[ccp4bb] anisotropic Bs
Hello Everyone There's probably an easy way to do this, but I haven't found it. I've refined a 1.1 A structure with refmac and want to inspect the thermal ellipsoids. Specifically I want to know if any of them are non-positive definite and I want to know which have very large anisotropy. (I can look at them in coot, but I'd like to have a list). I'm concerned because I get messages in the refmac log file - problem with make u positive and I want to know what the cause of the error messages. I thought anisoanl would be the most likely program, but it doesn't seem to do it. (Perhaps I'm using the program wrongly.) Thanks Sue Dr. Sue A. Roberts Dept. of Chemistry and Biochemistry University of Arizona 1041 E. Lowell St., Tucson, AZ 85721 Phone: 520 621 8171 s...@email.arizona.edu http://www.biochem.arizona.edu/xray
Re: [ccp4bb] homology modeling
A metaserver such as bioinfobank is helpful if your sequence is not super-secret, especially if one is not an experienced modeller. http://meta.bioinfo.pl/submit_wizard.pl It submits your sequence to a range of sequence-based and threading- based servers. Models (c-alpha, built with modeller) can be downloaded, inspected, and compared. Alignment files for input to modeller can also be downloaded, allowing you to easily build all-atom models. Sue Dr. Sue A. Roberts Biochemistry Molecular Biophysics University of Arizona 520 621 8171 s...@email.arizona.edu http://www.biochem.arizona.edu/xray
Re: [ccp4bb] structure (factor) amplitude
My preference is also for the full structure factor amplitude. I would have said that I'd never seen the term structure amplitude used. However, I just looked this up in my old Stout Jensen (1968 edition - brown cover) and find that (on p. 195) where |F| is introduced they define it as: 'the most important quantity derived from the intensities is the structure factor modulus (structure amplitude). (Italics are theirs, not mine). Sue On Jan 12, 2009, at 8:37 AM, Andrew Purkiss-Trew wrote: On Mon, 2009-01-12 at 10:42 +, Ian Tickle wrote: I was taught 'structure amplitude' - makes perfect sense to me! Why does 'structure amplitude' make any less sense than 'structure factor'? It also clearly made sense to Phil Coppens, a crystallographer of considerable repute, see ITC Vol. B (2nd Ed.), sect 1.2., p.10: 'The Structure Factor'. To quote the introduction to the section: The 'structure factor' is the central concept in structure analysis by diffraction methods. Its modulus is called the 'structure amplitude'. Also I did a 'Google vote' for the two terms. 'Structure amplitude' has 11300 hits. 'Structure factor amplitude' has only 4750. So all round I would say that 'structure amplitude' wins by a considerable margin. Having had a quick look at the google results myself, I think that there is a problem is the methodology. Google doesn't take into account punctuation when searching. So the first search includes results such as 'structure. Amplitude', where the two words are in different sentences, or 'structure, amplitude' where the words are part of a list. Given this case, the winning margin is likely to be less. My preference would also be for the full 'Structure factor amplitude'. 'Structure amplitude' leaves me with visions of comparing the pdb files of a small single domain protein and a ribosome. Two structures having different sizes (or amplitudes). Cheers -- Ian -Original Message- From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Pavel Afonine Sent: 11 January 2009 03:01 To: Ethan A Merritt Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] structure (factor) amplitude On 1/10/2009 5:14 PM, Ethan A Merritt wrote: On Saturday 10 January 2009, Bernhard Rupp wrote: Dear All, I am getting conflicting comments on the use of 'structure factor amplitude' vs. just 'structure amplitude' for |F|. ??? That's just... odd. |F| is the amplitude of F. But no way F is a structure. I agree. If F is a structure factor then |F| is a structure factor amplitude. structure amplitude doesn't make much sense... Pavel. Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674 Dr. Sue A. Roberts Biochemistry Molecular Biophysics University of Arizona 520 621 8171 s...@email.arizona.edu http://www.biochem.arizona.edu/xray
