Re: [ccp4bb] Coot and OS X Leopard
Hi Paul, and everyone else who responded, Yes, Bill does provide a standalone version, but this required an X-window update which I was not at the time comfortable doing, as my iMac had been updating itself fairly regularly and I didn't know what I was letting myself in for. The consensus appears to be that the updates don't usually downgrade the X installation (Xcode 3.1 was the only one which was highlighted - thanks Randy) so it may not be too much of a problem in real life. It has to be noted that everything else (ccp4, xds, shelx, ...) worked out of the box, so the only problem I had encountered was coot. Thanks to everyone who got in touch, Best, Graeme -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Paul Emsley Sent: 20 August 2008 15:34 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Coot and OS X Leopard Winter, G (Graeme) wrote: I have an OS X leopard machine which I would really like to get coot working on, but it appears to involve messing with the X system and / or fink, neither of which I really fancy. Now I appreciate that there is something broken about the X window (no idea what though) but I was wondering if it is possible to get coot working with it anyway? I looked at the X window update on Bill Scott's page, but the idea of having to reinstall it every time Apple decide to update my machine didn't really appeal. Doesn't Bill provide a stand-alone version? If not that then the answer, I think, is no not yet - I intend to make such a thing after returning from IUCr. You are not alone. Paul.
[ccp4bb] Running Resolve after Sharp?
Hi Sorry for a mixed up question about two great software. Has anybody tried to use Resolve after sharp / autosharp? i.e., escaping the Solomon step other than handedness determination and doing the density modification ( maybe NCS / building) directly with the sharp output? If so, I would appreciate any input.. I am confused with the eden file.. Cheers, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515
[ccp4bb] Protein concentration
Dear all, I would be glad to hear what (simple) method I should use to determine protein concentrations as accurately as possible. Presently, I'm measuring absorption at 280nm with a nanodrop device. I either have 0 or 1 tryptophan and no activity test. Many thanks in advance! Best regards, Mark Mark Hilge Protein Biophysics NCMLS 274 3rd floor M850.03.035 Geert Grooteplein 28 6525 GA Nijmegen The Netherlands http://www.mark-hilge.com Phone: 0031 24 36 10 525 Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud University Nijmegen Medical Centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.
Re: [ccp4bb] Protein concentration
Dear Mark Most easy way to have relative estimation is to run PAGE of your protein with known proteins of known different concentration so u can have a good relative estimation. but for more accurate estimation u can go for Biochemical methods such as Lowry method or BCA method which are more senstive then UV spectro method although they depend upon oxidation of total aromatic amino acid in protein u can try or wait for other suggestions.# . Puneet Juneja On Thu, Aug 21, 2008 at 12:54 PM, Mark Hilge [EMAIL PROTECTED] wrote: Dear all, I would be glad to hear what (simple) method I should use to determine protein concentrations as accurately as possible. Presently, I'm measuring absorption at 280nm with a nanodrop device. I either have 0 or 1 tryptophan and no activity test. Many thanks in advance! Best regards, Mark Mark Hilge Protein Biophysics NCMLS 274 3rd floor M850.03.035 Geert Grooteplein 28 6525 GA Nijmegen The Netherlands http://www.mark-hilge.com Phone: 0031 24 36 10 525 Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud University Nijmegen Medical Centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.
