Re: [ccp4bb] Refinement with refmac05 and methionine density
Hi Jeorge, The simplest answer is that you have multiple positions for the Methionine. So you can try adding in an alternate position for it. However, you didn’t mention the sigma cutoff or e-/A^3 for either of your density maps. Its quite possible that your fofc map is just scaled way down and what you are seeing is an exaggeration of what’s barely there. Hope this helps. Cheers! - Greg --- Greg Costakes, Ph.D. Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge, CB2 1GA United Kingdom From: jeorgemarley thomas Sent: Wednesday, November 12, 2014 8:16 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Refinement with refmac05 and methionine density Dear All, I am refining the structure with refmac05, and after each refinement the density around this methionine is flipping. and it is difficult to say where this methionine actually have the density. please suggest what I should I do. I am attaching the snap here. Thanks in Advance for your kind suggestions Jeorge --- This email is free from viruses and malware because avast! Antivirus protection is active. http://www.avast.com
[ccp4bb] XRD basic requirement
Hi everyone, My institute is decided to purchase an in-house X-ray diffractometer. Unfortunately i do not know what is the basic requirement that we should look for before we can select the equipment. I hope to get some guideline that will be useful for me to make a better decision on which XRD that we should purchase. That you in advance for your generosity. Anuar Young Scientist
[ccp4bb] Event for the website: Advertising the 2015 Young Scientists' Forum in Berlin
Dr Claudia Alen Amaro Scientific Project Manager Instruct: An Integrated Structural Biology Infrastructure for Europe, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington OX3 7BN, UK Tel: +44 1865 287808 email: clau...@strubi.ox.ac.uk Follow us on twitter @instructhub Original message Date: Mon, 10 Nov 2014 15:31:49 +0100 From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Tales Rocha tale...@gmail.com) Subject: [ccp4bb] Advertising the 2015 Young Scientists' Forum in Berlin To: CCP4BB@JISCMAIL.AC.UK Dear Young Scientists It’s our great pleasure to invite you to the 15th FEBS Young Scientists’ Forum (YSF) next year in Berlin, Germany. It will take place just before the main FEBS meeting, from 2nd to 4th July 2015. The YSF is a forum for PhD students and junior postdocs to discuss their research and career plans in an informal setting, away from the large FEBS congress. It will feature keynote lectures by young principal investigators and selected talks by participants. We aim to provide not only an excellent environment for scientific discussion, but also to give training in key skills through our roundtable session. The meeting will also include a social event at a premier location in the heart of Berlin. For more information please see the attached flyer and visit www.febs2015.org. Registration is now open! The deadline for registration and abstract submission is 31st January 2015. Be sure to sign up soon, so you don’t miss out. Please pay close attention to the eligibility criteria. Note that applicants selected for participation in the YSF will be automatically registered at the FEBS congress and will not have to pay any additional fees. We look forward to seeing you in Berlin in 2015 Karine Santos YSF Chair 2015 Fabian Gerth, Claudia Gras, Olga Herdt, Janine Lützkendorf, Jan Wollenhaupt, David Yadin Organising Committee -- flyer_YSF.pdf (519k bytes)
Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Wolfram Tempel, there might be some confusion about terms. It is correct that xscale scales several data sets together. However, in crystallography, 'merging' might be the better term for this process. Crystallographic 'Scaling' is far more complicated than 'merging'. It applies correction factors which try to make up for experimental errors in your data set. These corrections include the sigma-values, which is particularly important for experimental phasing. In that respect it can actually hamper the data quality if you (crystallographically) scale your data twice, although the effect is rather subtle. CORRECT carries out these corrections, hence CORRECT scales your data set, while XSCALE does not repeat this step - it only merges your data in the sense that it puts your data on a common scale. This is the application of a not too difficult mathematical formula (which is listed in the xds wiki, but I don't remember the URL). Regards, Tim On 11/11/2014 10:07 PM, Sudhir Babu Pothineni wrote: http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xscale XSCALE http://www.mpimf-heidelberg.mpg.de/%7Ekabsch/xds/html_doc/xscale_parameters.html is the scaling program of the XDS suite. It scales reflection files (typically called XDS_ASCII.HKL) produced by XDS. Since the CORRECT step of XDS already scales an individual dataset, XSCALE is only /needed/ if several datasets should be scaled relative to another. However, it does not deterioriate a dataset if it is scaled again in XSCALE, since the supporting points of the scalefactors are at the same positions in detector and batch space. The advantage of using XSCALE for a single dataset is that the user can specify the limits of the resolution shells. _Scaling with scala/aimless_ http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Scaling_with_SCALA_%28or_better:_aimless%29 -Sudhir *** Sudhir Babu Pothineni GM/CA @ APS 436D Argonne National Laboratory 9700 S Cass Ave Argonne IL 60439 Ph : 630 252 0672 On 11/11/14 14:42, wtempel wrote: Thank you Boaz. So if CORRECT can do a fully corrected scaling, are there no corrections that XSCALE might apply to XDS_ASCII.HKL data that are beyond CORRECT's capabilities? Wolfram On Tue, Nov 11, 2014 at 3:05 PM, Boaz Shaanan bshaa...