instead of refined models, as the latter will make way less sense. So again - you got lucky with your thick dataset -- use it and don't sweat the 90% completeness! HTH, Jens On Fri, 2014-02-21 at 18:41 -0600, Chris Fage wrote: Dear CCP4BB Users, I recently collected a number of datasets from plate-shaped crystals that diffracted to 1.9-2.0 angstroms and yielded very nice electron density maps. There is no major density unaccounted for by the model; however, I am unable to decrease Rwork and Rfree beyond ~0.25 and ~0.30, respectively. Probably due to the more 2-dimensional nature of my crystals, there is a range of phi angles in which the reflections are smeared, and I am wondering if the problem lies therein. I would be grateful if anyone could provide advice for improving my refinement statistics, as I was under the impression that the R-factors should be ~5% lower for the given resolution. A few more pieces of information: -Space group = P21, with 2 monomers per asymmetric unit; -Chi square = 1.0-1.5; -Rmerge = 0.10-0.15; -Data were processed in HKL2000 and refined in Refmac5 and/or phenix.refine; -PHENIX Xtriage does not detect twinning, but hints at possible weak translational pseudosymmetry; -I was previously able to grow one atypically thick crystal which diffracted to 1.65 angstroms with Rwork/Rfree at 0.18/0.22. Unfortunately, the completeness of the dataset was only ~90%. Regards, Chris
[ccp4bb] XDS vs SADABS absorption correction factors
All, Sorry, this is a little bit off topic. I could not find a thorough definition of the Correction Factors for absorption correction in XDS nor of the Transmittance factors in SADABS. We collected small molecule samples on a synchrotron beamline, processed the data with XDS and the user now needs to know the Minimum and Maximum T for their cif. From what I could gather, the XDS correction factors in the ABSORP.CBF are multiplied by 1000; the values are around 1 (i.e a little smaller /and/ a little larger). The cif dictionary for _exptl_absorpt_correction_T_ states The permitted range is 0.0 - 1.0, which clearly has to be a different definition. Any pointers are welcome, Cheers, Jens
Re: [ccp4bb] Symmetry problem
Monika, There are several possible causes for the problem you are encountering, but your description is a little too vague to discern them. Scenario 1) You ran phaser with the option all possible spacegroups, for several different components of your crystal, setup individually, and the runs do not agree on the best spacegroup? -- In that case, phaser had problems determining the correct spacegroup, I'd suggest you search for all components, but in separate runs for each possible spacegroup. Scenario 2) You assumed your spacegroup assignment was correct, and ran MR for each of your components individually, and when you display the solutions, they overlap. In this case, you might have your solutions on different origins. The best way out is to use the first solution as a fixed solution, which is possible in most MR programs, and then search for the next component. There might be other scenarios, if you describe your situation in more detail (how many components in the crystal setup, what program you used, how you used it, and what you mean by different symmetries), we might be able to help you better, Cheers, Jens On Tue, 2014-02-18 at 14:59 -0300, Monika Coronado wrote: Dear, Does anyone know how to merge two molecules with different symmetry? I will explain: I have done the molecular replacement using the domains of the molecules separately, now I have to put all together, however they have a different symmetry. I will appreciate any kind of help. Regards, Mônika -- __o _`\,_ (*)/ (*) -+-+-+-+-+-+- * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ...E tudo muda... * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
Re: [ccp4bb] small crystals
Careina, If your target is interesting enough, try to reproduce the small crystals in batch and apply for FELS time. Small crystals are actually an advantage there. Cheers, Jens On Wed, 2013-12-04 at 21:41 -0800, Careina Edgooms wrote: Hi all Any advice on how to get bigger crystals from conditions that give showers of tiny crystals? I am getting small pretty looking individual crystals but they are too small and they don't seem to grow. In fact, in some instances if left for a couple of days they actually dissolve. I have fiddled around with mother liquor volume, protein concentration as well as drop volume (I am using hanging drop method) but none seem to make any difference and I always get the same tiny crystals. I think I might try microseeding but I haven't tried that yet. Any suggestions or tricks would be welcome Careina.
[ccp4bb] scala discrepancy between versions
Dear developers, We have been doing the local scaling with scala of multiple wavelengths for some time. We scaled one dataset collected remotely from the absorption edge, and input this to scala as a reference as one batch without any problems. With the latest release of CCP4, though, we get the following error (reference dataset is assigned to batch 9): Missing phi limits for batch 9 No valid orientation data for batch 9: this is not allowed with TAILS, SECONDARY, ABSORPTION or BEAMS options Scala: Failed in SETSCL Times: User: 0.0s System:0.0s Elapsed: 0:00 Our current workaround is to use the last, not the latest, release of CCP4. Any help is appreciated, Jens
Re: [ccp4bb] [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from twinned crystals; Sorry for HTML.
Fulvio,
First, to your point 2): Iobs(h1) and Iobs(h2) as well as Itrue(h1)
and Itrue(h2) are /not/ correlated! The Iobses are /related/ to the
Itrues by alpha (and the twin law), but the Itrues are totally
uncorrelated to each other, and so are the Iobses, in my opinion (even
though those will become more and more equal as alpha approaches 0.5,
but this is not a correlation! And at alpha = 0.5 this formalism breaks
down, anyways). So I do think that the simple error propagation is valid
here.
Now for your point 1): The formula I gave is only valid if you have an
analytical relationship between the magnitudes you measure and the
magnitudes you extract (and no correlation between them). For
non-merohedral twins, this is not true, as you'll have to make that
decision on a reflection by reflection base, so this is definitely /not/
generally applicable in that situation.
And yes, the uncertainties associated with /detwinned/ intensities are
much larger than the uncertainties associated with your measured data.
This is one (but not the most important) reason, to refine against
intensities and make the twin law part of your model.
Hope that makes sense,
Jens
On Thu, 2013-11-07 at 09:22 +0100, fulvio.saccoc...@uniroma1.it wrote:
Dear all,
thank you for your reply. I would summarize my concerns and opinions,
so
far:
1) for QTLS (non-merohedral twinning - non intersecting lattices) I think one
should consider the variables as independent and random and it is possible to
recover the true intensities of a unique lattice from the stronger
diffracting
one (see for example Jenni Ban, 2009, Acta D65, 101-111). Hence, the
quadratic formula (reported fomr Jens Kaiser) can be applied;
2) for TLS (merohedral twinning - perfectly overlapping spots) I think one
should not consider the two variable independent since they are related by
alpha (see the formulas I reported in my first message). In this case, I
think
the right formula should be that reported by Tim Grune, that as far as I know
overestimates the true error but in this case the quadratic is not applicable.
