Re: [ccp4bb] shelxl, refinement of occupany
Refining a common occupancy (using one free variable) for a loop that is in poor density is well worth trying. The loop may well have multiple conformations and this may make it easier to find a second conformation in the difference map. I also recommend refining the occupancies of any selenium atoms present (e.g. by changing '11' to '1'), this allows for partial incorporation and radiation damage. Hydrogen atoms should be included in all final refinements, they cost no extra parameters and can reduce the free R by 0.5 to 1.0%; the antibumping restraints involving them (BUMP) are also useful. However I do not include OH hydrogens because the stupid program sometimes puts them in the wrong place (e.g. two on the same H-bond) and the combination of the riding model and antibumping restraints can tear the structure apart. For amide sidechains and histidines I would recommend checking the conformations with the molprobity server before adding the hydrogens in SHELXL. It is however less work to model all alternative conformations before adding hydrogens with HFIX, the program will then set up the disorder correctly for the hydrogens too. In such cases the disorder should be modeled one atom further back than you can see in the maps; if CG has two positions then there should be two pairs of alternative H-atoms on CB, which the program will set automatically if you have included PART 1 and PART 2 alternatives for CB. This is appreciably more work to set up later by hand if you add the hydrogens before modeling the disorder! It is worth trying to make the waters anisotropic (with an ISOR restraint) to see if this reduces R free significantly. If the .lst file gives NPD warnings the restraints on the anisotropic atoms are too soft. And I am surprised that after all your emails on the subject you still can't spell 'SHELX'! George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Wed, 21 Mar 2007, U Sam wrote: I am looking for some advice. (1) In shelex what should I mention to refine occupancy. I have two molecule in asym unit. In A molecule residues 89-92 is present, but in B these residues are missing. So I believe in B these residues should not be with zero occupancy, although I donot find any prominent density (Fo-Fc). Occupancy could be anywhere between 0.0 to 1.0. How can I refine this parameter. Or, I should neglect this missing part of residues in B indicating a occupancy of 0.0 or keep a gap of these residues with no information including coordinates. Right now R1=14% and R1(free) =18%, without making water anisotropic. (2) I am using 1.4 A data. Should I refine water anisotropically ? If answer is yes, when. (3) Should I add hydrogen at this resolution. If yes, when should I do. Thanks Sam _ The average US Credit Score is 675. The cost to see yours: $0 by Experian. http://www.freecreditreport.com/pm/default.aspx?sc=660600bcd=EMAILFOOTERAVERAGE
Re: [ccp4bb] Scale factor in ccp4
A less convoluted method is to read both .sca files into xprep, scale them together and write out the combined .sca file. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Thu, 22 Mar 2007, Eleanor Dodson wrote: When youu run scalepack2mtz the GUI always follows this by TRUNCATE to convert Is to Fs At that stage there is an attempt to put the data on roughly an absolute scale, either using the NRES you gave as input or if that is not set, I think assuming 50% of the cell volume is protein. Anyway the scales WILL be different after TRUNCATE. If you want to scale them together more carefully you will need to run cad, then SCALEIT ( on the GUI undr exptl phases) THEN convert each I1 and I2 back to a sca file .. Seems a lot of trouble! Why do you need this? Eleanor yang li wrote: Hi: I have two set of data from the same crystal with the names 1.sca and 2.sca, they have different Intensity values due to different scale factors. Now I use Scalepack2mtz convert them to 1.mtz and 2.mtz, then use cad to merge to a cad.mtz, then convert it to cad.sca file, I find that the Intensity values in this cad.sca arediffrent from 1.sca and 2.sca, I wonder if the program has scaled the values itself? If that is true, which program did this, Scalepack2mtz or cad? Thanks! Li Yang
[ccp4bb] Workshop: Macromolecular Crystallography at PETRA III