[ccp4bb] RAxis fiber diffraction
Hello Everyone Since I'm convinced that ccp4bb is the repository of all knowledge about all diffraction phenomena... A colleague would like to do some fiber diffraction studies. I have an RAxis - I know we can put the fiber in the beam and shoot it and get some pattern on the detector. Can anyone recommend some reading material or tutorials for me to learn more about what I've agreed to do? Assuming the material is actually crystalline enough to give a pattern on the detector, I can pick peaks and get d-spacings. What more sophisticated, readily available methods (software?) is out there for, perhaps, data reduction (if there is such a thing for fiber diffraction) or subsequent analysis. Thanks, Sue Sue Roberts Department of Biochemistry Molecular Biophysics University of Arizona [EMAIL PROTECTED]520 621-8171
Re: [ccp4bb] SUMMARY: losing zinc during crystallization
Hello I wish to thank everyone for all the helpful replies. A summary follows: While some expressed surprise at the zinc lability, others related tales of difficulty keeping zinc in a protein. Suggested ways of overcoming the problem included: 1) Use of TCEP as a reducing agent 2) Allowing Zn to leave and filling the site with Au or Cd 3) Limiting oxygen during crystallization - crystallization in a glove bag or degassed solutions. One person noted that TCEP decomposition products include phosphate and as a result ZnPO4 crystals can form. I'm off to try suggestion (3). Hope it works and I don't have to resort to suggestion (2). Thanks again for the help. Sue Hello Everyone I've been trying to crystallize a zinc-containing enzyme for what seems to me to be an eternity. The protein contains stoichiometric zinc (1 zinc/ protein monomer) when isolated and the zinc is required for activity. Each crystal we've obtained has lost the zinc and contains a disulfide bond between two cysteine residues that should be zinc ligands (based on structures of similar proteins). We've tried crystalizing in the presence of reducing agents, crystallizing with substrate analogs, and supplementing the crystallization drops with zinc with no success (and combinations of these approaches). We've obtained a variety of crystals and determined structures, but none contain any zinc. Attempts to insert zinc into the crystal (zinc + reducting agent or zinc alone) have not been successful. Does anyone have any tricks to suggest that might help? Thanks in advance. Sue Dr. Sue A. Roberts Biochemistry Molecular Biophysics University of Arizona 520 621 8171 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Dr. Sue A. Roberts Biochemistry Molecular Biophysics University of Arizona 520 621 8171 [EMAIL PROTECTED]
[ccp4bb] losing zinc during crystallization
Hello Everyone I've been trying to crystallize a zinc-containing enzyme for what seems to me to be an eternity. The protein contains stoichiometric zinc (1 zinc/ protein monomer) when isolated and the zinc is required for activity. Each crystal we've obtained has lost the zinc and contains a disulfide bond between two cysteine residues that should be zinc ligands (based on structures of similar proteins). We've tried crystalizing in the presence of reducing agents, crystallizing with substrate analogs, and supplementing the crystallization drops with zinc with no success (and combinations of these approaches). We've obtained a variety of crystals and determined structures, but none contain any zinc. Attempts to insert zinc into the crystal (zinc + reducting agent or zinc alone) have not been successful. Does anyone have any tricks to suggest that might help? Thanks in advance. Sue Dr. Sue A. Roberts Biochemistry Molecular Biophysics University of Arizona 520 621 8171 [EMAIL PROTECTED]
Re: [ccp4bb] poll: cutoff for high resolution