Therefore, one would be prone to conclude that the uncertainties associated
to
merohedral-twinned crystals are higher than regular crystals or
non-merohedral
crystals. What's your opinion about?
In data mercoledì 6 novembre 2013 23:29:01, Jens Kaiser ha scritto:
Tassos,
I'm no expert either, and there are caveats for using this formula on
correlated magnitudes. But I would assume that the intensities of twin
related reflections should be independent from each other (that's my
understanding of the sigmoid cumulative intensity distribution of
twins). Thus, I think the simple Gaussian error propagation should be
applicable to uncertainty estimates in detwinned intensities.
Cheers,
Jens
On Thu, 2013-11-07 at 08:09 +0100, Anastassis Perrakis wrote:
Dear Jens,
That formula for error propagation is correct for independent
measurements.
Does this assumption stand true for Intensities in twinning? I am no
expert, but I would think not.
Tassos
On 7 Nov 2013, at 7:53, Jens Kaiser wrote:
Fulvio, Tim,
error propagation is correct, but wrongly applied in Tim's
example.
s_f= \sqrt{ \left(\frac{\partial f}{\partial {x} }\right)^2 s_x^2 +
\left(\frac{\partial f}{\partial {y} }\right)^2 s_y^2 +
\left(\frac{\partial f}{\partial {z} }\right)^2 s_z^2 + ...} (see
http://en.wikipedia.org/wiki/Propagation_of_uncertainty#Simplification)
The uncertainty in a derived magnitude is always larger than any
individual uncertainty, so no subtraction, anytime. Furthermore, in
Tim's example you could end up with negative sigmas..
HTH,
Jens
On Thu, 2013-11-07 at 04:44 +0100, Tim Gruene wrote:
Dear Fulvio,
with simple error propagation, the error would be
sigma(I(h1)) = (1-α)sigma(Iobs(h1))-α*sigma(Iobs(h2))/(1-2α)
would it not?
Although especially for theoretical aspects you should be concerned
about division by zero.
Best,
Tim
On 11/06/2013 05:54 PM, Fulvio Saccoccia wrote:
Thank you for reply. My question mostly concern a theoretical
aspect rather than practical one. To be not misunderstood, what is
the mathematical model that one should apply to be able to deal
with twinned intensities with their errors? I mean, I+_what? I ask
this In order to state some general consideration on the accuracy
about the recovery the true intensities on varying of alpha. Thanks
Fulvio
Fulvio Saccoccia PhD Dept. of Biochemical Sciences Sapienza
University of Rome 5, Piazzale A. Moro 00185 phone +39 0649910556
Messaggio Originale Da: herman.schreu...@sanofi.com
Inviato: 06/11/2013, 17:25 A: CCP4BB@JISCMAIL.AC.UK Oggetto
Re: [ccp4bb] R: [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from twinned crystals; Sorry for HTML.
Fulvio, Tim,
error propagation is correct, but wrongly applied in Tim's example.
s_f= \sqrt{ \left(\frac{\partial f}{\partial {x} }\right)^2 s_x^2 +
\left(\frac{\partial f}{\partial {y} }\right)^2 s_y^2 +
\left(\frac{\partial f}{\partial {z} }\right)^2 s_z^2 + ...} (see
http://en.wikipedia.org/wiki/Propagation_of_uncertainty#Simplification)
The uncertainty in a derived magnitude is always larger than any
individual uncertainty, so no subtraction, anytime. Furthermore, in
Tim's example you could end up with negative sigmas..
HTH,
Jens
On Thu, 2013-11-07 at 04:44 +0100, Tim Gruene wrote:
Dear Fulvio,
with simple error propagation, the error would be
sigma(I(h1)) = (1-α)sigma(Iobs(h1))-α*sigma(Iobs(h2))/(1-2α)
would it not?
Although especially for theoretical aspects you should be concerned
about division by zero.
Best,
Tim
On 11/06/2013 05:54 PM, Fulvio Saccoccia wrote:
Thank you for reply. My question mostly concern a theoretical
aspect rather than practical one. To be not misunderstood, what is
the mathematical model that one should apply to be able to deal
with twinned intensities with their errors? I mean, I+_what? I ask
this In order to state some general consideration on the accuracy
about the recovery the true intensities on varying of alpha. Thanks
Fulvio
Fulvio Saccoccia PhD Dept. of Biochemical Sciences Sapienza
University of Rome 5, Piazzale A. Moro 00185 phone +39 0649910556
Messaggio Originale Da: herman.schreu...@sanofi.com
Inviato: 06/11/2013, 17:25 A: CCP4BB@JISCMAIL.AC.UK Oggetto:
[ccp4bb] AW: [ccp4bb] uncertainites associated with intensities
from twinned crystals
Dear Fulvio, you cannot detwin perfectly twinned data with this
formula. The term (1-2α) becomes zero, so you are dividing by zero.
With good refinement programs (ShelX, Refmac), refinement is done
against twinned data, which is better than to detwin the data with
the formula you mention.
As I understand it, to get map coefficients, the calculated
contribution of the twin domain (Fcalc’s) is substracted from Fobs
(with the appropriate weighting factors), so what you see in coot
is detwinned electron density. In practical terms, the only thing
you have to do is to specify the TWIN keyword in Refmac.
Best regards, Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag
von Fulvio Saccoccia Gesendet: Mittwoch, 6. November 2013 16:58 An:
CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] uncertainites associated
with intensities from twinned crystals
Dear ccp4 users
a question about the recovering of true intensities from merohedral
twinned crystal. Providing alpha and the twin operator one should
be able to recover the intensities from the formulas:
I(h1) = (1-α)Iobs(h1)-αIobs(h2)/(1-2α)
I(h2) = -αIobs(h1)+(1+α)Iobs(h2)/(1-2α)
as stated in many papers and books*.
However I was wondering about the uncertainties associated to these
measurements, I mean: for all physical observable an uncertainty
should be given.
Hence, what is the uncertainty associated to a perfect merohedrally
twinned crystal (alpha=0.5)? It is clear that in this case we drop
in a singular value of the above formulas.
Please, let me know your hints or your concerns on the matter.
Probably there is something that it is not so clear to me.
Thanks in advance
Fulvio
ref. **(C. Giacovazzo, H. L. Monaco, G. Artioli, D. Viterbo, M.
Milaneso, G. Ferraris, G. Gilli, P. Gilli, G. Zanotti and M. Catti.