[ccp4bb] Thermal control
Dear all, We are studying the possibility to control the temperature of our optical hutch room at MX beam line (length ~ 15 m, width ~ 3 m, height ~ 2,2 m). If somebody already had experience in the subject, I would like to know the adopted solution and have a notion of its cost. Thanks. Fernando de Mattos ([EMAIL PROTECTED]) - Physicist Brazilian Sychrotron Light Laboratory - Center for Structural Molecular Biology
[ccp4bb] postdoctoral positions in protein crystallography available at Bethesda Maryland, USA
Two postdoctoral positions are available at the Department of Biochemistry, Uniformed Services University to perform structural and biochemical research on potential drug target proteins from Mycobacterium tuberculosis. The candidates will be involved in recombinant protein expression and purification, biochemical analysis, and crystal structure determination. Candidates must have a recent Ph.D. degree in biochemistry or a related field, with experience in protein expression and purification. Prior experience in X-ray crystallography is preferred. Uniformed Services University is located across the street from the National Institute of Health (NIH) campus in Bethesda, Maryland. Interested persons please send CV with names of at least two referees by e-mail to: Shuishu Wang Assistant Professor Department of Biochemistry Uniformed Services University 4301 Jones Bridge Road Bethesda, Maryland 20814 e-mail: [EMAIL PROTECTED]
Re: [ccp4bb] Protein concentration
Often the exact concentration is not so important compared to the ability to establish proportional read-out, ease and reproducibility so that systematic variations and comparisons can be made. For considerations of molar ratios of for example protein:ligand complexes one would often screen a range or add in excess in any case, so probably again you are fine. For an accurate calibration of your method of choice you can opt for a total aminoacid analysis. Poul On 21/08/2008, at 15.07, Puneet juneja wrote: Dear Mark Most easy way to have relative estimation is to run PAGE of your protein with known proteins of known different concentration so u can have a good relative estimation. but for more accurate estimation u can go for Biochemical methods such as Lowry method or BCA method which are more senstive then UV spectro method although they depend upon oxidation of total aromatic amino acid in protein u can try or wait for other suggestions.# . Puneet Juneja On Thu, Aug 21, 2008 at 12:54 PM, Mark Hilge [EMAIL PROTECTED] wrote: Dear all, I would be glad to hear what (simple) method I should use to determine protein concentrations as accurately as possible. Presently, I'm measuring absorption at 280nm with a nanodrop device. I either have 0 or 1 tryptophan and no activity test. Many thanks in advance! Best regards, Mark Mark Hilge Protein Biophysics NCMLS 274 3rd floor M850.03.035 Geert Grooteplein 28 6525 GA Nijmegen The Netherlands http://www.mark-hilge.com Phone: 0031 24 36 10 525 Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud University Nijmegen Medical Centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.
Re: [ccp4bb] Protein concentration
Mark, A little more information on the protein and need would be nice. Is it a large peptide, a small protein, or a recombinant protein? Do you want real quantitative results or semi quantitative (like BCA, Bradford, or Lowry which can be off by 20% or more relative to the [BSA])? Do you want it to be rapid assay? Is it to measure the protein concentration of a pure sample or to follow a purification? Do you want it to be non-invasive (like the A280 measurement) or how much protein are you willing to waste? Some thoughts for a pure sample: 1) If you denature a sample, and label the lysines and N-terminus with a fluorophore (e.g., fluoroscein), you can unambiguously measure the absorption or fluouresence emission. But that a longish procedure and you lose your protein. If you have Cys residues, labeling those with DTNB or mercurichrome can allow you to do the same thing. You just need to ensure all labeling sites are accessible. 2) Many people who recombinantly express a protein without Trp residues have mutated a Phe or Tyr residue to Trp. Thus, the protein has a built-in means to measure protein concentration by Trp absorption or fluorescence. 3) If you have protein to waste or it survives being lyophilized, dialyze it into ammonium acetate, lyophilize it, then weigh it on a microbalance. Measuring protein concentration is not an exact science if you want it to be rapid and not waste lots of your precious protein sample. Good luck, Michael R. Michael Garavito, Ph.D. Professor of Biochemistry Molecular Biology 513 Biochemistry Bldg. Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334Email: [EMAIL PROTECTED] On Thu, Aug 21, 2008 at 12:54 PM, Mark Hilge [EMAIL PROTECTED] wrote: Dear all, I would be glad to hear what (simple) method I should use to determine protein concentrations as accurately as possible. Presently, I'm measuring absorption at 280nm with a nanodrop device. I either have 0 or 1 tryptophan and no activity test. Many thanks in advance! Best regards, Mark Mark Hilge Protein Biophysics NCMLS 274 3rd floor M850.03.035 Geert Grooteplein 28 6525 GA Nijmegen The Netherlands http://www.mark-hilge.com Phone: 0031 24 36 10 525 Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud University Nijmegen Medical Centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.