Beamline Design Workshop Macromolecular Crystallography at PETRA III EMBL-Hamburg Outstation, April 23 to 25, 2007 Starting in 2007, the PETRA storage ring in Hamburg, Germany, will be converted into a 3rd generation source for synchrotron radiation. The new PETRA III storage ring will be operational in 2009 and provide X-rays of extreme brilliance. EMBL Hamburg is in charge of building and operating three undulator beamlines on PETRA III. Two of these beamlines will be dedicated to macromolecular X-ray crystallography and one to small angle X-ray scattering (Further information can be obtained under http://www.embl-hamburg.de/services/petra/). The beamlines will be integrated with facilities for sample preparation, high-throughput crystallization, data processing and data evaluation. The workshop will bring together structural biologists and beamline scientists to discuss scientific and experimental challenges in macromolecular crystallography. The results of this discussion will directly enter into the design of the two beamlines for macromolecular crystallography in the [EMAIL PROTECTED] project. The workshop will start on 23rd April at 15:00 and finish on 25th April at 18:00. There is no registration fee, but participants are expected to cover their own travel and accommodation. For further information and registration, please go to: http://www.embl-hamburg.de/workshops/2007/mx/ The number of participants will be limited to 50. The registration deadline is April 4th, 2007. Applicants will be informed about the acceptance of their applications by April 9th, 2007. Organising committee: Thomas R. Schneider, Michele Cianci, Gleb Bourenkov
Re: [ccp4bb] Highest shell standards
I will agree with Ulrich. Even at 3.0 A, it is possible to have a structure with reasonable accuracy which can explain the biological function/ or is consistent with available biochemical data. Ranvir --- Ulrich Genick [EMAIL PROTECTED] wrote: Here are my 2-3 cents worth on the topic: The first thing to keep in mind is that the goal of a structure determination is not to get the best stats or to claim the highest possible resolution. The goal is to get the best possible structure and to be confident that observed features in a structure are real and not the result of noise. From that perspective, if any of the conclusions one draws from a structure change depending on whether one includes data with an I/sigI in the highest resolution shell of 2 or 1, one probably treads on thin ice. The general guide that one should include only data, for which the shell's average I/sigI 2 comes from the following simple consideration. F/sigF = 2 I/sigI So if you include data with an I/sigI of 2 then your F/sigF =4. In other words you will have a roughly 25% experimental uncertainty in your F. Now assume that you actually knew the structure of your protein and you would calculate the crystallographic R-factor between the Fcalcs from your true structure and the observed F. In this situation, you would expect to get a crystallographic R- factor around 25%, simply because of the average error in your experimental structure factor. Since most macromolecular structures have R-factors around 20%, it makes little sense to include data, where the experimental uncertainty alone will guarantee that your R-factor will be worse. Of course, these days maximum-likely-hood refinement will just down weight such data and all you do is to burn CPU cycles. If you actually want to do a semi rigorous test of where you should stop including data, simply include increasingly higher resolution data in your refinement and see if your structure improves. If you have really high resolution data (i.e. better than 1.2 Angstrom) you can do matrix inversion in SHELX and get estimated standard deviations (esd) for your refined parameters. As you include more and more data the esds should initially decrease. Simply keep including higher resolution data until your esds start to increase again. Similarly, for lower resolution data you can monitor some molecular parameters, which are not included in the stereochemical restraints and see, if the inclusion of higher-resolution data makes the agreement between the observed and expected parameters better. For example