Fundamentals of Crystallography, 3rd edition. IUCr Texts on
Crystallography No. 15, IUCr/Oxford University Press, 2011;
Chandra, N., Acharya, K. R., Moody, P. C. (1999). Acta Cryst. D55.
1750-1758)
--
Fulvio Saccoccia, PhD
Dept. of Biochemical Sciences A. Rossi Fanelli
Sapienza University of Rome
Tel. +39 0649910556
Re: [ccp4bb] [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from twinned crystals; Sorry for HTML.
Tassos,
I'm no expert either, and there are caveats for using this formula on
correlated magnitudes. But I would assume that the intensities of twin
related reflections should be independent from each other (that's my
understanding of the sigmoid cumulative intensity distribution of
twins). Thus, I think the simple Gaussian error propagation should be
applicable to uncertainty estimates in detwinned intensities.
Cheers,
Jens
On Thu, 2013-11-07 at 08:09 +0100, Anastassis Perrakis wrote:
Dear Jens,
That formula for error propagation is correct for independent
measurements.
Does this assumption stand true for Intensities in twinning? I am no
expert, but I would think not.
Tassos
On 7 Nov 2013, at 7:53, Jens Kaiser wrote:
Fulvio, Tim,
error propagation is correct, but wrongly applied in Tim's
example.
s_f= \sqrt{ \left(\frac{\partial f}{\partial {x} }\right)^2 s_x^2 +
\left(\frac{\partial f}{\partial {y} }\right)^2 s_y^2 +
\left(\frac{\partial f}{\partial {z} }\right)^2 s_z^2 + ...} (see
http://en.wikipedia.org/wiki/Propagation_of_uncertainty#Simplification)
The uncertainty in a derived magnitude is always larger than any
individual uncertainty, so no subtraction, anytime. Furthermore, in
Tim's example you could end up with negative sigmas..
HTH,
Jens
On Thu, 2013-11-07 at 04:44 +0100, Tim Gruene wrote:
Dear Fulvio,
with simple error propagation, the error would be
sigma(I(h1)) = (1-α)sigma(Iobs(h1))-α*sigma(Iobs(h2))/(1-2α)
would it not?
Although especially for theoretical aspects you should be concerned
about division by zero.
Best,
Tim
On 11/06/2013 05:54 PM, Fulvio Saccoccia wrote:
Thank you for reply. My question mostly concern a theoretical
aspect rather than practical one. To be not misunderstood, what is
the mathematical model that one should apply to be able to deal
with twinned intensities with their errors? I mean, I+_what? I ask
this In order to state some general consideration on the accuracy
about the recovery the true intensities on varying of alpha. Thanks
Fulvio
Fulvio Saccoccia PhD Dept. of Biochemical Sciences Sapienza
University of Rome 5, Piazzale A. Moro 00185 phone +39 0649910556
Messaggio Originale Da: herman.schreu...@sanofi.com
Inviato: 06/11/2013, 17:25 A: CCP4BB@JISCMAIL.AC.UK Oggetto:
[ccp4bb] AW: [ccp4bb] uncertainites associated with intensities
from twinned crystals
Dear Fulvio, you cannot detwin perfectly twinned data with this
formula. The term (1-2α) becomes zero, so you are dividing by zero.
With good refinement programs (ShelX, Refmac), refinement is done
against twinned data, which is better than to detwin the data with
the formula you mention.
As I understand it, to get map coefficients, the calculated
contribution of the twin domain (Fcalc’s) is substracted from Fobs
(with the appropriate weighting factors), so what you see in coot
is detwinned electron density. In practical terms, the only thing
you have to do is to specify the TWIN keyword in Refmac.
Best regards, Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag
von Fulvio Saccoccia Gesendet: Mittwoch, 6. November 2013 16:58 An:
CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] uncertainites associated
with intensities from twinned crystals
Dear ccp4 users
a question about the recovering of true intensities from merohedral
twinned crystal. Providing alpha and the twin operator one should
be able to recover the intensities from the formulas:
I(h1) = (1-α)Iobs(h1)-αIobs(h2)/(1-2α)
I(h2) = -αIobs(h1)+(1+α)Iobs(h2)/(1-2α)
as stated in many papers and books*.
However I was wondering about the uncertainties associated to these
measurements, I mean: for all physical observable an uncertainty
should be given.
Hence, what is the uncertainty associated to a perfect merohedrally
twinned crystal (alpha=0.5)? It is clear that in this case we drop
in a singular value of the above formulas.
Please, let me know your hints or your concerns on the matter.
Probably there is something that it is not so clear to me.
Thanks in advance
Fulvio
ref. **(C. Giacovazzo, H. L. Monaco, G. Artioli, D. Viterbo, M.
Milaneso, G. Ferraris, G. Gilli, P. Gilli, G. Zanotti and M. Catti.
Fundamentals of Crystallography, 3rd edition. IUCr Texts on
Crystallography No. 15, IUCr/Oxford University Press, 2011;
Chandra, N., Acharya, K. R., Moody, P. C. (1999). Acta Cryst. D55.
1750-1758)
--
Fulvio Saccoccia, PhD
Dept. of Biochemical Sciences A. Rossi Fanelli
Sapienza University of Rome
Tel. +39 0649910556
Re: [ccp4bb] atomic coloring for the color blind
Phoebe, I'm red green blind myself, and it is not as straight forward as it sounds. The problem is that we see red and green despite lacking one of the color receptors (I actually prepared a figure using red and green once and got a referee comment that red/green blind people would have difficulties with - which I could attest to being wrong...). We can distinguish between bright green and bright red! But in between, things are sketchy. Our brains learned to associate certain gray levels with either green or red (e.g. on our old BW TV, I did see all the grass as green, I was flabbergasted at the age of 6 to learn that our neighbor did not see the colors in our BW TV; Also, I called one of my class mates in junior high on his ugly green jeans, only to learn they were washed out black). My advice: Convert the image to gray scales. If you can't tell the difference, people with color seeing problems can't tell them apart. Actually, chose your color scheme so it gives good contrast in a gray scale image. This also should take care of the much rarer blue deficiency; and it might cut down on reproduction cost - as everything should be reproducible on a BW copy machine. HTH, Jens I feel badly that one of my undergrads had trouble telling an O from a C in a pymol homework set because he's color blind. (The assignment involved telling me why the a GTP analog (GDPCP) wasn't hydrolyzed). Is there a handy by-atom coloring scheme I can recommend that works for the red-green color blind? thanks, Professor Rice ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago 773 834 1723; pr...@uchicago.edumailto:pr...@uchicago.edu http://bmb.bsd.uchicago.edu/Faculty_and_Research/ http://www.rsc.org/shop/books/2008/9780854042722.asp
Re: [ccp4bb] Which program sequence to use in transforming from P1 to orthorhombic?