I don't think the term high resolution has any real definition or meaning anymore. If you're proud of the resolution, put the number in the title of the paper and let the reader decide. At one time 2 A was high resolution, but I wouldn't consider that high resolution today for a plain vanilla protein structure. The optical resolution is ~ 0.7 x the spacing at which the diffraction is cut off as a best possible case - SFCHECK gives an estimate of the optical resolution. Since hydrogen atoms are not really visible, even at very high resolution, I'd call atomic resolution that resolution at which atoms in C=O bonds are resolved or ~ 1.2 A. I used to think using atomic resolution as a descriptor was safe (I think the shelx and acorn documentation uses 1.2 A in this definition) until I attended a seminar entitled Atomic resolution structure of (some membrane protein - I don't remember which one) and found it to be a solid state NMR study where they could figure out the direction in which a helix was running (and could therefore build a helix.) Sue On May 15, 2008, at 9:11 AM, [EMAIL PROTECTED] wrote: On 14 May, Mark Del Campo wrote: At what refinement resolution or resolution ranges would you call a structure high resolution vs. low resolution? I realize that this may boil down to semantics (e.g. some may classify structures as medium resolution), but I wanted to get an opinion from the pros. A sensible definition of high resolution would be that resolution at which the structure is computationally over-determined, which is about 2 angstroms or better for a complete data set. This would also be a sensible definition for what is called atomic resolution, because the atoms are resolved as spheres or better, so that the position is over-determined. Regards, -- Michael L. Love Ph.D Department of Biophysics and Biophysical Chemistry School of Medicine Johns Hopkins University 725 N. Wolfe Street Room 608B WBSB Baltimore MD 21205-2185 Interoffice Mail: 608B WBSB, SoM office: 410-614-2267 lab:410-614-3179 fax:410-502-6910 cell: 443-824-3451 http://www.gnu-darwin.org/ Visit proclus realm! http://proclus.tripod.com/ -BEGIN GEEK CODE BLOCK- Version: 3.1 GMU/S d+@ s: a+ C UBULI$ P+ L+++() E--- W++ N- !o K- w--- !O M++@ V-- PS+++ PE Y+ PGP-- t+++(+) 5+++ X+ R tv-(--)@ b !DI D- G e h--- r+++ y --END GEEK CODE BLOCK-- Dr. Sue A. Roberts Biochemistry Biophysics University of Arizona 520 621 8171 [EMAIL PROTECTED]
Re: [ccp4bb] [phenixbb] Rant: B vs TLS, anisou, and PDB headers
I suspect there's not going to be consensus on anything except that there needs to be a standardization regarding deposited TLS parameters.Probably the first step is to convince the pdb to not throw away the record describing what's actually in the B-factor column. In my (probably unimportant) opinion, I agree that the B value on the ATOM card should be the equivalent isotropic thermal parameter of the atom. I personally don't like to see ANISOU records when anisotropic thermal parameters weren't refined. I agree anisotropic values derived from TLS are useful, but I'd like there to be a flag on the ANISOU record, or maybe a different name on the ANISOU record (Yeah, I know that suggestion won't fly) so that one could distinguish between refined anisotropic thermal parameters and those derived from TLS parameters. If the TLS groups used are contained in the pdb file, I can manage to generate a close-enough facsimile of the refinement (although not automatically) so that I can look at the ellipsoids and learn what I want to learn. Since I'm not a bioinformatics center, this has been, so far, good enough for me. Sue On Mar 29, 2008, at 1:56 PM, George M. Sheldrick wrote: I think that it is essential that the PDB file that actually gets deposited contains ANISOU records that have had the isotropic contributions added already, and that the B on the atom record is one third of the trace of the orthogonalised Bij tensor that can be derived from the ANISOU record, just as it is for an anisotropic refinement without TLS (or a refinement with TLS restraints rather than constraints, as in the next version of SHELXL, release NOT imminent). Then if you are not interested in anisotropy you still have meaningful B values on the ATOM record, and a structure factor calculation (e.g. with SFCALC) will get the R factors right. If I have understood the rather convoluted discussion on this question, phenix.refine does this correctly, but if you use REFMAC you need to use another program (TLSANL ?) to convert the PDB file before you deposit it. Apparantly many people have forgotten to do this and the RCSB/EBI has unfortunately not checked it (which would be trivial for them to do). If they could be persuaded to check that the ATOM and ANISOU records are consistent as explained above, the problem would sort itself out, at least for new depositions. 