SHELX does not restrain torsion angles in aliphatic portions of side chains. If your structure improves, those angles should cluster more tightly around +60 -60 and 180... Cheers, Ulrich Could someone point me to some standards for data quality, especially for publishing structures? I'm wondering in particular about highest shell completeness, multiplicity, sigma and Rmerge. A co-worker pointed me to a '97 article by Kleywegt and Jones: http://xray.bmc.uu.se/gerard/gmrp/gmrp.html To decide at which shell to cut off the resolution, we nowadays tend to use the following criteria for the highest shell: completeness 80 %, multiplicity 2, more than 60 % of the reflections with I 3 sigma(I), and Rmerge 40 %. In our opinion, it is better to have a good 1.8 Å structure, than a poor 1.637 Å structure. Are these recommendations still valid with maximum likelihood methods? We tend to use more data, especially in terms of the Rmerge and sigma cuttoff. Thanks in advance, Shane Atwell TV dinner still cooling? Check out Tonight's Picks on Yahoo! TV. http://tv.yahoo.com/
Re: [ccp4bb] Highest shell standards
There are journals that have specific specifications for these parameters, so it matters where you publish. I've seen restrictions that the highest resolution shell has to have I/sig 2 and completeness 90%. Your mileage may vary. I typically process my data to a maximum I/sig near 1, and completeness in the highest resolution shell to 50% or greater. It's reasonable to expect the multiplicity/redundancy to be greater than 2, though that is difficult with the lower symmetry space groups in triclinc and monoclinic systems (depending upon crystal orientation and detector geometry). The chi^2's should be relatively uniform over the entire resolution range, near 1 in the highest resolution bins, and near 1 overall. With this set of criteria, R(merge)/R(sym) (on I) can be as high as 20% and near 100% for the highest resolution shell. R is a poor descriptor when you have a substantial number of weak intensities because it is dominated by the denominator; chi^2's are a better descriptor since it has, essentially, the same numerator. One should also note that the I/sig criteria can be misleading. It is the *average* of the I/sig in a resolution shell, and as such, will include intensities that are both weaker and stronger than the average. For the highest resolution shell, if you discard intensities greater than 2sig, then you are also discarding intensities substantially greater than 2sig as well. The natural falloff of the intensities is reflected (no pun intended) by the average B-factor of the structure, and you need the higher resolution, weaker data to best define that parameter. Protein diffraction data is inherently weak, and far weaker than we obtain for small molecule crystals. Generally, we need all the data we can get, and the dynamic range of the data that we do get is smaller than that observed for small molecule crystals. That's why we use restraints in refinement. An observation of a weak intensity is just as valid as the observation of a strong observation, since you are minimizing a function related to matching Iobs to Icalc. This is even more valid with refinement targets like the maximum likelihood function. The ONLY reasons that we ever used I/sig or F/sig cutoffs in refinements was to make the calculations faster (since we were substantially limited by computing power decades ago), the sig's were not well-defined for weak intensities (especially for F's), and the detectors were not as sensitive. Now, with high brilliance x-ray sources and modern detectors, you can, in fact, measure weak intensities well--far better than we could decades ago. And while the dynamic range of intensities for a protein set is relatively flat, in comparison to a small molecule dataset, those weak terms near zero are important in restraining the Fcalc's to be small, and therefore helping to define the phases properly. In 2007, I don't see a valid argument of severe cutoff's in I/sig at the processing stage. I/sig = 1 and a reasonable completeness of 30-50% in the highest resolution shell should be adequate to include most of the useful data. Later on, during refinement, you can, indeed, increase the resolution limit, if you wish. Again, with