@bgu.ac.il mailto:bshaa...@bgu.ac.il wrote: Hi, I actually choose the option 'constant' further down in the aimless gui but I guess the effect is similar to 'onlymege'. Boaz /Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il mailto:bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 / // // / / *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK] on behalf of wtempel [wtem...@gmail.com mailto:wtem...@gmail.com] *Sent:* Tuesday, November 11, 2014 9:50 PM *To:* CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS Hello all, in a discussion https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1307L=CCP4BBH=1P=186901 on this board, Kay Diederichs questioned the effect of scaling data in AIMLESS after prior scaling in XDS (CORRECT). I understand that the available alternatives in this work flow are to specify the AIMLESS ‘onlymerge’ command, or not. Are there any arguments for the preference of one alternative over the other? Thank you for your insights, Wolfram Tempel - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) iD8DBQFUYzT7UxlJ7aRr7hoRAuO2AJ9P3kJAjP+8wWjXRvkZwgDs9UOo3ACfb1En 67VgyyqCTX6j5vOz3xMVwqE= =ooTC -END PGP SIGNATURE-
Re: [ccp4bb] Refinement with refmac05 and methionine density
That looks really odd - the whole MET has a negative/positive ghost Second conformations usually branch at the CB, and dont look like that. Are you sure you havent somehow got two MET residues in the coordinate set ? Turn on cysmmetry display in coot and look for clashes around there. Does the rest of the map look OK? I would set the occupancies of the MET and nearby side chains to 0.00 (you can do that in coot) then refine and look at the maps again. This is very old fashioned but you can do this: distang xyzin coords.pdb dist inter end to get a list of close symmetry clashes contacts Eleanor On 12 November 2014 09:17, Greg Costakes gcost...@purdue.edu wrote: Hi Jeorge, The simplest answer is that you have multiple positions for the Methionine. So you can try adding in an alternate position for it. However, you didn’t mention the sigma cutoff or e-/A^3 for either of your density maps. Its quite possible that your fofc map is just scaled way down and what you are seeing is an exaggeration of what’s barely there. Hope this helps. Cheers! - Greg --- Greg Costakes, Ph.D. Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge, CB2 1GA United Kingdom *From:* jeorgemarley thomas kirtswab...@gmail.com *Sent:* Wednesday, November 12, 2014 8:16 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Refinement with refmac05 and methionine density Dear All, I am refining the structure with refmac05, and after each refinement the density around this methionine is flipping. and it is difficult to say where this methionine actually have the density. please suggest what I should I do. I am attaching the snap here. Thanks in Advance for your kind suggestions Jeorge -- http://www.avast.com/ This email is free from viruses and malware because avast! Antivirus http://www.avast.com/ protection is active.
Re: [ccp4bb] XRD basic requirement
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Anuar, this depends on the crystal you are planning to measure. Will they be small so that you need to go for high intensity, or will they be large so that you can go for high quality (flat profile beam). Your budget will also be a limiting factor both for the source (rotating anode vs. liquid jet) and the detector (image plate vs. CMOS etc). Small molecule crystals also have different requirements than macromolecular samples. You need to figure out in better detail what your needs are - there are quite a few applications. Regards, Tim On 11/12/2014 10:06 AM, Dr Mohd Anuar Jonet wrote: Hi everyone, My institute is decided to purchase an in-house X-ray diffractometer. Unfortunately i do not know what is the basic requirement that we should look for before we can select the equipment. I hope to get some guideline that will be useful for me to make a better decision on which XRD that we should purchase. That you in advance for your generosity. Anuar Young Scientist - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) iD8DBQFUYzZ6UxlJ7aRr7hoRAnALAJ49J3bqN9PNSjLq9pIe8zV1EX87owCgrmVL lGc3xTadiW7cAKomTC05LrA= =vxqv -END PGP SIGNATURE-
Re: [ccp4bb] Refinement with refmac05 and methionine density