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 Sat, 29 Mar 2008, Pavel Afonine wrote: Hi Frank, Hi Frank, All your reasons are there for the convenience of the *crystallographer*, mine are for the end user (=unsuspecting biologist) -- who doesn't know TLS even exists (none of used to), never mind about Hirshfeld's test and how it relates to TLS (I didn't), and certainly not how run it (I still don't). This is exactly what phenix.refine does: it puts all together so you are not expected to have any knowledge about magic TLS matrices in PDB file header, about right programs to convert one into another and so on. In contrast, if one split things apart: - you must know that what's in ATOM record is incomplete; - you must know that there are TLS matrices that you have to convert to appropriate B and add to residual ones; - you must know that there are the programs out there to do that; - and you must know how to use these programs too. So, having complete record doesn't require any manipulations on the model (and so extra knowledge) . Imagine the situation when you got a model with partial B-factors and another part encoded in PDB header as TLS and you want to do a refinement in SHELXL. In this case you will need to compute the total B to start with the correct values. In contrast, if the values are complete, you do not need to do anything. In the end what's important I believe is that the output information is clearly accompanied with the explanations about what it represents and that there are tools available from both ends (phenix, ccp4) to easily go from partial to total and back. The rest is the matter of personal preferences. Cheers, Pavel. --- Pavel V. Afonine, Ph.D. Lawrence Berkeley National Lab, Berkeley CA, USA (http:// www.lbl.gov/) CCI: Computational Crystallography Initiative (http://cci.lbl.gov/) PHENIX (http://phenix-online.org/) Sue Roberts Department of Biochemistry Molecular Biophysics University of Arizona [EMAIL PROTECTED]520 621-8171
Re: [ccp4bb] ccp4i - Directories Project Directory Error
I also thought the problem was using the Terminal window and not the X11 window, but, interestingly, typing ccp4i in a Terminal window, not an X11 window does work. X11 does need to be installed and running, -- that could be the problem. (Caveat, this is in 10.4, not 10.5 - I have 10.5 but haven't installed it yet because of the coot discussions) Sue On Mar 25, 2008, at 8:37 AM, Anastassis Perrakis wrote: Hi - You need to add to your .chrc, or type in an ***X11*** window (and not in the Terminal). source /usr/local/ccp4-6.0.2//bin/ccp4.setup-csh then it will work. it does not really install a real application in the OSX sense. A. On Mar 25, 2008, at 15:47, Kurt Padilla wrote: William, Thanks for your advice. I intend to give it a try in the next few days. Hopefully, I will have some positive results to share. Anastassis, I tried using the binary from the link you provided, but I was unable to get the program to run even though Installer said that the installation was successful. I don't remember the details, but the installation did not produce an executable .app file and typing ccp4i into Terminal didn't launch the program either. Kurt On Tue, Mar 25, 2008 at 10:35 AM, Anastassis Perrakis [EMAIL PROTECTED] wrote: Hi - I am sure that its not a fink problem really, but why not try the CCP4 distribution? http://www.ccp4.ac.uk/download/ A. On Mar 22, 2008, at 5:34, Kurt Padilla wrote: Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/ directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut Sue Roberts Biochemistry Biophysics University of Arizona [EMAIL PROTECTED]
Re: [ccp4bb] an over refined structure