Re: [ccp4bb] Protein concentration
Mark, There are two very easy alternatives. First is the Bradford Coomassie Dye binding assay. You can buy a kit from Biorad at the following link: http://www.bio-rad.com/B2B/BioRad/product/br_category.jsp?BV_SessionID=0349900713.1219329576BV_EngineID=ccchadeemgdfflfcfngcfkmdhkkdfll.0categoryPath=%2fCatalogs%2fLife+Science+Research%2fSample+Quantitation%2fProtein+Assay+Kits+and+Cuvettes%2fBio-Rad+Protein+AssaydivName=CorporateloggedIn=falselang=Englishcountry=HQcatLevel=5catOID=-12777isPA=falseserviceLevel=Lit+RequestsearchStr=coomassiecateName=Ordering+Information Second is the BCA assay which can be purchased from Pierce (now bought out by Thermo/Fisher): http://www.piercenet.com/Products/Browse.cfm?fldID=02020101 Cheers, Jim On Thu, Aug 21, 2008 at 6:54 AM, Mark Hilge [EMAIL PROTECTED] wrote: Dear all, I would be glad to hear what (simple) method I should use to determine protein concentrations as accurately as possible. Presently, I'm measuring absorption at 280nm with a nanodrop device. I either have 0 or 1 tryptophan and no activity test. Many thanks in advance! Best regards, Mark Mark Hilge Protein Biophysics NCMLS 274 3rd floor M850.03.035 Geert Grooteplein 28 6525 GA Nijmegen The Netherlands http://www.mark-hilge.com Phone: 0031 24 36 10 525 Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud University Nijmegen Medical Centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629. -- Jim Fairman Graduate Research Assistant Department of Biochemistry, Cellular, and Molecular Biology (BCMB) University of Tennessee -- Knoxville 216-368-3337 [EMAIL PROTECTED] [EMAIL PROTECTED]
[ccp4bb] HKL2MAP
Dear, I'm looking to obtain a copy from HKL2MAP..? Does anyone know who to contact and the correct email address please..? The email of Thomas Schneider ([EMAIL PROTECTED]) is apparently not working anymore. 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
Re: [ccp4bb] Running Resolve after Sharp?
Your native structure factors and their stand.deviations are named FP and SIGFP in the eden.mtz. Further you need the phases and the figure of merit, PHIB and FOM, also from the edem.mtz. If you want to use some other density modification program the Hendrickson-Lattman coefficients might come handy. It is all written in the SHARP manual at http://www.globalphasing.com/sharp/manual/appendix1.html There you can find also the explanations for the columns in all the eden* files. I found RESOLVE to be most helpful for data worse than 2.3 resolution. ARP/wARP (which is implemented also in SHARP) is good for high resolution data but is very strict in its data quality requests. What is your resolution? Do you have problems with the output of the ARP/wARP at the end of autoSHARP? Good luck, Djordje Francuski What is the resolution of your data? Hi Sorry for a mixed up question about two great software. Has anybody tried to use Resolve after sharp / autosharp? i.e., escaping the Solomon step other than handedness determination and doing the density modification ( maybe NCS / building) directly with the sharp output? If so, I would appreciate any input.. I am confused with the eden file.. Cheers, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515
[ccp4bb] GNU-Darwin Package set of Molecules Machine
I am starting to get questions about how the Molecules site was constructed. http://molecules.gnu-darwin.org/ I think that it is a good example of what is possible using GNU-Darwin OS and FOSS, free and open source software. I also thought that GNU-Darwinists and others would be interested in the package set. It should be noted that these are alpha, first run packages, but we are putting them to good use. Here is the uname -a output for the current darwintel machine, which is doing all the heavy lifting. Darwin darwintel 8.0.1 Darwin Kernel Version 8.0.1: Fri Apr 29 12:18:40 PDT 2005; root:xnu-792.obj/RELEASE_I386 x86 i386 AMD Phenom(tm) X4 Quad-Core Processor GP-9500 Darwin This system has been stripped of all proprietary software, except two hardware driver binaries unfortunately, which is why we don't distribute the OS installer. One of the reasons why we operate this way is so that we can build and distribute free software that runs under current Darwin-based operating systems, like GNU-Darwin and Mac OS. Here is a link to the package directory. http://www.gnu-darwin.org/www001/packages-1.5a-CURRENT/ GNU-Darwinists with familiarity regarding our architecture may find these packages useful. If that is not the case, please consult our online help files and examples before trying this package set. Here is a link to the ports tree. http://www.gnu-darwin.org/www001/ports-1.5a-CURRENT If there are any further questions about how we are operating the Molecules site, please feel free to ask, or get a GNU-Darwin account, and look for yourself. Accounts are free for 30 days. Regards, proclus http://www.gnu-darwin.org/ -- 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-- pgpJ5AeUEBCw1.pgp Description: PGP signature
[ccp4bb] Phaser fails with malloc error
Hello, I am running phaser from the ccp4 6.0.99 suite on an OSX 10.5.4 Leopard , Mac Pro machine . I get the rather ominous error given below . We have gotten similar malloc errors with large datasets before on this machine. In those cases the same jobs ran fine on regular linux. Thought I would write in. I can send the mtz and search model over if needed for testing/ reproducing this error Thanks a lot for your help Hari Jayaram Postdoc , Brandeis Univerity EXIT STATUS: SUCCESS CPU Time: 0 days 0 hrs 9 mins 0.67 secs (540.67 secs) Finished: Thu Aug 21 13:45:26 2008 /pre /html *** * Information from CCP4Interface script *** The program run with command: /sw/share/xtal/ccp4-6.0.99e/bin/phaser has failed with error message phaser(36682) malloc: *** mmap(size=1999872000) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug *** #CCP4I TERMINATION STATUS 0 phaser(36682) malloc: *** mmap(size=1999872000) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug #CCP4I TERMINATION TIME 21 Aug 2008 13:45:26 #CCP4I MESSAGE Task failed
Re: [ccp4bb] Running Resolve after Sharp?