targets like maximum likelihood, there is no statistical reason to do that. You do it because it makes the R(cryst), R(free), and FOM look better. You do it because you want to have a 2.00A vs. 1.96A resolution structure. What is always true is that you need to look at the maps, and they need as many terms in the Fourier summation as you can include. There should never be an argument that you're savings on computing cycles. It's takes far longer to look carefully at an electron density map and make decisions on what to do than to carry out refinement. We're rarely talking about twice the computing time, we're probably thinking 10% more. That's definately not a reason to throw out data. We've got lots of computing power and lots of disk storage, let's use to our advantage. That's my nickel. Bernie Santarsiero On Thu, March 22, 2007 7:00 am, Ranvir Singh wrote: I will agree with Ulrich. Even at 3.0 A, it is possible to have a structure with reasonable accuracy which can explain the biological function/ or is consistent with available biochemical data. Ranvir --- Ulrich Genick [EMAIL PROTECTED] wrote: Here are my 2-3 cents worth on the topic: The first thing to keep in mind is that the goal of a structure determination is not to get the best stats or to claim the highest possible resolution. The goal is to get the best possible structure and to be confident that observed features in a structure are real and not the result of noise. From that perspective, if any of the conclusions one draws from a structure change depending on whether one includes data with an I/sigI in the highest resolution shell of 2 or 1, one probably treads on thin ice. The general guide that one should include only data, for which the shell's average I/sigI 2
Re: [ccp4bb] Highest shell standards
I have a question about how the experimental sigmas are affected when one includes resolution shells containing mostly unobserved reflections. Does this vary with the data reduction software being used? One thing I've noticed when scaling data (this with d*trek (Crystal Clear) since it's the program I use most) is that I/sigma(I) of reflections can change significantly when one changes the high resolution cutoff. If I set the detector so that the edge is about where I stop seeing reflections and integrate to the corner of the detector, I'll get a dataset where I/sigma(I) is really compressed - there is a lot of high resolution data with I/sigma(I) about 1, but for the lowest resolution shell, the overall I/sigma(I) will be maybe 8-9. If the data set is cutoff at a lower resolution (where I/sigma(I) in the shell is about 2) and scaled, I/sigma(I) in the lowest resolution shell will be maybe 20 or even higher (OK, there is a different resolution cutoff for this shell, but if I look at individual reflections, the trend holds). Since the maximum likelihood refinements use sigmas for weighting this must affect the refinement. My experience is that interpretation of the maps is easier when the cut-off datasets are used. (Refinement is via refmac5 or shelx). Also, I'm mostly talking about datasets from well- diffracting crystals (better than 2 A). Sue On Mar 22, 2007, at 2:29 AM, Eleanor Dodson wrote: I feel that is rather severe for ML refinement - sometimes for instance it helps to use all the data from the images, integrating right into the corners, thus getting a very incomplete set for the highest resolution shell. But for exptl phasing it does not help to have many many weak reflections.. Is there any way of testing this though? Only way I can think of to refine against a poorer set with varying protocols, then improve crystals/data and see which protocol for the poorer data gave the best agreement for the model comparison? And even that is not decisive - presumably the data would have come from different crystals with maybe small diffs between the models.. Eleanor Shane Atwell wrote: Could someone point me to some standards for data quality, especially for publishing structures? I'm wondering in particular about highest shell completeness, multiplicity, sigma and Rmerge. A co-worker pointed me to a '97 article by Kleywegt and Jones: _http://xray.bmc.uu.se/gerard/gmrp/gmrp.html_ To decide at which shell to cut off the resolution, we nowadays tend to use the following criteria for the highest shell: completeness 80 %, multiplicity 2, more than 60 % of the reflections with I 3 sigma(I), and Rmerge 40 %. In our opinion, it is better to have a good 1.8 Å structure, than a poor 1.637 Å structure. Are these recommendations still valid with maximum likelihood methods? We tend to use more data, especially in terms of the Rmerge and sigma cuttoff. Thanks in advance, *Shane Atwell* Sue Roberts Biochemistry Biopphysics University of Arizona [EMAIL PROTECTED]