Ethan, The last time I attempted similar things, I had to run rotaprep to convince scala of using most things that did not come directly out of mosflm, but that was before the pointless days. As the reflections are already scaled in P1, I would consider it safe to rely on the Pointless Rmerge -- but that's just a guess (and you can't do much with the data downstream). I would assume sftools might be able to merge the reindexed file output by pointless. Nevertheless, if I were faced with the same problem nowadays, I would convert to a shelx hkl file and use xprep for the merging and statistics -- that's painless. Cheers, Jens On Mon, 2013-02-11 at 13:56 -0800, Ethan Merritt wrote: Hi all, I've downloaded a structure factor file from the PDB that presents itself as being triclinic. It contains F, sig(F), and Rfree only. The P1-ness of this structure is dubious, however. Pointless is 99.6% sure it's orthorhombic and puts out an mtz file in P212121 containing I SIGI BATCH M/ISYM where the batch numbers are all 1 and ISYM runs from 1 to 8. So far so good, but now I'm stuck. I can't persuade Scala or Aimless to merge the symmetry mates and report a merging R factor.Is there a trick to this? Some other program sequence? Ethan
Re: [ccp4bb] Perfluoropolyether as cryoprotectant for membrane proteins ?
Ulrike, I usually suggest it as the second try (the first try is mother liquor alone), as it does not involve mixing any new buffer concoctions. I do not have hard data, but I'd estimate it worked in about 50% of cases; it seemed not to matter if you try it on a soluble or membrane protein crystal. In my hands it performs better than mineral oil, silicon oil or paratone. Problematic cases are crystals in heavy precipitate, which has to be removed prior to transfer into the oil, otherwise it sticks around the crystal and you can't get the crystal dry. hth, Jens On Mon, 2012-12-03 at 13:07 +, Ulrike Demmer wrote: Dear crystallographers, does anyone have experience using Perfluoropolyether (Hampton Research) as cryoprotectant for membrane proteins ? Cheers, Ulrike
Re: [ccp4bb] One little clash
Christine, As interesting as the di-Tyrosine idea is, from the picture you provided, it looks more like the two tyrosines share a C=C bond. Given your slightly elevated R-factors and the high symmetry space group, I would thoroughly check for even the slightest sign of twinning. I once had a case of a coiled coil that seemed to be sitting on a crystallographic two-fold. R-factors were a bit too high for the resolution. Lowering the symmetry and redefining that two-fold axis as a twinning operator lead to very reasonable R-factors, and the ends of the helices (in the original model disordered) to adopt obviously different conformations. At the time, we did not feel too confident with that interpretation (swapping crystallographic symmetry for a twinning operator and an NCS operator at the same time) and screened for a crystal that seemed not to suffer from that malady (which we found); therefore it was - in hindsight unfortunately - never published in that form. Nowadays, I feel very strongly, that reducing the symmetry and reassigning certain crystallographic operators to a mix of twinning operators/NCS operators to be actually a legitimate - and often probably more correct - way of interpreting certain problematic crystals. Just 2 cents Jens On Wed, 2012-07-11 at 13:37 -0600, Lukacs, Christine wrote: Hi all- I have a protein that crystallizes in I422, and diffracts well, between 1.3-1.7A. Beautiful density, slightly higher final R-factors than you might expect at this resolution (low to mid 20s). The density is all beautiful, except that I have this one little clash, between a few atoms from a tyrosine and its symmetry mate. In this picture I have it modeled as an Alanine and you can see the two tyrosine rings interlocking; and there is clearly no alternate conformation. Since it is not near my site of interest, I have been pretty much ignoring it, going through refinement with it as an alanine, then changing it at the very end to a tyrosine and just minimizing B-s, no positional. Now that I plan to publish a bunch of these, I should probably figure out what is really going on. Any insights? Thanks Christine Christine Lukacs Roche This message is intended for the use of the named recipient(s) only and may contain confidential and/or proprietary information. If you are not the intended recipient, please contact the sender and delete this message. Any unauthorized use of the information contained in this message is prohibited.
Re: [ccp4bb] Off-topic: PDB deposition of multiple structure factor files
It might be a portal issue. But the pdb staff is very helpful in getting this deposited. We deposited data of I think 4 crystals and 3 wavelengths with different phase sets in 2008. (The data was anisotropic, 3.5/4.2 A resolution, model building was not straight forward, so we wanted to preserve as much information as possible. If memory serves right, we have experimental fobs, anisotropy corrected fobs, a derivative and a semet dataset; if you're interested, pdb code is 3dhw, have a look at the sf-file) hth, Jens On Fri, 2012-04-27 at 20:35 +0200, Mark J van Raaij wrote: again, it looks like this is particular to the US portal. We submit via the European www.pdbe.org and can submit multiple datasets. See 2XGF for an example. Note: I think from www.rcsb.org only one file can be downloaded, but www.pdbe.org clearly shows both. Although you are in the US, you can use the pdbe deposition tool AUTODEP - or the Japanese one, if you like. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 27 Apr 2012, at 20:23, Florian Schmitzberger wrote: Dear All, With my most recent PDBe deposition, in addition to the native data, I had intended to deposit the anomalous data, used for structure determination, and make it available for download. This turned out to be less straightforward than I had anticipated, because the current PDB convention is to only allow a single structure factor file for experimental data (usually the native dataset), available for download from the PDB. In my case, the anomalous data were concatenated with the native data into a single cif file (this worked and made sense, because both for both datasets the unit cell dimensions are virtually identical). I imagine it would be beneficial to be able to make available more than a single structure factor file, including the ones derived from experimental phasing, in the PDB, along with the final coordinates, without concatenating the data into a single file (which may lead to confusion to users when downloaded). Is this anything the PDB is already working to implement in the near future (perhaps via the coming PDBx format)? Best regards, Florian
Re: [ccp4bb] Disorder or poor phases?