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jeorge, the 'ghost' could be explained by a shift of an entire section, i.e. you have to split several residues into A+B, not only the MET. The cylR2 structure in 2XJ3 is one example where this was necessary. Best, Tim On 11/12/2014 11:23 AM, Eleanor Dodson wrote: That looks really odd - the whole MET has a negative/positive ghost Second conformations usually branch at the CB, and dont look like that. Are you sure you havent somehow got two MET residues in the coordinate set ? Turn on cysmmetry display in coot and look for clashes around there. Does the rest of the map look OK? I would set the occupancies of the MET and nearby side chains to 0.00 (you can do that in coot) then refine and look at the maps again. This is very old fashioned but you can do this: distang xyzin coords.pdb dist inter end to get a list of close symmetry clashes contacts Eleanor On 12 November 2014 09:17, Greg Costakes gcost...@purdue.edu wrote: Hi Jeorge, The simplest answer is that you have multiple positions for the Methionine. So you can try adding in an alternate position for it. However, you didn’t mention the sigma cutoff or e-/A^3 for either of your density maps. Its quite possible that your fofc map is just scaled way down and what you are seeing is an exaggeration of what’s barely there. Hope this helps. Cheers! - Greg --- Greg Costakes, Ph.D. Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge, CB2 1GA United Kingdom *From:* jeorgemarley thomas kirtswab...@gmail.com *Sent:* Wednesday, November 12, 2014 8:16 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Refinement with refmac05 and methionine density Dear All, I am refining the structure with refmac05, and after each refinement the density around this methionine is flipping. and it is difficult to say where this methionine actually have the density. please suggest what I should I do. I am attaching the snap here. Thanks in Advance for your kind suggestions Jeorge -- http://www.avast.com/ This email is free from viruses and malware because avast! Antivirus http://www.avast.com/ protection is active. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) iD8DBQFUY0O/UxlJ7aRr7hoRArkIAJsHP6gLpSkRtJPEE7/P/R453uGvJACeMfus jFS3EEDy7g7ss5A6L3D3cco= =uLjH -END PGP SIGNATURE-
[ccp4bb] 2014 BCA Biological Structures Group Winter Meeting: registration is now open!
*2014 BCA-BSG Winter Meeting* *The 2014 BCA-BSG Winter Meeting will take place on the European Photon and Neutron (EPN) Campus (hosting the European Synchrotron Radiation Facility and the Institute Laue Langevin), Grenoble, France on 15-17 **December 2014. *The meeting will be themed around opportunities for Structural Biology at large-scale research infrastructure and will include sessions addressing the combination of structural information from X-rays neutrons in Structural Biology, Structural Biology on the EPN Campus, and Emerging Techniques in Structural Biology. Confirmed speakers include: Arwen Pearson, CUI, Hamburg, Germany Cecilia Casadei, University of Leicester, UK Julia Richardson, University of Edinburgh, UK Selma Maric, Karolinska Institute, Sweden Stephen Cusack, EMBL, Grenoble Andrea Dessen, IBS, Grenoble Catarina da Silva, CEA, Grenoble Antoine Royant, IBS, Grenoble Gemma Newby, ESRF, Grenoble Manfred Burghammer, ESRF, Grenoble Matthew Bowler, EMBL, Grenoble Ulrich Zander, ESRF, Grenoble Estelle Mossou, University of Keele, UK/ILL, Grenoble Helmut Schober, Director of Science, ILL, Grenoble Elizabeth Duke, Diamond Light Source, UK The first half of the meeting - supported by the UK Science Technology Funding Council (STFC) - aims at presenting the strategic significance to the structural biology community of UK investment in large-scale research infrastructure. This part of the meeting will include visits to ESRF and ILL Experimental Facilities, a round table discussion and speakers including: Florent Bernaudat, Partnership for Structural Biology, Grenoble Harald Reichert, ESRF, Grenoble Colin Miles, BBSRC, UK Pamela Williams, Astex, UK David Scott, University of Nottingham, UK Adrian Mancuso, European XFEL, Hamburg, Germany Andrew Harrison, Diamond Light Source, UK Gordon Leonard, ESRF, Grenoble Trevor Forsyth, ILL, Grenoble *A provisional programme and details of how to register for the meeting can be found at: *** *http://www.esrf.fr/home/events/conferences/2014-bca-bsg-winter-meeting.html*** ** ** ** *The deadline for registration is the 8**December.* *The programme includes a poster session. Contributions from younger and more senior scientists on any aspect of Structural Biology are actively encouraged.* In order to help reduce the costs of attending the meeting, the registration fee (32EUR for students; 64EUR for regular participants) will include the cost of all meals during the meeting, including the meeting dinner on 16 December and as many participants as possible will be housed - at participants' own cost - in the cost effective ESRF/ILL Guesthouse. The registration fee also includes membership of the BCA for the year 2015. *Five Travel Bursaries, each of up to £200, are available from the BCA to support participation in the meeting by research students and postdoctoral workers who are BCA members.* Please see http://crystallography.org.uk/prizes/bursaries/abbf-bursaries/ for details. looking forward to seeing you over in Grenoble! Gordon Leonard, Trevor Forsyth and Ed Mitchell.
Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS
Hi Tim, this is incorrect. XSCALE determines the relative scale and B in a first step (this is what you describe). It then, in a second step, re-determines all scale factors (exactly as CORRECT does for the individual data sets), at the exact same supporting points that CORRECT used. (This avoids over-fitting which would result from a scaling model with different basis functions; a worry that I have when people use SCALA/AIMLESS after CORRECT without taking precautions.) The resulting scale factors are written to files MODPIX*.cbf, DECAY*.cbf, ABSORP*.cbf for inspection. Thirdly, it produces statistics and writes output files. best, Kay On Wed, 12 Nov 2014 11:22:51 +0100, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Wolfram Tempel, there might be some confusion about terms. It is correct that xscale scales several data sets together. However, in crystallography, 'merging' might be the better term for this process. Crystallographic 'Scaling' is far more complicated than 'merging'. It applies correction factors which try to make up for experimental errors in your data set. These corrections include the sigma-values, which is particularly important for experimental phasing. In that respect it can actually hamper the data quality if you (crystallographically) scale your data twice, although the effect is rather subtle. CORRECT carries out these corrections, hence CORRECT scales your data set, while XSCALE does not repeat this step - it only merges your data in the sense that it puts your data on a common scale. This is the application of a not too difficult mathematical formula (which is listed in the xds wiki, but I don't remember the URL). Regards, Tim On 11/11/2014 10:07 PM, Sudhir Babu Pothineni wrote: http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xscale XSCALE http://www.mpimf-heidelberg.mpg.de/%7Ekabsch/xds/html_doc/xscale_parameters.html is the scaling program of the XDS suite. It scales reflection files (typically called XDS_ASCII.HKL) produced by XDS. Since the CORRECT step of XDS already scales an individual dataset, XSCALE is only /needed/ if several datasets should be scaled relative to another. However, it does not deterioriate a dataset if it is scaled again in XSCALE, since the supporting points of the scalefactors are at the same positions in detector and batch space. The advantage of using XSCALE for a single dataset is that the user can specify the limits of the resolution shells. _Scaling with scala/aimless_ http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Scaling_with_SCALA_%28or_better:_aimless%29 -Sudhir *** Sudhir Babu Pothineni GM/CA @ APS 436D Argonne National Laboratory 9700 S Cass Ave Argonne IL 60439 Ph : 630 252 0672 On 11/11/14 14:42, wtempel wrote: Thank you Boaz. So if CORRECT can do a fully corrected scaling, are there no corrections that XSCALE might apply to XDS_ASCII.HKL data that are beyond CORRECT's capabilities? Wolfram On Tue, Nov 11, 2014 at 3:05 PM, Boaz Shaanan bshaa...@bgu.ac.il mailto:bshaa...@bgu.ac.il wrote: Hi, I actually choose the option 'constant' further down in the aimless gui but I guess the effect is similar to 'onlymege'. Boaz /Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il mailto:bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 / // // / / *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK] on behalf of wtempel [wtem...@gmail.com mailto:wtem...@gmail.com] *Sent:* Tuesday, November 11, 2014 9:50 PM *To:* CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS Hello all, in a discussion https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1307L=CCP4BBH=1P=186901 on this board, Kay Diederichs questioned the effect of scaling data in AIMLESS after prior scaling in XDS (CORRECT). I understand that the available alternatives in this work flow are to specify the AIMLESS ‘onlymerge’ command, or not. Are there any arguments for the preference of one alternative over the other? Thank you for your insights, Wolfram Tempel - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) iD8DBQFUYzT7UxlJ7aRr7hoRAuO2AJ9P3kJAjP+8wWjXRvkZwgDs9UOo3ACfb1En 67VgyyqCTX6j5vOz3xMVwqE= =ooTC -END PGP SIGNATURE-
Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS
On Wed, 12 Nov 2014 15:32:04 +, Kay Diederichs kay.diederi...@uni-konstanz.de wrote: ... It then, in a second step, re-determines all scale factors (exactly as CORRECT does for the individual data sets), at the exact same supporting points that CORRECT used. (This avoids over-fitting which would result from a scaling model with different basis functions; a worry that I have when people use SCALA/AIMLESS after CORRECT without taking precautions.) The resulting scale factors are written to files MODPIX*.cbf, DECAY*.cbf, ABSORP*.cbf for inspection. Maybe needless to add, but I'll write it nevertheless. XSCALE _also_ adjust the error model in this step, and adjusts the sigmas accordingly. Kay
Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS
Hi Kay, thank you for the clarification. I had understood that using XSCALE after CORRECT does no harm, but did not understand that the reason lies in the consistent choice of support points rather than not repeating what might already having been done. Regards, Tim On 11/12/2014 04:32 PM, Kay Diederichs wrote: Hi Tim, this is incorrect. XSCALE determines the relative scale and B in a first step (this is what you describe). It then, in a second step, re-determines all scale factors (exactly as CORRECT does for the individual data sets), at the exact same supporting points that CORRECT used. (This avoids over-fitting which would result from a scaling model with different basis functions; a worry that I have when people use SCALA/AIMLESS after CORRECT without taking precautions.) The resulting scale factors are written to files MODPIX*.cbf, DECAY*.cbf, ABSORP*.cbf for inspection. Thirdly, it produces statistics and writes output files. best, Kay On Wed, 12 Nov 2014 11:22:51 +0100, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Wolfram Tempel, there might be some confusion about terms. It is correct that xscale scales several data sets together. However, in crystallography, 'merging' might be the better term for this process. Crystallographic 'Scaling' is far more complicated than 'merging'. It applies correction factors which try to make up for experimental errors in your data set. These corrections include the sigma-values, which is particularly important for experimental phasing. In that respect it can actually hamper the data quality if you (crystallographically) scale your data twice, although the effect is rather subtle. CORRECT carries out these corrections, hence CORRECT scales your data set, while XSCALE does not repeat this step - it only merges your data in the sense that it puts your data on a common scale. This is the application of a not too difficult mathematical formula (which is listed in the xds wiki, but I don't remember the URL). Regards, Tim On 11/11/2014 10:07 PM, Sudhir Babu Pothineni wrote: http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xscale XSCALE http://www.mpimf-heidelberg.mpg.de/%7Ekabsch/xds/html_doc/xscale_parameters.html is the scaling program of the XDS suite. It scales reflection files (typically called XDS_ASCII.HKL) produced by XDS. Since the CORRECT step of XDS already scales an individual dataset, XSCALE is only /needed/ if several datasets should be scaled relative to another. However, it does not deterioriate a dataset if it is scaled again in XSCALE, since the supporting points of the scalefactors are at the same positions in detector and batch space. The advantage of using XSCALE for a single dataset is that the user can specify the limits of the resolution shells. _Scaling with scala/aimless_ http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Scaling_with_SCALA_%28or_better:_aimless%29 -Sudhir *** Sudhir Babu Pothineni GM/CA @ APS 436D Argonne National Laboratory 9700 S Cass Ave Argonne IL 60439 Ph : 630 252 0672 On 11/11/14 14:42, wtempel wrote: Thank you Boaz. So if CORRECT can do a fully corrected scaling, are there no corrections that XSCALE might apply to XDS_ASCII.HKL data that are beyond CORRECT's capabilities? Wolfram On Tue, Nov 11, 2014 at 3:05 PM, Boaz Shaanan bshaa...@bgu.ac.il mailto:bshaa...@bgu.ac.il wrote: Hi, I actually choose the option 'constant' further down in the aimless gui but I guess the effect is similar to 'onlymege'. Boaz /Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il mailto:bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 / // // / / *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK] on behalf of wtempel [wtem...@gmail.com mailto:wtem...@gmail.com] *Sent:* Tuesday, November 11, 2014 9:50 PM *To:* CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS Hello all, in a discussion https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1307L=CCP4BBH=1P=186901 on this board, Kay Diederichs questioned the effect of scaling data in AIMLESS after prior scaling in XDS (CORRECT). I understand that the available alternatives in this work flow are to specify the AIMLESS ‘onlymerge’ command, or not. Are there any arguments for the preference of one alternative over the other? Thank you for your insights, Wolfram Tempel -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature
[ccp4bb] Test
This is a test Sent from my Windows Phone
Re: [ccp4bb] Incubator for crystallization
Hi, Our experience was the opposite. Ours did not work well and completely broke soon after. This incubator quickly turned into the largest door stop in the lab. I'm sure ours was just a lemon, but I thought I'd still mention it to warn others. I am still interested in hearing what models of crystal incubators people are using, small or large. Engin On 11/11/14 5:17 AM, jai mohan wrote: Dear Ulrike, Molecular dimensions incubator model MD5-601 works pretty good in our lab. -Peltier type -low vibration -fully programmable up to 99 days -temperature up to 4C -accommodate low space -with RS232 Check the following links | From archives related to your question posted previously. DT2-MP-38: DigiTherm(R) 38-liter Heating/Cooling Incubator - Tritech Research, Inc. http://www.tritechresearch.com/DT2-MP-38.html image http://www.tritechresearch.com/DT2-MP-38.html DT2-MP-38: DigiTherm(R) 38-liter Heating/Cooling Incu... http://www.tritechresearch.com/DT2-MP-38.html View on www.tritechresearch... http://www.tritechresearch.com/DT2-MP-38.html Preview by Yahoo EchoTherm™ IN30, IN35, IN40, IN45, IN50 and IN55 Bench Top Incubators | Torrey Pines Scientific https://www.torreypinesscientific.com/products/incubators/echotherm-in30-in35-in40-and-in45-bench-top-incubators image https://www.torreypinesscientific.com/products/incubators/echotherm-in30-in35-in40-and-in45-bench-top-incubators EchoTherm™ IN30, IN35, IN40, IN45, IN50 and IN55 B... https://www.torreypinesscientific.com/products/incubators/echotherm-in30-in35-in40-and-in45-bench-top-incubators EchoTherm™ IN30, IN40 and IN50 Series Bench Top, Chilling/Heating Incubators with Fully Programmable or Non-programmable Controls Chill or heat... View on www.torreypinesscien... https://www.torreypinesscientific.com/products/incubators/echotherm-in30-in35-in40-and-in45-bench-top-incubators Preview by Yahoo Cheers Dr.S.M.Jaimohan
Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS
Hello Kay, you said the o-word, and you are familiar with the inner workings of XDS. Has the data-to-parameter ratio in even complex scaling models become so small that a doubling (worst case) of model parameters would be a serious concern? Could one detect such overfitting by, say, comparing (molecular) model R-factors between refinement against the once (CORRECT) scaled or twice (CORRECT+AIMLESS) scaled data? Thank you, Wolfram On Wed, Nov 12, 2014 at 10:32 AM, Kay Diederichs kay.diederi...@uni-konstanz.de wrote: Hi Tim, this is incorrect. XSCALE determines the relative scale and B in a first step (this is what you describe). It then, in a second step, re-determines all scale factors (exactly as CORRECT does for the individual data sets), at the exact same supporting points that CORRECT used. (This avoids over-fitting which would result from a scaling model with different basis functions; a worry that I have when people use SCALA/AIMLESS after CORRECT without taking precautions.) The resulting scale factors are written to files MODPIX*.cbf, DECAY*.cbf, ABSORP*.cbf for inspection. Thirdly, it produces statistics and writes output files. best, Kay On Wed, 12 Nov 2014 11:22:51 +0100, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Wolfram Tempel, there might be some confusion about terms. It is correct that xscale scales several data sets together. However, in crystallography, 'merging' might be the better term for this process. Crystallographic 'Scaling' is far more complicated than 'merging'. It applies correction factors which try to make up for experimental errors in your data set. These corrections include the sigma-values, which is particularly important for experimental phasing. In that respect it can actually hamper the data quality if you (crystallographically) scale your data twice, although the effect is rather subtle. CORRECT carries out these corrections, hence CORRECT scales your data set, while XSCALE does not repeat this step - it only merges your data in the sense that it puts your data on a common scale. This is the application of a not too difficult mathematical formula (which is listed in the xds wiki, but I don't remember the URL). Regards, Tim On 11/11/2014 10:07 PM, Sudhir Babu Pothineni wrote: http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xscale XSCALE http://www.mpimf-heidelberg.mpg.de/%7Ekabsch/xds/html_doc/xscale_parameters.html is the scaling program of the XDS suite. It scales reflection files (typically called XDS_ASCII.HKL) produced by XDS. Since the CORRECT step of XDS already scales an individual dataset, XSCALE is only /needed/ if several datasets should be scaled relative to another. However, it does not deterioriate a dataset if it is scaled again in XSCALE, since the supporting points of the scalefactors are at the same positions in detector and batch space. The advantage of using XSCALE for a single dataset is that the user can specify the limits of the resolution shells. _Scaling with scala/aimless_ http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Scaling_with_SCALA_%28or_better:_aimless%29 -Sudhir *** Sudhir Babu Pothineni GM/CA @ APS 436D Argonne National Laboratory 9700 S Cass Ave Argonne IL 60439 Ph : 630 252 0672 On 11/11/14 14:42, wtempel wrote: Thank you Boaz. So if CORRECT can do a fully corrected scaling, are there no corrections that XSCALE might apply to XDS_ASCII.HKL data that are beyond CORRECT's capabilities? Wolfram On Tue, Nov 11, 2014 at 3:05 PM, Boaz Shaanan bshaa...@bgu.ac.il mailto:bshaa...@bgu.ac.il wrote: Hi, I actually choose the option 'constant' further down in the aimless gui but I guess the effect is similar to 'onlymege'. Boaz /Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il mailto:bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 / // // / / *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK] on behalf of wtempel [wtem...@gmail.com mailto:wtem...@gmail.com] *Sent:* Tuesday, November 11, 2014 9:50 PM *To:* CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS Hello all, in a discussion https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1307L=CCP4BBH=1P=186901 on this board, Kay Diederichs questioned the effect of scaling data in AIMLESS after prior scaling in XDS (CORRECT). I understand that the available alternatives in this work flow are to specify the AIMLESS ‘onlymerge’ command, or not. Are there any
[ccp4bb] merging anisotropic datasets