Re: [ccp4bb] Highest shell standards
I typically process my data to a maximum I/sig near 1, and completeness in the highest resolution shell to 50% or greater. It What about maps computed of very incomplete datasets at high resolution? Don't you get a false sense of details when the missing reflections are filled in with DFc when computing a 2MFo-DFc map? P
[ccp4bb] Postdoc and Ph.D. student positions
Postdoctoral Position in Structural Biology / Biochemistry We are looking for a highly motivated Postdoc for our laboratory at the Institute for Physiological Chemistry at Ruhr-University Bochum, Germany. Our work involves biochemical and structural studies on cellular signaling systems with relevance to cancer, metabolic diseases, or aging. A main focus of the group is the mechanism of metabolic sensing and cyclic nucleotide signaling. Our laboratory is located at the Medical School of the Ruhr-University Bochum which harbours outstanding research groups and facilities. The group is further associated with the Max-Planck-Institute of Molecular Physiology in Dortmund giving us access to state-of the art x-ray facilities and synchrotron beamlines. Our lab offers excellent research opportunities and a stimulating environment for research in structural biology. The ideal candidate is a highly motivated Ph.D. with an interest in medically relevant questions; experience in protein biochemistry and protein crystallization is mandatory. Additional experience in molecular biology would be an asset. Applications (including CV, research experience, and two names and contact information for references) should be sent to Dr. Clemens Steegborn Ruhr-University Bochum MA 2/141 Universitaetsstr. 150 44801 Bochum Germany Email: mailto:[EMAIL PROTECTED][EMAIL PROTECTED] mailto:[EMAIL PROTECTED][EMAIL PROTECTED] Jun.-Prof. Dr. Clemens Steegborn Ruhr-University Bochum Dept. Physiol. Chemistry, MA 2/141 Universitaetsstr. 150 44801 Bochum, Germany phone: 0049 234 32 27041 fax: 0049 234 32 14193 email: [EMAIL PROTECTED]
Re: [ccp4bb] Highest shell standards
I have observed something similar myself using Saint in a Bruker Smart6K detector and using denzo in lab and syncrotron detectors. First the I over sigma never really drops to zero, no mater how much over your real resolution limit you integrate. Second, if I integrate to the visual resolution limit of, say, 1.5A, I get nice dataset statistics. If I now re-integrate (and re-scale) to 1.2A, thus including mostly empty (background) pixels everywhere, then cut the dataset after scaling to the same 1.5A limit, the statistics are much worse, booth in I over sigma and Rint. (Sorry, no numbers here, I tried this sometime ago). I guess the integration is suffering at profile fitting level while the scaling suffers from general noise (those weak reflections between 1.5A and 1.2A will be half of your total data!). I would be careful to go much over the visual resolution limit. Jose. ** Jose Antonio Cuesta-Seijo Cancer Genomics and Proteomics Ontario Cancer Institute, UHN MaRs TMDT Room 4-902M 101 College Street M5G 1L7 Toronto, On, Canada Phone: (416)581-7544 Fax: (416)581-7562 email: [EMAIL PROTECTED] ** On Mar 22, 2007, at 10:59 AM, Sue Roberts wrote: I have a question about how the experimental sigmas are affected when one includes resolution shells containing mostly unobserved reflections. Does this vary with the data reduction software being used? One thing I've noticed when scaling data (this with d*trek (Crystal Clear) since it's the program I use most) is that I/sigma(I) of reflections can change significantly when one changes the high resolution cutoff. If I set the detector so that the edge is about where I stop seeing reflections and integrate to the corner of the detector, I'll