Hello, Kay is absolutely right. Just to make this clear: We all know that in many cases, you start out with poor phases (i.e. a weak SIR/MIR/MAD or a borderline replacement model) and your density is modest. The prudent thing to do at this stage is, to build only things you trust and have a look at the improved density. Well, we all know also, that an improved density means in most cases a density with improved phases. The term disorder means, a region of higher uncertainty. Logically, the more information you have (more actual data points - i.e. reflections == resolution/completeness; more reliable Fs; etc.; _better phases_) the better you can pinpoint these areas. The phase is a magnitude we cannot measure, but that affects the density the most. We determine it through refinement (which encompasses density interpretation and computational optimization of atomic parameters with regards to the reflection data). Gedankenexperiment: If you collect data on a crystal, let's say on a sealed tube from 1950 with a photon counter, and you collect the same data from the same crystal on a modern synchrotron with a PAD, you might find certain areas of your molecule disordered that you might be able to interpret with (more) data collected from the better collected data. Probably more so - if you have the same amount of data and poorer or better phases, you have a similar problem. My point being: the term disorder is related to the amount of data you have (be it collected (I's) or deduced (phi's)). With very few exceptions (see for example the paper for 1M1N), it's not the method (diffraction) that tricks us, it's just the amount of information that we have, that prevents us from building complete models. Most importantly, the term disordered - as used in macromolecular terminology - depends on resolution /and/ quality of the phases. (As a side note: What we call alternative conformations in macromolecular crystallography is called disorder in small molecule crystallography. I don't know what the SM word for the MM disorder is...) Cheers, Jens On Wed, 2012-04-11 at 06:44 +0100, Kay Diederichs wrote: Hi Dale, my experience is that high-B regions may become visible in maps only late in refinement. So my answer to the original poster would be - both global reciprocal-space (phase quality) and local real-space (high mobility) features contribute to a region not appearing ordered in the map. This would be supported by your experience if those residues that you could not model in 3BCL had high (or at least higher) B-factors compared to the rest of the model. Is that so? best, Kay
Re: [ccp4bb] Collecting small-molecule diffraction on a Macromolecular xtallography beam line
Giorgo, We have done that routinely for quite some time now. We had problems when using a normal CCD detector, where we had to collect two or three sweeps to avoid overloads (see below). Since we have the PILATUS this is not necessary anymore and the data behaves fine. Problems still persisting are: we have only a single axis goniometer, which can lead to low completeness in P1 and P-1. Highest energy (17keV) and closest distance (188mm) at our beamline have many SM crystals (even the ones that don't diffract in house -- that is a 300 or 500 u sealed tube) with an I/sig of 5-10 at the edge of the detector. Crunch, Acorn, ShelxCDE and ShelxS don't have any problem with any of the data we collected to 0.9A resolution. The multipass caused some inexplicable non definite positives during refinement. We haven't tracked that down systematically, so it might just have happened haphazardly. HTH, Jens On Wed, 2012-02-08 at 11:41 +, Giorgio Giardina wrote: Hello, I have some interesting small molecule xtals. I was wondering if it is possible to collect a small molecule data-set using a sincrotron macromolecular xtallography beam line, maybe with a very low beam intensity and moving the detector as close as possible? Has anybody experienced that? And if I get the images back home, can I process them using standard macromolecular software or do I need ab-initio special programs? Will MR work for phasing? Thanks in advance, Giorgio
Re: [ccp4bb] odd behaviour of reindex
Ian, Ah! the old the row is the column depiction of matrices in CCP4 - ha had forgotten about that! Now at least the output makes sense and the caveat is to never use brackets. Thanks to all replies!! Jens On Tue, 2012-01-31 at 10:17 +, Ian Tickle wrote: On 31 January 2012 02:30, Jens Kaiser kai...@caltech.edu wrote: Hi all, we encountered an odd behaviour of REINDEX. Snip form logfile: Data line--- reindex HKL (h+l)/2, -k, (h-l)/2 Data line--- end Reflections will be reindexed, and unit cell recalculated Reindexing transformation: (h' k' l') = ( h k l ) ( 1.0 0.0 1.0 ) ( 0.0 -1.0 0.0 ) ( 0.5 0.0 -0.5 ) Obviously, the first line of the matrix is not what we intended to create. inputting the transformation as HKL h/2+l/2, -k, h/2-l/2 produces the desired result: Data line--- reindex HKL h/2+l/2, -k, h/2-l/2 Data line--- end Reflections will be reindexed, and unit cell recalculated Reindexing transformation: (h' k' l') = ( h k l ) ( 0.5 0.0 0.5 ) ( 0.0 -1.0 0.0 ) ( 0.5 0.0 -0.5 ) Admittedly, the documentation does not use any brackets in the examples, but i would expect REINDEX either to throw an error or treat (h+l)/2 like (h-l)/2 but not treat them in the way encountered. Jens Reindex is not treating (h+l)/2 any differently from (h-l)/2, they are being treated identically, i.e. it is simply ignoring the brackets in both cases (which is why expanding the expressions without brackets works).. So (h+l)/2 is being treated as though you had specified h+l/2 and (h-l)/2 becomes h-l/2. Don't forget that the rule for matrix multiplication is row-by-column, not row-by-row! Cheers -- Ian
[ccp4bb] odd behaviour of reindex
Hi all, we encountered an odd behaviour of REINDEX. Snip form logfile: Data line--- reindex HKL (h+l)/2, -k, (h-l)/2 Data line--- end Reflections will be reindexed, and unit cell recalculated Reindexing transformation: (h' k' l') = ( h k l ) ( 1.0 0.0 1.0 ) ( 0.0 -1.0 0.0 ) ( 0.5 0.0 -0.5 ) Obviously, the first line of the matrix is not what we intended to create. inputting the transformation as HKL h/2+l/2, -k, h/2-l/2 produces the desired result: Data line--- reindex HKL h/2+l/2, -k, h/2-l/2 Data line--- end Reflections will be reindexed, and unit cell recalculated Reindexing transformation: (h' k' l') = ( h k l ) ( 0.5 0.0 0.5 ) ( 0.0 -1.0 0.0 ) ( 0.5 0.0 -0.5 ) Admittedly, the documentation does not use any brackets in the examples, but i would expect REINDEX either to throw an error or treat (h+l)/2 like (h-l)/2 but not treat them in the way encountered. Cheers, Jens -- +-+-+ | Jens T. Kaiser | Office: +1(626)395-2662 | | California Institute of Technology | Lab:+1(626)395-8392 | | m/c 114-96 | Cell: +1(626)379-1650 | | 1200 E. California Blvd.| Xray: +1(626)395-2661 | | Pasadena, CA 91125 | Email: kai...@caltech.edu | | USA | Skype: jens.t.kaiser | +-+-+
Re: [ccp4bb] writing scripts-off topic
Yuri, I second everythig Ethan Merritt said, but would add: awk is easier and as functional as Perl for quick and dirty projects. Once you need Perl's complexity, you're probably better off moving to Python or a compiled language; Perl is powerful, but it allows you to do really dirty coding; I found myself writing an elegant Perl script that I did not understand anymore 1/2y later. I would also add Fortran (maybe Fortran90) to the list of higher level languages. Disclaimer: I'm not a programmer, I hack things together... Cheers, Jens -Original message- From: Ethan Merritt merr...@u.washington.edu To: CCP4BB@JISCMAIL.AC.UK Sent: 1970 Jan, Thu, 1 00:00:00 GMT+00:00 Subject: Re: [ccp4bb] writing scripts-off topic On Monday, 23 January 2012, Yuri Pompeu wrote: Hello Everyone, I want to play around with some coding/programming. Just simple calculations from an input PDB file, B factors averages, occupancies, molecular weight, so forth... What should I use python,C++, visual basic? What you describe is primarily a task of processing the text in a PDB file. I would recommend perl, with python as a more trendy alternative. If this is to be a springboard for a larger project, then you might choose instead to use a standard library like cctbx to do the fiddly stuff and call it from a higher level language (C or C++). Ethan
Re: [ccp4bb] From non-twinned to twinned?