Yes, I did that recently and it worked although I found SOLOMON maps to be (subjectively) better. You should probably use the 'centroid' phases from the eden.mtz (SHARP gurus might want to correct me :)) Artem Hi Sorry for a mixed up question about two great software. Has anybody tried to use Resolve after sharp / autosharp? i.e., escaping the Solomon step other than handedness determination and doing the density modification ( maybe NCS / building) directly with the sharp output? If so, I would appreciate any input.. I am confused with the eden file.. Cheers, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515
[ccp4bb] CCP4 windows installation error: 1603: Error installing Microsoft(R).NET Framework.
Hi, We were trying to install the windows version of new ccp4 but met the following error: 1603: Error installing Microsoft(R).NET Framework. Anyone expeienced similar problem, and how to solve it ? Thanks. Hongmin IMPORTANT NOTICE: This e-mail and any attachments may contain confidential or sensitive information which is, or may be, legally privileged or otherwise protected by law from further disclosure. It is intended only for the addressee. If you received this in error or from someone who was not authorized to send it to you, please do not distribute, copy or use it or any attachments. Please notify the sender immediately by reply e-mail and delete this from your system. Thank you for your cooperation.
Re: [ccp4bb] Phaser fails with malloc error
Hello Phil and thanks for your email..I was running a VMware fusion Ubuntu session which was grabbing onto a large chunk of memory ( entirely my fault). I didnt realize that virtualized sessions can divert memory away from even the OS and make it essentially unavailable. I am waiting for my ubuntu job to finish to retry the phaser run. Sorry I jumped the gun and emailed ccp4bb Thanks again hari On Thu, Aug 21, 2008 at 2:55 PM, Phil Jeffrey [EMAIL PROTECTED]wrote: I would take a look at how much physical memory is on the machine, how much disk space there is on the system drive (often used as virtual swap), and what other processes are running. This would seem to be a failure to allocate 2Gb of memory, which isn't the smallest chunk I've ever seen. Phil hari jayaram wrote: Hello, I am running phaser from the ccp4 6.0.99 suite on an OSX 10.5.4 Leopard , Mac Pro machine . I get the rather ominous error given below . We have gotten similar malloc errors with large datasets before on this machine. In those cases the same jobs ran fine on regular linux. Thought I would write in. I can send the mtz and search model over if needed for testing/ reproducing this error Thanks a lot for your help Hari Jayaram Postdoc , Brandeis Univerity EXIT STATUS: SUCCESS CPU Time: 0 days 0 hrs 9 mins 0.67 secs (540.67 secs) Finished: Thu Aug 21 13:45:26 2008 /pre /html *** * Information from CCP4Interface script *** The program run with command: /sw/share/xtal/ccp4-6.0.99e/bin/phaser has failed with error message phaser(36682) malloc: *** mmap(size=1999872000) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug *** #CCP4I TERMINATION STATUS 0 phaser(36682) malloc: *** mmap(size=1999872000) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug #CCP4I TERMINATION TIME 21 Aug 2008 13:45:26 #CCP4I MESSAGE Task failed
[ccp4bb] How best to scale together absolute and Fo-Fc density maps?