Back in the old days, when I worked on crystal structures with 15 or 20 atoms or so, the symptoms of missed crystallographic symmetry included instability of the refinement, high correlations between parameters, and (relatively) large deviations between equivalent bond distances and bond angles. There can be real consequences of missing symmetry and divergences between copies of molecules, even when resolution and data quality were not an issue, because the refinement can become unstable. Hence, I'm always skeptical of the assumption that structures can be safely refined in space groups of too low symmetry. I've assumed that, when people chose to (or accidently) refine protein structures in lower symmetry space groups, geometrical and NCS restraints keep the refinement under control. Is there a publication somewhere that has looked at the effect of deliberate refinement in space groups of lower than correct symmetry? Sue On Feb 8, 2008, at 11:07 AM, Edward Berry wrote: Dirk Kostrewa wrote: Dear Dean and others, Peter Zwart gave me a similar reply. This is very interesting discussion, and I would like to have a somewhat closer look to this to maybe make things a little bit clearer (please, excuse the general explanations - this might be interesting for beginners as well): 1). Ccrystallographic symmetry can be applied to the whole crystal and results in symmetry-equivalent intensities in reciprocal space. If you refine your model in a lower space group, there will be reflections in the test-set that are symmetry-equivalent in the higher space group to reflections in the working set. If you refine the (symmetry-equivalent) copies in your crystal independently, they will diverge due to resolution and data quality, and R-work and R-free will diverge to some extend due to this. If you force the copies to be identical, the R-work R-free will still be different due to observational errors. In both cases, however, the R-free will be very close to the R-work. Sue Roberts Biochemistry Biophysics University of Arizona [EMAIL PROTECTED]
Re: [ccp4bb] convert .cif to .mtz
In recent coots, (This is 0.4.1, kendall, on a mac or linux) you no longer need to calculate fcalc and phases. If you choose auto open mtz and have at least one pdb file open, coot will ask you which pdb file to use to calculate fcalc and phases. (I guess it runs refmac then) and, voila, the maps are displayed. Sue On Jan 29, 2008, at 8:37 AM, Eleanor Dodson wrote: It has just worked for me? convert to mtz file type mmCIF then I had to put in my own cell and spacegroup. And I will have to calculate phases before I can use coot with it.. Eleanor Eleanor It looks like this.. # _audit.revision_id1_0 _audit.creation_date 2005-03-22 _audit.update_record 'Initial release' # loop_ _refln.wavelength_id _refln.crystal_id _refln.index_h _refln.index_k _refln.index_l _refln.F_meas_au _refln.F_meas_sigma_au _refln.status 1 100 -51 0.0 0.000 1 110 -51 0.0 0.000 1 140 -51 0.0 0.000 1 101 -51 0.0 0.000 1 111 -51 0.0 0.000 1 121 -51 0.0 0.000 Kristof Van Hecke wrote: Dear all, I'm looking for a convenient way of converting a .cif structure factor file (from PDB) to a map-file (e.g. .mtz) to open with COOT for example..? Already tried ccp4i with 'Convert to/modify/extend MTZ', but got a bunch of errors when opening with coot.. Many thanks Kristof -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm Sue Roberts Biochemistry Biophysics University of Arizona [EMAIL PROTECTED]
Re: [ccp4bb] Primary source for detergent properties
There is a series of books - Surfactant science series which has some of this information. I'm familiar with the Nonionic Surfactants, Anionic Surfactants, and Cationic Surfactants books (they have unattractive green covers) from the days when I used to work for a soap company. One problem with published phase diagrams is that the behavior of surfactants can vary considerably among manufacturers and even from batch to batch, especially for commercial-grade material, but even for supposedly pure reagents. Sue On Oct 22, 2007, at 2:48 PM, Jacob Keller wrote: Dear CCP4BB, Although this is not exactly CCP4-related, I thought somebody here might know whether there is somewhere a definitive list or tabulation of detergent properties which are not simply copied out of catalogs, but have been traceably experimentally determined. In particular, it would be great to have phase diagrams for common detergents with detergent concentration versus pH, salt concentration, temperature, etc. Would this not be incredibly helpful for the scientific community? And yet, this is not so easy to find Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.467.4049 cel: 773.608.9185 email: [EMAIL PROTECTED] *** Sue Roberts Biochemistry Biophysics University of Arizona [EMAIL PROTECTED]