get a dataset where I/sigma(I) is really compressed - there is a lot of high resolution data with I/sigma(I) about 1, but for the lowest resolution shell, the overall I/sigma(I) will be maybe 8-9. If the data set is cutoff at a lower resolution (where I/sigma(I) in the shell is about 2) and scaled, I/sigma(I) in the lowest resolution shell will be maybe 20 or even higher (OK, there is a different resolution cutoff for this shell, but if I look at individual reflections, the trend holds). Since the maximum likelihood refinements use sigmas for weighting this must affect the refinement. My experience is that interpretation of the maps is easier when the cut-off datasets are used. (Refinement is via refmac5 or shelx). Also, I'm mostly talking about datasets from well-diffracting crystals (better than 2 A). Sue On Mar 22, 2007, at 2:29 AM, Eleanor Dodson wrote: I feel that is rather severe for ML refinement - sometimes for instance it helps to use all the data from the images, integrating right into the corners, thus getting a very incomplete set for the highest resolution shell. But for exptl phasing it does not help to have many many weak reflections.. Is there any way of testing this though? Only way I can think of to refine against a poorer set with varying protocols, then improve crystals/data and see which protocol for the poorer data gave the best agreement for the model comparison? And even that is not decisive - presumably the data would have come from different crystals with maybe small diffs between the models.. Eleanor Shane Atwell wrote: Could someone point me to some standards for data quality, especially for publishing structures? I'm wondering in particular about highest shell completeness, multiplicity, sigma and Rmerge. A co-worker pointed me to a '97 article by Kleywegt and Jones: _http://xray.bmc.uu.se/gerard/gmrp/gmrp.html_ To decide at which shell to cut off the resolution, we nowadays tend to use the following criteria for the highest shell: completeness 80 %, multiplicity 2, more than 60 % of the reflections with I 3 sigma(I), and Rmerge 40 %. In our opinion, it is better to have a good 1.8 Å structure, than a poor 1.637 Å structure. Are these recommendations still valid with maximum likelihood methods? We tend to use more data, especially in terms of the Rmerge and sigma cuttoff. Thanks in advance, *Shane Atwell* Sue Roberts Biochemistry Biopphysics University of Arizona [EMAIL PROTECTED]
Re: [ccp4bb] Highest shell standards
My guess is that the integration is roughly the same, unless the profiles are really poorly defined, but that the scaling that is suffering from using a lot of high-resolution weak data. We've integrated data to say I/sig = 0.5, and sometimes seem more problems with scaling. I then cut back to I/sig = 1 and it's fine. The major difficulty arises that if the crystal is dying, and the decay/scaling/absorption model isn't good enough. So that's definately a consideration when trying to get a more complete data set and higher resolution (so more redundancy). Bernie On Thu, March 22, 2007 12:21 pm, Jose Antonio Cuesta-Seijo wrote: I have observed something similar myself using Saint in a Bruker Smart6K detector and using denzo in lab and syncrotron detectors. First the I over sigma never really drops to zero, no mater how much over your real resolution limit you integrate. Second, if I integrate to the visual resolution limit of, say, 1.5A, I get nice dataset statistics. If I now re-integrate (and re-scale) to 1.2A, thus including mostly empty (background) pixels everywhere, then cut the dataset after scaling to the same 1.5A limit, the statistics are much worse, booth in I over sigma and Rint. (Sorry, no numbers here, I tried this sometime ago). I guess the integration is suffering at profile fitting level while the scaling suffers from general noise (those weak reflections between 1.5A and 1.2A will be half of your total data!). I would be careful to go much over the visual resolution limit. Jose. ** Jose Antonio Cuesta-Seijo Cancer Genomics and Proteomics Ontario Cancer Institute, UHN MaRs TMDT Room 4-902M 101 College Street M5G 1L7 Toronto, On, Canada Phone: (416)581-7544 Fax: (416)581-7562 email: [EMAIL PROTECTED] ** On Mar 22, 2007, at 10:59 AM, Sue Roberts wrote: I have