What are your cell constants and space group? It sounds to me you misindexed and then artificially twinned your structure by integrating/merging in too high of a symmetry. I've seen that happen for primitive hexagonal which was actually C-centered monoclinic. Also, in my experience this is more likely to happen with denzo/scalepack as it refines every image and does postrefinement in scalepack. XDS will decide for you on a symmetry after integration, and in MOSFLM you should see earlier that something is wrong. HTH Jens On Wed, 2012-01-04 at 21:42 +0800, Zhiyi Wei wrote: Dear all, I recently collected a dataset (~2000 frames) from a single crystal. If merge first 600 frames (sca1) or last 600 frames (sca2), Rmerge values from scalepack seem to be ok (~10%) though rejection ratios are high (~5%). But if I merge all frames together, Rmerge value goes up to ~20% and rejection is extremely high (~20%). Then, I checked sca1 and sca2 by xtriage in phenix. Surprisingly, the logfiles told me that sca1 is no twining while sca2 is very likely to be twinned. I never met this case before. So, I am wondering if it is possible from a non-twinned structure to a twinned structure just due to radiation damage. If the answer is yes, does it mean that I should not collect a large number of frames to amplify anomalous signals by using this crystal? Thanks a lot! Best, Zhiyi
Re: [ccp4bb] PHENIX vs REFMAC refinement had me fooled
My money is on the the wrong test set (as Jonathan Elegheert suggested). I have seen this several times with newbies, when the test set is created by phenix. It does it the xplor-way. When it comes to the free set, refmac defaults to 0, phenix tries to be intelligent (i.e. if 1/0 it uses 1, if more 0/1/2... it uses 0). Additionally, refmac (and I think phenix) produces Fc filled maps. So if you swap R/freeR reflections, the maps always look spectacular, as they essentially are Fcalc maps. Inspection of the logfiles should help: #of reflections free and #of reflections for refinement are reported by both programs, and IIRC, you should get a warning that your free-R-set is not sensible. One way out is to /always/ use ccp4 to assign the test-set, then both programs run fine. Otherwise you have to explicitly tell refmac to use 1 as the test reflections. HTH, Jens On Thu, 2011-12-08 at 18:36 +0100, Christopher Browning wrote: Dear All, Question: Has anybody ever refined the same structure using PHENIX and then tried REFMAC to see what happens? I did and I stumbled on something funny. I'm refining a structure at 1.1A resolution which was solved with Iodine phasing using PHENIX AutoSolve. Got a great map and the structure was built almost completely. I had to build a few residues myself, and using the published sequence, I started filling in the residues, but as I came nearer the N-terminus, it looked like the density did not match residues from the sequence. I kept the residues as in the sequence, but as you can see from the PHENIX refined picture (below is the link) it still looks like the amino acid sequence in the crystal does not match the published protein sequence. Out of interest I refined the same file in REFMAC, and now the electron density is correct, and the sequence of the amino acids in the crystal matches the published sequence (see link for picture below). Not only that. my R/Rfree improved (16.5/19 for PHENIX, 10/18 for REFMAC). I've also refined the occupancies of the iodide, however the the output FO-FC map from PHENIX complains and the REFMAC map is fine. How can this be and what causes this? Link for the pictures: Both maps are at identical Sigma levels in both pictures. PHENIX: http://dl.dropbox.com/u/51868657/PHENIX_refined.png REFMAC: http://dl.dropbox.com/u/51868657/REFMAC_refined.png Cheers, Chris Browning
Re: [ccp4bb] cryo protection
Hey Len, I had this problem, too. As you know, my favorite first try is always fomblin (no need to mix anything). I had quite a bit success in stubborn cases to inject about 4uL fomblin through the tape on top of the drop and then looping crystals through the oil layer. You can wick the mother liquor off and try them right away or continue manipulation under oil Cheers, Jens On Wed, 2011-10-26 at 11:46 -0500, Leonard Thomas wrote: Hi All, I have run into a very sensitive crystals system when it comes to cryo protecting them. I have run through the usual suspects and trays are going to be setup with a cryo protectant as part of crystallization cocktail. The one problem that seems to be occurring is that the crystals crack as soon as they are transfered out of the original drop. I am running out of ideas and really would love some new ones. Thanks in advance. Len Leonard Thomas Ph.D. Macromolecular Crystallography Laboratory Manager University of Oklahoma Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019-5251 lmtho...@ou.edu http://barlywine.chem.ou.edu Office: (405)325-1126 Lab: (405)325-7571
Re: [ccp4bb] Anomalous map average by NCS
Hui/Phoenix, It is pretty hard to say from what you describe which method is right. The NCS maps in coot will give you a correct - but not as good of an estimate of your density - if, and only if, you have enough of a model and you have defined your NCS master and slave chains correctly. If you have chemically different but similar subunits and you don't check them correctly in the NCS ghosts dialog, you'll get bad results. CCP4 map average (from the map and mask utilities) is pretty tricky, most of the times; When I had to do averaging of anomalous difference maps, I found it most useful to do cyclic averaging of your normal (i.e. non-anomalous) map, either with dm, ave/rave or MAIN (and probably phenix, though I have not tried it); that will give you good indications of the quality and validity of your averaging (i.e. backtransformation R factors; correlation coefficients tend to be also more reliable). Then use these phases (rotated, but the ccp4i fft task will do that for you if you select anomalous map) to calculate your averaged anomalous map with your DANOs and the averaged phases. This seems to me the most robust and reliable method of averaging anomalous maps in the general case. If you have your NCS related molecules defined properly, you might want to add coot's average maps on top of that, but it is unlikely to improve the outcome. Cheers, Jens On Wed, 2011-09-21 at 16:45 -0700, Hui Wang wrote: Dear all, I am wondering if anybody did NCS average for Anomalous map. Based on my knowledge, there are two days to do it. 1, Use Map average in CCP4 program (input from map which cover unit cell, create averaged density for whole unite cell ) 2, Use NCS map in coot program. However, I got different results from both ways. I am not sure which one is corret. Someone can help me with that? Thanks a lot Phoenix
Re: [ccp4bb] viewing and scoring diffraction using the PX Scanner