Re: [ccp4bb] ADIT Validation server Ramachandran outliers
OK, I'm properly chastised - outlier does not equal bad. However, residues which are not flagged as problematic or unusual during validation should not be flagged in the final pdb file. And I have read Gerard's paper, and the molprobity paper. Recently. Sue On Sep 21, 2007, at 9:57 AM, Gerard DVD Kleywegt wrote: Has anyone successfully fought this bad residue listing? I understand that the pdb wishes to flag problem regions, but this is not a valid way of doing so. I can tell them where the problem regions are in the structure if they wish. oh dear, oh dear - touchy, touchy! coordinate-based validation (no matter which test, no matter which program) can only produce a list of OUTLIERS. it's up to the depositor or user of the model to figure out whether each individual outlier is an ERROR in the MODEL or a (unusual and possibly interesting) FEATURE of the STRUCTURE (typically by inspection of the density). there's no need to take the output of such programs as a personal insult, or to start a fight with the pdb, or ... [rest of diatribe mercifully deleted before hitting the send-button] warmly recommended review paper (really, i sometimes wonder what the half-life of papers on quality control and validation, and more generally on methods, is): http://xray.bmc.uu.se/cgi-bin/gerard/ reprint_mailer.pl?pref=56 warmly recommended tutorial (have a look at question 13 in particular): http://xray.bmc.uu.se/gerard/embo2001/modval/index.html --dvd ** Gerard J. Kleywegt [Research Fellow of the Royal Swedish Academy of Sciences] Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED] ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** Sue Roberts Biochemistry Biophysics University of Arizona [EMAIL PROTECTED]
[ccp4bb] anisotropic atoms, refmac, ccp4, coot the pdb
Hello Everyone This isn't really a question, just a warning to check your anisotropic temperature factors both after refinement and after deposition at the pdb. We've been having a lot of trouble with anisotropic temperature factors lately. Here's what's been going on. We have three different proteins, each diffracting better than 1.2 A - the best resolution is ~ 0.8 A. All have been refined with refmac (yes I know shelxl is great for such problems, but that's not the issue here). For structures refined with some versions of refmac (including the ccp4-6.0.2 linux distribution from early this year), the anisotropic components output on the ANISOU card are ridiculous. When we run anisoanl, ALL atoms are flagged as non-positive definite. When I ask coot to show anisotropic ellipsoids, they have only two dimensions (coot doesn't crash, Paul has the negative numbers trapped). Refinement of the same data set/coordinates with shelxl produces anisotropic temperature factors which are reasonable as judged by these two methods. I can fix the refmac problem by installing the latest version of refmac from Garib's web page (not the version in ccp4-6.0.2). The anisotropic ellipsoids are now good (as judged by anisoanl and coot). (Repeating myself, these are all very high resolution structures). So, I thought the problem was solved. We reviewed structures we'd deposited with the pdb but were as yet unreleased and found one with unrealistic thermal ellipsoids, which confused us since the depositor had done the sanity checks before depositing the coordinates. When we compared the file we submitted to the pdb and the file which was returned to us, the numbers on ALL the ANISOU cards had been rotated in this fashion: ANISOU1 N MET A 1 1612 1818 1492 2 -160 -14 AN has become ANISOU1 N MET A 1 1612 2-14 1818 1492 -160 N In other words the aniso card, (u11,u22,u33,u12,u13,u23) has been rearranged to be (u11,u12,u23,u22,u33,u13) (this doesn't make any sense to me) I can speculate that the refmac/pdb issues are interlinked and one arises from an attempt to fix the other, but I don't know that that's true. I did a quick check of structures released by the pdb in the last year with resolution 1.1 A and found at least one with the same problems (I stopped looking after I'd found one). Sue Sue Roberts Biochemistry Biopphysics University of Arizona [EMAIL PROTECTED]
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]