I have three datasets of varying quality collected from different regions of a single crystal. In each case, the data are anisotropic (from Aimless using CC1/20.5): Dataset 1: 3.5, 3.5 5.5 A Dataset 2: 4.2, 4.3, 4.8 A Dataset 3: 3.7, 3.9, 4.4 A I initially took a simple-minded approach and processed each dataset at the appropriate resolution limit (set 1: 3.5A; set 2: 4.2A; set 3: 3.7A) using XDS/XSCALE as implemented in xia2. The resulting merged dataset seems fine (albeit with ugly stats in the high-res bins because of the anisotropy), and it allowed me to solve the structure (Rfree/Rcryst ~31/26). Now I am wondering if I can improve the maps further by first applying an ellipsoidal truncation (using the UCLA diffraction anisotropy server) and then scaling/merging the three datasets together. However, it seems that the UCLA anisotropy server only allows input of one dataset at a time, and it outputs merged amplitudes. Is there some way to obtain the elliptically truncated but unmerged data for each of the three datasets? More generally, are there preferred strategies for dealing with strongly anisotropic data? Bob Robert Keenan Associate Professor Dept. of Biochemistry Molecular Biology GCIS W238 University of Chicago 929 East 57th Street Chicago, IL 60637 (o) 773.834.2292 (f) 773.834.5416 (e) bkee...@uchicago.edumailto:bkee...@uchicago.edu http://keenanlab.bsd.uchicago.edu
Re: [ccp4bb] merging anisotropic datasets
Hi Bob, we have done elliptic truncation before merging/scaling as lined out in 2012 Zebisch (JMB). However, I see no reason not to scale the 3 runs together with aimless (to lets say 3.4A) and then subject the resulting merged file to the sawata server. Best, Matthias - Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax (+44) 1865 287547 Email matth...@strubi.ox.ac.uk Website http://www.strubi.ox.ac.uk - On 11/12/2014 9:26 PM, Robert Keenan wrote: I have three datasets of varying quality collected from different regions of a single crystal. In each case, the data are anisotropic (from Aimless using CC1/20.5): Dataset 1: 3.5, 3.5 5.5 A Dataset 2: 4.2, 4.3, 4.8 A Dataset 3: 3.7, 3.9, 4.4 A I initially took a simple-minded approach and processed each dataset at the appropriate resolution limit (set 1: 3.5A; set 2: 4.2A; set 3: 3.7A) using XDS/XSCALE as implemented in xia2. The resulting merged dataset seems fine (albeit with ugly stats in the high-res bins because of the anisotropy), and it allowed me to solve the structure (Rfree/Rcryst ~31/26). Now I am wondering if I can improve the maps further by first applying an ellipsoidal truncation (using the UCLA diffraction anisotropy server) and then scaling/merging the three datasets together. However, it seems that the UCLA anisotropy server only allows input of one dataset at a time, and it outputs merged amplitudes. Is there some way to obtain the elliptically truncated but unmerged data for each of the three datasets? More generally, are there preferred strategies for dealing with strongly anisotropic data? Bob Robert Keenan Associate Professor Dept. of Biochemistry Molecular Biology GCIS W238 University of Chicago 929 East 57th Street Chicago, IL 60637 (o) 773.834.2292 (f) 773.834.5416 (e) bkee...@uchicago.edu mailto:bkee...@uchicago.edu http://keenanlab.bsd.uchicago.edu
Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS
Hi Wolfram, it took me a while until I realized that you mean overfitting when you said o-word. You can abuse XDS in a number of ways, and I would call them overfitting the data although that would be using the word in a somewhat strained way: reducing WFAC1 below 1, decreasing REFLECTIONS/CORRECTION_FACTOR below 50 come to mind, but in an extended sense there are other ways: rejecting frames for no other reason than that they have low I/sigma or high Rmeas, ... People always seem to find ways to beautify their precision indicators, but they are just fooling themselves, because rejecting data just for cosmetic reasons creates bias. In other words, they trade random error against systematic error. Guess what is worse. A deeper reason of the problem is that crystallographers have been fixated on data R-factors for decades, and have become really spoilt by this. Our science has been completely mis-lead when it comes to data statistics, and is recovering only slowly. Concerning non-cautious use of SCALA/AIMLESS after CORRECT: actually I know of no systematic studies in this respect. But I know one thing: it is better to be critical with respect to recipes, than to follow them blindly. So I suggest the following project: compare SAD structure solution with the following routes a) INTEGRATE - CORRECT scaling - SHELXD b) INTEGRATE - AIMLESS scaling - SHELXD c) INTEGRATE - CORRECT+AIMLESS scaling - SHELXD d) INTEGRATE - CORRECT but scaling switched off - AIMLESS scaling - SHELXD e) INTEGRATE - CORRECT scaling - AIMLESS but scaling switched off - SHELXD and report here. You can add XSCALE into the mix but that won't change the picture, since it does the exact same calculations for multiple datasets as CORRECT does for single datasets. Personally, I don't understand why people would _want_ to do c),d) or e) because that's just added complexity, and additional sources of error. I'm looking forward to the results of such studies! Kay On Wed, 12 Nov 2014 12:41:28 -0500, wtempel wtem...