I've computed an electron density map, on an absolute scale, from the atomic positions of a molecular dynamics simulation. I would like to compare this map, in particular a few peaks in it, to a (sigmaA-weighted) Fo-Fc map, calculated from a randomly-shaken refined (with a few key atoms at zero occupancy) x-ray structure. Although I don't know F(000) exactly, I could estimate it, as well as [F(000),obs - F(000),calc], if needed (i.e., I know which atoms are missing in the Fo-Fc map, and there are no atoms in the model that need to be removed). Three ways I've considered doing this: 1. Shift the Fo-Fc map values so that it's minimum value becomes zero, then scale it so that it's total electron count equals my (absolute) MD map. I see this as applying [F(000),obs - F(000),calc], followed by (arbitrary) scaling. 2. Match map means and sigmas, and scale them together. 3. Match histograms from each map, applying a linear transformation to get the Fo-Fc map non-negative and its histogram peak position the same as the MD map. Are any of 1 - 3 absurd or stupid? Preferred? A better way altogether? Thanks! David Borhani, Ph.D. D. E. Shaw Research, LLC 120 West Forty-Fifth Street, 39th Floor New York, NY 10036 [EMAIL PROTECTED] 212-478-0698 http://www.deshawresearch.com http://www.deshawresearch.com/
Re: [ccp4bb] How best to scale together absolute and Fo-Fc density maps?
Hi David One big problem you have here is that, depending on the low high resolution cutoffs and the completeness of your X-ray data, there will be Fourier series termination and phase error effects on both the electron density maxima and minima. The effects will be to reduce the peak heights and broaden the peak widths of your atoms (by an amount that is B-factor dependent), and also to introduce both +ve -ve 'ripples', which means that you can't assume that the Fo-Fc map is all positive, even if there are no wrongly placed atoms (or atoms with errors in occupancy or B factor) in your model. So I think correction for the missing F000 term is the least of your worries! That said, I would say the answer to your question is to match the map means since these depend directly on F000. Matching the map sigmas and/or the histograms as you suggest will also take out some of the differences due to the aforementioned resolution phase error effects, but by no means all. Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Borhani, David Sent: 21 August 2008 23:20 To: CCP4BB@JISCMAIL.AC.UK Subject: How best to scale together absolute and Fo-Fc density maps? I've computed an electron density map, on an absolute scale, from the atomic positions of a molecular dynamics simulation. I would like to compare this map, in particular a few peaks in it, to a (sigmaA-weighted) Fo-Fc map, calculated from a randomly-shaken refined (with a few key atoms at zero occupancy) x-ray structure. Although I don't know F(000) exactly, I could estimate it, as well as [F(000),obs - F(000),calc], if needed (i.e., I know which atoms are missing in the Fo-Fc map, and there are no atoms in the model that need to be removed). Three ways I've considered doing this: 1. Shift the Fo-Fc map values so that it's minimum value becomes zero, then scale it so that it's total electron count equals my (absolute) MD map. I see this as applying [F(000),obs - F(000),calc], followed by (arbitrary) scaling. 2. Match map means and sigmas, and scale them together. 3. Match histograms from each map, applying a linear transformation to get the Fo-Fc map non-negative and its histogram peak position the same as the MD map. Are any of 1 - 3 absurd or stupid? Preferred? A better way altogether? Thanks! David Borhani, Ph.D. D. E. Shaw Research, LLC 120 West Forty-Fifth Street, 39th Floor New York, NY 10036 [EMAIL PROTECTED] 212-478-0698 http://www.deshawresearch.com http://www.deshawresearch.com/ 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 [EMAIL PROTECTED] 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
Re: [ccp4bb] Running Resolve after Sharp?
Dear all, funny, I just gave a talk partly abuot this at the IUCr computing school in Kyoto today. Weird coincidences .. Anyway, to explain things a bit more (although previous posts already did most of it): - FP/SIGFP are the 'native' amplitude and sigma - HLA/HLB/HLC/HLD is the phase probability from SHARP as Hendrickson-Lattmann coefficients: these are in sync with FP/SIGFP - you can calculate an initial map in two ways: FB/PHIB = map including (average) heavy atom contribution Fcent/PHIcent = map of light atoms only This is all that's needed for running DM (I don't know RESOLVE, but I guess it is similar in the input it wants): LABIN FP=FP SIGFP=SIGFP - HLA=HLA HLB=HLB HLC=HLC HLD=HLD - FDM=FDM PHIDM=PHIDM The important points are a) use FP/SIGFP as amplitude and sigma (even if these don't really correspond to measured data) b) use HLA-D for phase combination (usually you should use the experimental phases _before_ density modification whenever you do phase combination, if you get HLs after density modifcation these will often be very biased) c) use FB/PHIB or Fcent/PHIcent to calculate starting map: this is only for the initial map, not for phase combination later during density modification. If you want to start from the SOLOMON result (eden_flat_XY.Zpc.mtz) the columns are named FPsha/SIGFPsha HLA/HLB/HLC/HLD FBshasol/PHIBshasol or Fcentshasol/PHIcentshasol For density modification at normal resolution (i.e. better than about 4A or so), in my experience SOLOMON gives excellent maps ... but doesn't handle NCS in a useable way. For a more theoretical background check our 2003 paper (Acta D) regarding this. Hope that helps ... Cheers Clemens On Thu, Aug 21, 2008 at 03:03:34PM -0400, [EMAIL PROTECTED] wrote: Yes, I did that recently and it worked although I found SOLOMON maps to be (subjectively) better. You should probably use the 'centroid' phases from the eden.mtz (SHARP gurus might want to correct me :)) Artem Hi Sorry for a mixed up question about two great software. Has anybody tried to use Resolve after sharp / autosharp? i.e., escaping the Solomon step other than handedness determination and doing the density modification ( maybe NCS / building) directly with the sharp output? If so, I would appreciate any input.. I am confused with the eden file.. Cheers, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515 -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] Running Resolve after Sharp?