a question about how the experimental sigmas are affected when one includes resolution shells containing mostly unobserved reflections. Does this vary with the data reduction software being used? One thing I've noticed when scaling data (this with d*trek (Crystal Clear) since it's the program I use most) is that I/sigma(I) of reflections can change significantly when one changes the high resolution cutoff. If I set the detector so that the edge is about where I stop seeing reflections and integrate to the corner of the detector, I'll get a dataset where I/sigma(I) is really compressed - there is a lot of high resolution data with I/sigma(I) about 1, but for the lowest resolution shell, the overall I/sigma(I) will be maybe 8-9. If the data set is cutoff at a lower resolution (where I/sigma(I) in the shell is about 2) and scaled, I/sigma(I) in the lowest resolution shell will be maybe 20 or even higher (OK, there is a different resolution cutoff for this shell, but if I look at individual reflections, the trend holds). Since the maximum likelihood refinements use sigmas for weighting this must affect the refinement. My experience is that interpretation of the maps is easier when the cut-off datasets are used. (Refinement is via refmac5 or shelx). Also, I'm mostly talking about datasets from well-diffracting crystals (better than 2 A). Sue On Mar 22, 2007, at 2:29 AM, Eleanor Dodson wrote: I feel that is rather severe for ML refinement - sometimes for instance it helps to use all the data from the images, integrating right into the corners, thus getting a very incomplete set for the highest resolution shell. But for exptl phasing it does not help to have many many weak reflections.. Is there any way of testing this though? Only way I can think of to refine against a poorer set with varying protocols, then improve crystals/data and see which protocol for the poorer data gave the best agreement for the model comparison? And even that is not decisive - presumably the data would have come from different crystals with maybe small diffs between the models.. Eleanor Shane Atwell wrote: Could someone point me to some standards for data quality, especially for publishing structures? I'm wondering in particular about highest shell completeness, multiplicity, sigma and Rmerge. A co-worker pointed me to a '97 article by Kleywegt and Jones: _http://xray.bmc.uu.se/gerard/gmrp/gmrp.html_ To decide at which shell to cut off the resolution, we nowadays tend to use the following criteria for the highest shell: completeness 80 %, multiplicity 2, more than 60 % of the reflections with I 3 sigma(I), and Rmerge 40 %. In our opinion, it is better to have a good 1.8 Å structure, than a poor 1.637 Å structure. Are these recommendations still valid with maximum likelihood methods? We tend to use more data, especially in terms of the Rmerge and sigma cuttoff. Thanks in advance, *Shane Atwell* Sue Roberts Biochemistry Biopphysics University of Arizona [EMAIL PROTECTED]
[ccp4bb] X-ray generator uninterruptible power supply
Hi Citizens: Does anyone use an uninterruptible power supply for their X-ray generator? Here at UCDIY, the electricity supply is pretty sketchy, and it is hammering our X-ray generator every time someone forgets to feed the hamster or grease his wheel. If so, how much does such a thing cost, and how unpleasant is it to maintain (since at UCDIY, you get to do all your own maintenance)? Thanks in advance. Bill
[ccp4bb] How to subtract one electron density map from another
Hi, I'm trying to get the difference map by subtracting the native electron density map from the complex electron density map. MAPMASK has a function of ADD/MULT, but I don't know how to use it? Any other ways to attack this problem in real space? Thanks in advance, Qing
Re: [ccp4bb] How to subtract one electron density map from another
On Thu, 2007-03-22 at 16:06 -0500, Qing Xie wrote: I'm trying to get the difference map by subtracting the native electron density map from the complex electron density map. MAPMASK has a function of ADD/MULT, but I don't know how to use it? Any other ways to attack this problem in real space? use overlapmap with ADD 1 -1 presuming your maps are on the correct scale (if not you can use mapmask to scale (one of) them). Paul.