@gmail.com wrote: Hello Kay, you said the o-word, and you are familiar with the inner workings of XDS. Has the data-to-parameter ratio in even complex scaling models become so small that a doubling (worst case) of model parameters would be a serious concern? Could one detect such overfitting by, say, comparing (molecular) model R-factors between refinement against the once (CORRECT) scaled or twice (CORRECT+AIMLESS) scaled data? Thank you, Wolfram On Wed, Nov 12, 2014 at 10:32 AM, Kay Diederichs kay.diederi...@uni-konstanz.de wrote: Hi Tim, this is incorrect. XSCALE determines the relative scale and B in a first step (this is what you describe). It then, in a second step, re-determines all scale factors (exactly as CORRECT does for the individual data sets), at the exact same supporting points that CORRECT used. (This avoids over-fitting which would result from a scaling model with different basis functions; a worry that I have when people use SCALA/AIMLESS after CORRECT without taking precautions.) The resulting scale factors are written to files MODPIX*.cbf, DECAY*.cbf, ABSORP*.cbf for inspection. Thirdly, it produces statistics and writes output files. best, Kay On Wed, 12 Nov 2014 11:22:51 +0100, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Wolfram Tempel, there might be some confusion about terms. It is correct that xscale scales several data sets together. However, in crystallography, 'merging' might be the better term for this process. Crystallographic 'Scaling' is far more complicated than 'merging'. It applies correction factors which try to make up for experimental errors in your data set. These corrections include the sigma-values, which is particularly important for experimental phasing. In that respect it can actually hamper the data quality if you (crystallographically) scale your data twice, although the effect is rather subtle. CORRECT carries out these corrections, hence CORRECT scales your data set, while XSCALE does not repeat this step - it only merges your data in the sense that it puts your data on a common scale. This is the application of a not too difficult mathematical formula (which is listed in the xds wiki, but I don't remember the URL). Regards, Tim On 11/11/2014 10:07 PM, Sudhir Babu Pothineni wrote: http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xscale XSCALE http://www.mpimf-heidelberg.mpg.de/%7Ekabsch/xds/html_doc/xscale_parameters.html is the scaling program of the XDS suite. It scales reflection files (typically called XDS_ASCII.HKL) produced by XDS. Since the CORRECT step of XDS already scales an individual dataset, XSCALE is only /needed/ if several datasets should be scaled relative to another. However, it does not deterioriate a dataset if it is scaled again in XSCALE, since the supporting points of the scalefactors
Re: [ccp4bb] merging anisotropic datasets
Would the CCP4 program BLEND be a suitable initial option? And then the anisotropic server? Tony. --- sent from my mobile account --- On 12 Nov 2014, at 21:29, Robert Keenan bkee...@uchicago.edumailto:bkee...@uchicago.edu wrote: I have three datasets of varying quality collected from different regions of a single crystal. In each case, the data are anisotropic (from Aimless using CC1/20.5): Dataset 1: 3.5, 3.5 5.5 A Dataset 2: 4.2, 4.3, 4.8 A Dataset 3: 3.7, 3.9, 4.4 A I initially took a simple-minded approach and processed each dataset at the appropriate resolution limit (set 1: 3.5A; set 2: 4.2A; set 3: 3.7A) using XDS/XSCALE as implemented in xia2. The resulting merged dataset seems fine (albeit with ugly stats in the high-res bins because of the anisotropy), and it allowed me to solve the structure (Rfree/Rcryst ~31/26). Now I am wondering if I can improve the maps further by first applying an ellipsoidal truncation (using the UCLA diffraction anisotropy server) and then scaling/merging the three datasets together. However, it seems that the UCLA anisotropy server only allows input of one dataset at a time, and it outputs merged amplitudes. Is there some way to obtain the elliptically truncated but unmerged data for each of the three datasets? More generally, are there preferred strategies for dealing with strongly anisotropic data? Bob Robert Keenan Associate Professor Dept. of Biochemistry Molecular Biology GCIS W238 University of Chicago 929 East 57th Street Chicago, IL 60637 (o) 773.834.2292 (f) 773.834.5416 (e) bkee...@uchicago.edumailto:bkee...@uchicago.edu http://keenanlab.bsd.uchicago.edu
[ccp4bb] PhD studentship at the University of Manchester
Dear All, Applications are invited for a PhD studentship at the Manchester Institute of Biotechnology, University of Manchester. The project will involve the structural and functional characterization of food allergens and their complexes. The techniques used will include cloning, protein purification, in vitro digestion, mass spectrometry (HDX-MS, IM-MS), crystallography, and cell-based assays. Project details and how to apply can be found at: - http://www.findaphd.com/search/projectDetails.aspx?PJID=58003 The deadline for applications is 26th November 2014. Informal enquires may be made to Balvinder Dhaliwal (email: balvinder.dhali...@manchester.ac.uk). Regards, Balvinder.