As a follow-up: About a week or two ago, SOLOMON worked very well at 2.4A Hg-SAD (1A) phased map for ~1100 amino acids and 6 mercury sites. Almost 70% solvent did help quite a bit, I am sure :) Resolve produced comparable maps that were 'subjectively' slightly less pretty. As a crude measure of 'goodness' I can only note that arp/warp was able to trace the SOLOMON maps further than the RESOLVE ones - about 60% versus 55% complete sequence. Having said this I hasten to add that the application of NCS evened things out, this time with about ~10% improved tracing for RESOLVE maps. Artem P.S. Ultimately both Resolve and SOLOMON produced high quality maps that were readily traceable by hand and via software. Both maps made me feel fuzzy and warm inside which was the desired outcome. In comparison, the 3.5A maps obtained using home-source MIR did not make me feel neither fuzzy nor warm. Non-isomorphism is a killer. P.P.S. soaking in Hg salts produced a new space group with considerably lower overall B (resolution went from 3.5 to 2.4A also). Mercury is indeed the sweetest of transition metals. -Original Message- From: Clemens Vonrhein [mailto:[EMAIL PROTECTED] Sent: Thursday, August 21, 2008 10:40 PM To: [EMAIL PROTECTED] Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Running Resolve after Sharp? Dear all, funny, I just gave a talk partly abuot this at the IUCr computing school in Kyoto today. Weird coincidences .. Anyway, to explain things a bit more (although previous posts already did most of it): - FP/SIGFP are the 'native' amplitude and sigma - HLA/HLB/HLC/HLD is the phase probability from SHARP as Hendrickson-Lattmann coefficients: these are in sync with FP/SIGFP - you can calculate an initial map in two ways: FB/PHIB = map including (average) heavy atom contribution Fcent/PHIcent = map of light atoms only This is all that's needed for running DM (I don't know RESOLVE, but I guess it is similar in the input it wants): LABIN FP=FP SIGFP=SIGFP - HLA=HLA HLB=HLB HLC=HLC HLD=HLD - FDM=FDM PHIDM=PHIDM The important points are a) use FP/SIGFP as amplitude and sigma (even if these don't really correspond to measured data) b) use HLA-D for phase combination (usually you should use the experimental phases _before_ density modification whenever you do phase combination, if you get HLs after density modifcation these will often be very biased) c) use FB/PHIB or Fcent/PHIcent to calculate starting map: this is only for the initial map, not for phase combination later during density modification. If you want to start from the SOLOMON result (eden_flat_XY.Zpc.mtz) the columns are named FPsha/SIGFPsha HLA/HLB/HLC/HLD FBshasol/PHIBshasol or Fcentshasol/PHIcentshasol For density modification at normal resolution (i.e. better than about 4A or so), in my experience SOLOMON gives excellent maps ... but doesn't handle NCS in a useable way. For a more theoretical background check our 2003 paper (Acta D) regarding this. Hope that helps ... Cheers Clemens On Thu, Aug 21, 2008 at 03:03:34PM -0400, [EMAIL PROTECTED] wrote: Yes, I did that recently and it worked although I found SOLOMON maps to be (subjectively) better. You should probably use the 'centroid' phases from the eden.mtz (SHARP gurus might want to correct me :)) Artem Hi Sorry for a mixed up question about two great software. Has anybody tried to use Resolve after sharp / autosharp? i.e., escaping the Solomon step other than handedness determination and doing the density modification ( maybe NCS / building) directly with the sharp output? If so, I would appreciate any input.. I am confused with the eden file.. Cheers, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515 -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