OK, I took the challenge. I got 7 out of 10. The three I missed were 2 questions about multi-well crystals which would be better (no problem) and the capillary (no problem either, because you can mount it)... I wouldn't be that snipe and braging (pun intended) if I would not agree with Klaus Jens On Tue, 2011-04-19 at 03:02 -0600, Marcus Winter wrote: Dear Klaus, Thanks for your note. Yes: we do understand the point that you make and, sincerely, we are sensitive to this possible criticism. However, we trust that you would agree that this was not a blatant advertisement. Also, my original posting was in direct response to a not unrelated one. Thank you for recognising the contributions made by the manufacturers. No doubt, we're – all of us, dependent upon public funding to some extent - directly or indirectly, and, similarly, we're taxpayers too... Anyway: why not entertain yourself by taking two minutes out for the PX Scanner Crystal Challenge: signature_crystalchall Many Thanks and Very Best Regards, Marcus (Agilent Technologies) -Original Message- From: Klaus Fütterer [mailto:k.futte...@bham.ac.uk] Sent: 19 April 2011 09:40 To: WINTER,MARCUS (A-UnitedKingdom,ex1) Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] viewing and scoring diffraction using the PX Scanner Dear Marcus, I always feel a bit uneasy about the advertisement-like posts that Agilent (and others) place on this BB. Of course, there are interactions between users and suppliers on many fronts, not least the support you guys provide in the form of sponsorship to meetings and conferences. Still, the original purpose of this bulletin board is the exchange of expertise and advice on a particular software package. No doubt, company-based crystallographers make valuable contributions to discussions on the BB. This is, however, different to placing an open sales pitch. I can remember that some in the community were miffed when discussions on non-CCP4 software packages became prominent. I think it is only fair to ask suppliers to minimise marketing of their products here. After all, the infrastructure for the BB is paid for by public money. With the obligatory '2 cents worth', Klaus === Klaus Fütterer, Ph.D. Reader in Structural Biology Undergraduate Admissions School of Biosciences P: +44-(0)-121-414 5895 University of Birmingham F: +44-(0)-121-414 5925 Edgbaston E: k.futte...@bham.ac.uk Birmingham, B15 2TT, UK W: http://tinyurl.com/futterer-lab === On 19 Apr 2011, at 08:22, Marcus Winter wrote: Dear Artem, Thanks for your reply. You raise a number of points. Immediately, I should comment that the price of the PX Scanner is very considerably less than the $400k that you mention. Whilst - with the proteins and crystallisation conditions that you may be working with, visual inspection may be sufficient to differentiate salt from protein crystals (as you suggest), you will accept that generally this may not be the case. Thus, ‘direct’ inspection, using X-rays, must surely be the most appropriate way ? As you will be aware, the best looking crystals are seldom the best diffracting. This is well demonstrated through the PX Scanner ‘Crystal Challenge’, of course. Clearly, that’s another prime purpose of the PX Scanner: to identify the ‘best’ crystals from amongst a multitude of candidates in a single droplet or across a plate, etc. Also, using the PX Scanner, we can check the effect of added cryo- protect. prior to freezing. Therefore, with this range of uses, the PX Scanner is clearly not intended for full ‘data-collection’ – but rather to most effectively support crystallisation optimisation and as a complement to in-house and central facility data-collection work. From the feedback that we receive, the PX Scanner is much valued by the number of groups which are now using these systems worldwide. However, even the proof of Grandma’s apple pie is not until the eating. Accordingly, we most cordially invite you to visit one of our application labs – or perhaps one of our customer
Re: [ccp4bb] linux flavors
David, I'm a big fan of SuSE. the nuveau problem exists, too, but blacklisting fixed it for me. For older hardware I love ultimate linux. The way I understand Zalman stereo it works with everything, given the program you use supports it. I'm sure you are aware of the problem with nVidia and emitters under Linux: you need the DIN pin on the card; USB emitters won't work. As far as I can tell, you also need the new nVidia DIN emitter, I had bad results with nuVision emitters and the new nVidia driver. Cheers, Jens linux.On Tue, 2011-02-22 at 10:16 -0500, David Roberts wrote: Hello all, Quick question on linux varieties. For years (and years) I have used fedora (after Ultrix of course). In fact, most of my computers are running FC7 (that long ago), it's very stable and works fine. However, since it is no longer supported, I'm toying with upgrading. I upgraded one machine to FC13. However, this nouveau driver thing is killing me, and getting my nvidia drivers installed is hopeless (I have followed every thread on this and I simply give up - it's not worth it). With a Zalman monitor it doesn't matter - nouveau works fine and my stereo is good - so I don't really care (or do I). The question is this - what flavors of linux out there are simplest to install - work instantly with various hardwares, and run stereo seamlessly (either Zalman stereo or hardware stereo with an emitter). For zalman anything works - which is why I'm going that way - but I still need hardware stereo on a few machines. So, for hardware, I need my nvidia drivers to install easily. I'm downloading ubuntu - is that a good choice? Can I run different flavors of linux with nfs and share drives in a local network (so one has fc7, one has fc13, and another has ubuntu)? Thanks Dave
Re: [ccp4bb] Difficult to solve MR - A mysterious case
Chen, First of all, it sounds funny that you can't integrate your data in C2 or P2. That should be possible if your lattice is hP. But then if your Rmrg is OK in P622, p622 is probably at least your (apparent) point group. Second, I'm usually suspicious of SG P622. I would almost bet you're missing at least one screw (that happens easily, especialy with hexagonal plates on single axis collection; a very long z-axis, e.g. is usually a good indication of P6(1/5)22). Check the end of the pointless output to make sure the assignement is not done because of 'no observations'. Try phaser in different runs with all possible spacegroups individually selected. If you get (for some reason) high Z-scores for multiple space groups early on, the 'automatic' space group assignement often fails, especially with high NCS. Don't dismiss twinning based on not beeing able to detect it. Some structures e.g. are hypercentric and present 'normal' intensity statistics when twinned. Some types of NCS could also mask twinning. Figuring that out requires more work. You basically have to scale your data in all possible 'real' symmetries (assuming merohedral twinning), do your replacement and define the 'left out' symop as twinlaw. But I guess when your merging stats are fine you most probably have a perfect twin (if you have one at all) and your refinement will suck anyways. Providing cell constants, pointless log (both for SG assignement), truncate log (maybe in comparision with your C222(1) dataset; for twinning) would help discerning between many of those possibilities. Good luck, Jens -Original message- From: Chen Guttman guttm...