Re: [ccp4bb] X-ray generator uninterruptible power supply
CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK wrote on 03/22/2007 04:46:35 PM: Hi Citizens: Does anyone use an uninterruptible power supply for their X-ray generator? Here at UCDIY, the electricity supply is pretty sketchy, and it is hammering our X-ray generator every time someone forgets to feed the hamster or grease his wheel. If so, how much does such a thing cost, and how unpleasant is it to maintain (since at UCDIY, you get to do all your own maintenance)? Thanks in advance. Bill Hi Bill - I'm afraid a UPS for that kind of power load may be very expensive. My 007HF needs a 20 amp, 200 VAC circuit, so let's say the UPS needs to be able to deliver 4 kW of power (you could probably get away with less). If you're talking about an older power hog like an RU-H3R, that wants an 85 amp (!) 200 VAC circuit, so your UPS needs to handle 17 kW load. Let's assume that you're trying to ride out little glitches (seconds to minutes), not long outages. So you don't need huge battery capacity, just high wattage. Here's a couple of sites that might help you - they helped me when I was looking for a UPS: http://www.powerware.com/UPS/selector/SolutionOverview.asp http://www.apcc.com/template/size/apc/index.cfm? http://www.advizia.com/tripplite/ You'll find that a UPS to run a low-power generator like the 007HF will cost you $5000 - $10,000, while something that can handle an RU-H3R looks like it'll cost $20k and up. I'm not even sure that all of these systems will deliver 3-phase power like the generator needs. I never considered getting a UPS for my generator, even though our building has no backup power and Con Ed also forgets to feed their hamsters occasionally. What I did get was a UPS for my cryostream - I figured that the data collection can always be restarted if the generator died in the middle of the night, but once the crystal is gone, it's gone. I paid less than $10k for a UPS that can run my Cryojet for over 15 hours, so even if the power goes out in the middle of the night, I can come in and rescue the crystal the next day. Email me if you want more info on my choice of UPS for my cryo. - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
Re: [ccp4bb] X-ray generator uninterruptible power supply
On Thu, 2007-03-22 at 18:54 -0400, [EMAIL PROTECTED] wrote: I never considered getting a UPS for my generator, even though our building has no backup power and Con Ed also forgets to feed their hamsters occasionally. What I did get was a UPS for my cryostream - I figured that the data collection can always be restarted if the generator died in the middle of the night, but once the crystal is gone, it's gone. I paid less than $10k for a UPS that can run my Cryojet for over 15 hours, so even if the power goes out in the middle of the night, I can come in and rescue the crystal the next day. That's a good idea, we do that now on our crystallography beamlines. -- === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED]
Re: [ccp4bb] How to subtract one electron density map from another
Why not simply scale the two data sets, and subtract corresponding Fs from one another and then calculate a map from those Fs. If you want to an error-weighted map, you should also perform error propagation on your sigF. Assuming that the two errors are independent of one another the formula for doing so would be sigmaFa-Fb = sqrt(sigFa^2 + sigFb^2). My advice would be to use omit phases for this map to avoid biasing your difference map by model phases. In other words calculate your phases from a model, in which you have removed atoms that show significant peaks in a preliminary difference map. Provided you use the same phases for both maps (which you should to avoid bias) subtracting the two maps structure factor by structure factor and subtracting them pixel by pixel is mathematically equivalent. Cheers, Ulrich On Mar 22, 2007, at 5:06 PM, Qing Xie wrote: Hi, I'm trying to get the difference map by subtracting the native electron density map from the complex electron density map. MAPMASK has a function of ADD/MULT, but I don't know how to use it? Any other ways to attack this problem in real space? Thanks in advance, Qing
Re: [ccp4bb] How to subtract one electron density map from another
Mapman (Uppsala software factory) allows you to subtract maps if they are on the same grid. You may need to multiply one map by a factor (again in mapman) to make the background flat in the regions you believe to be identical. Linearity of the Fourier Transform implies you could get the same result by subtracting in reciprocal space. However if the crystals are not perfectly isomorphous, it may help to skew one map onto the others before subtracting, i.e. apply a rotation-translation operator to superimpose equivalent areas, which could be a reason for doing it in real space. You can do this with mave (also USF), getting the operator by superimposing models in O or lsqman, or, if the refinement has not progressed that far, refining the operator from identity with the improve option of mave. I expect mapmask and friends of dmmulti can do all this too, but I am less familiar with the CCP4 tools. Either way, there is certain amount of documentation you will need to read in order to know how to use it. But that is time well spent in the long run, as it will help you to interpret the results or modify the procedure as new situations arise. If you get stuck and have specific questions, the BB is hear to help! Ed