@bgu.ac.il To: CCP4BB@JISCMAIL.AC.UK Sent: 1970 Jan, Thu, 1 00:00:00 GMT+00:00 Subject: [ccp4bb] Difficult to solve MR - A mysterious case Dear Colleagues, Im on the bring of giving up on a very difficult and puzzling structure and my last hope lies here with you folks... Background: Im working on a point mutated protein with a known w.t. structure. This specific mutation have been crystallized in the form of plates (C2221 SG) and hexagons (P622 SG). Whilst the plate form structure was solved without of a hiccup, the later was a different story. I am attaching two images of the obtained diffractions of the hexagon crystal, 90 degrees apart (the 905 images were collected at a synchrotron beamline with a delta phi of 0.2). What I've done so far: - Diffracted images were indexed integrated with iMosflm (used pointless to asses the correct SG). This was later scaled in SCALA to 2.4A with the attached statistics. - HKL2000 was also used but it couldn't lock on the P622 symmetry (gave either C2 or P2 which fit to the first section of the data set but didn't fit the 90 degree diffraction pattern); Splitting the data into two data sets at the 90degree gave a P6 option but once it finished the first 90 degree, it missed-fitting the 2nd data set. - Scaled data was phased using Phaser with the known w.t. structure which gave a single solution with the following statistics: RFZ=7.6 TFZ=33.4 PAK=0 LLG=1316 LLG=1426 and with an initial R-factor of 48.7 - Looking at density map, I could distinguish areas which had excellent fit while other areas demonstrated poor fit. The ligand, which was soaked with the crystal and was also solved with the w.t. protein, fitted almost perfectly with the identified positive peaks. However, apparently there were also major changes (mainly positive peaks) that could not be accounted for by the structural restraints and were hard to figure out. These major changes, which might as well be ghosts of a problematic data set, are the reason I want to solve this structure - Rigid body, Restrained refinement and real space refinement didn't improve Rwork/Rfree beyond 0.4/0.46. I've also tried the following steps: - Used AMore and Molrep - didn't yield any improvement in density map nor in the R factor statistics - Used Phenix Refine with different settings including simulated annealing, didn't work either - Tried rebuilding using Autosol and generation of OMIT map - this yielded some sort of improvement to 0.39/0.44 but still the map was not drastically improved and there where areas which were hard to fit with the current model. - Tried removing stretches of residues and check the map after refinement - mostly i've noticed spots of positive peaks related to the backbone. - I've also checked for wrong use of symmetry with several programs, including Zanuda, and still the best SG is P622. - I've checked for twining with Phenix, CCP4 and web hosted programs and no twining was detected (not even perfect twining). So, I've pretty much hit a brick wall. I would be happy to hear any suggestion to what might be the problem with this Data set. Thanks for the help and time, Chen -- Chen Guttman The Zarivach laboratory, Building 39, Room 009B Ben-Gurion University
Re: [ccp4bb] pymol movies scripts
I used to do that in POVray. you can use any program that writes POV output and can generate all the objects you want. I used to write each object I want to manipulate to a separate file and #declare ed it as a POVray object. Then I wrote a 'master' povray file, that #include d the aforementioned ones and added (with the time variable) the transformations I wanted to have. It is then really simple to e.g. rotate your molecule while you're flying towards the active site and slowly display a surface. The upside is, you have tremendous control, the downside is that it's not really reusable for other projects and the planning (which objects to create, and the writing out of them) takes quite a while. well, and you'll have to look a bit into povray (#declare, #include, transform, texture, camera, clock). I think it's well worth the effort. ah, and be careful, for some graphics programs it is important that you don't move anything between writing ou the objects as they translate your scene into a povray frame. good luck and have fun jens On Tue, 2007-09-18 at 11:22 +0200, Sebastiano Pasqualato wrote: Hi all, I'm starting using pymol to generate movies to show my structure. While its seems fairly easy to generate simple movies with rocking or rotating molecules, I have been finding some difficulties understanding how to generate more complex movies. For instance, I'd love to generate a movie in which the molecule rotate along the x axis, then along the y axis, while the surface slowly shows up... or even more complicated scenarios, involving changes in colors of the objects (of course not sudden ones!)... Does anybody have some scripts to share with me, or can point me to some web pages that would explain me how to do that? Thanks a lot in advance, best, Sebastiano -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 Milano Italy tel +39 02 9437 5094 fax +39 02 574 303 310 No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.5.487 / Virus Database: 269.13.22/1013 - Release Date: 9/17/2007 1:29 PM
Re: [ccp4bb] microscope
I had some pretty good experience with MOTIC SMZ140/143 microscopes. compared to Leica (which are my favorites) they seem a little flimsy but image quality is good, they come with a built in video cam and grabber, they have a large table and at 1,700 bucks (with camera, 10x and 20x eyepieces and a 1.5x 'objective' and yes, that's one-thousand-seven-hundred!) they're unbeatable. the two big negatives: they come with built in halogen light, so the can get warm (yoo can use the reflective light to avoid that) and no polariser option (they have one on their webpage - don't buy that, unless you want to disassemble it, getting polarisers from somewhere else and jerry rig them in is easier) cheers jens On Mon, 2007-06-11 at 06:12 -0700, Frank Lees wrote: Hi, I apologize if this has been posted here before, but I will need to buy a standard stereo microscope for viewing crystals. Could anyone give me some suggestions regarding the brand, model, and retailer? Thanks in advance! Frank __ Get the Yahoo! toolbar and be alerted to new email wherever you're surfing.
