Dear Evgenii, it indeed makes sense to (optionally) use F+/- for refinement, but it just hasn't been requested before and I didn't think about it myself. I'm opening a ticket to not forget about it: https://github.com/ccp4/dimple/issues/13 and I'll get back to it later.
Best wishes, Marcin On Tue, 3 Dec 2019 at 13:36, Eugene Osipov <e.m.osi...@gmail.com> wrote: > > Dear Richard, > yes, it has I(+)/I(-) and corresponding sigmas. I tried the command you've > specified - final mtz still contains only "normal" maps but now I see > anomalous phases in anode.pha > In order to get difference anomalous maps I still have to run refmac5 with > LABIN F+=F(+) SIGF+=SIGF(+) F-=F(-) SIGF-=SIGF(-) FREE=FreeR_flag > Is it possible to specify in dimple which columns I want it to use during > restrained refinement, either F/SIGF or anomalous pairs F+/SIGF+ and F-/SIGF-? > May be it is possible to modify source code to tell dimple to run refmac5 > with specified LABINs? > Kind regards, > Evgenii > > > вт, 3 дек. 2019 г. в 12:31, Gildea, Richard (DLSLtd,RAL,LSCI) > <richard.gil...@diamond.ac.uk>: >> >> Dear Evgenii, >> >> Does your input mtz file contain I(+)/I(-) and SIGI(+)/SIGI(-) columns? >> Dimple runs shelxc to obtain the input reflection file for anode, which >> requires anomalous intensities as input. >> >> I.e. it essentially runs the following commands: >> >> $ mtz2sca AUTOMATIC_DEFAULT_free.mtz anode.sca >> >> $ shelxc anode << EOF >> SAD anode.sca >> CELL 57.9066 57.9066 150.3051 90.0 90.0 90.0 >> SPAG P 41 21 2 >> EOF >> >> $ cp dimple/final.pdb anode.pdb >> >> $ anode anode >> >> At Diamond we run dimple --anode on the free.mtz file generated by xia2, >> which contains the following columns: >> >> label #valid %valid min max type >> F 32162 99.75% 0.01 3130.76 F: amplitude >> SIGF 32162 99.75% 0.01 102.51 Q: standard deviation >> DANO 31745 98.46% -271.19 227.37 D: anomalous difference >> SIGDANO 31745 98.46% 0.00 124.40 Q: standard deviation >> F(+) 31777 98.55% 0.01 3130.76 G: F(+) or F(-) >> SIGF(+) 31777 98.55% 0.01 102.51 L: standard deviation >> F(-) 27431 85.08% 0.02 2758.00 G: F(+) or F(-) >> SIGF(-) 27431 85.08% 0.01 91.95 L: standard deviation >> ISYM 32243 100.00% -1.00 2.00 Y: M/ISYM, packed partial/reject >> flag and symmetry number >> IMEAN 32162 99.75% -0.31 780.55 J: intensity >> SIGIMEAN 32162 99.75% 0.00 24.65 Q: standard deviation >> I(+) 31777 98.55% -0.48 780.55 K: I(+) or I(-) >> SIGI(+) 31777 98.55% 0.00 24.65 M: standard deviation >> I(-) 27431 85.08% -0.44 609.14 K: I(+) or I(-) >> SIGI(-) 27431 85.08% 0.00 16.78 M: standard deviation >> >> E.g.: >> >> $ dimple AUTOMATIC_DEFAULT_free.mtz 1RQW dimple --anode -fpng >> >> Cheers, >> >> Richard >> >> Dr Richard Gildea >> Data Analysis Scientist >> Tel: +441235 77 8078 >> >> Diamond Light Source Ltd. >> Diamond House >> Harwell Science & Innovation Campus >> Didcot >> Oxfordshire >> OX11 0DE >> ________________________________ >> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Eugene Osipov >> <e.m.osi...@gmail.com> >> Sent: 03 December 2019 10:22 >> To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> >> Subject: [ccp4bb] Dimple anomalous peaks >> >> Dear CCP4 community, >> I can't figure out how to tell Dimple to use F(+)/F(-) columns and search >> for anomalous peaks. >> I was trying to run dimple in the next form: >> dimple -R free.mtz --anode --fcolumn F output.mtz test.pdb dimple_dir >> In the output mtz I get only 2Fo-Fc and Fo-Fc maps. When I try to use >> --fcolumn F(+) I gen an error. >> My mtz file contains both averaged F/SIGF, anomalous pairs F(+)/F(-) and >> their differences in DANO. >> Can someone tell how to calculate anomalous difference maps from dimple run? >> Thanks in advance, >> -- >> Evgenii Osipov >> Laboratory for Biocrystallography, >> Department of Pharmaceutical Sciences, >> KU Leuven O&N2 >> >> ________________________________ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >> >> >> >> -- >> >> This e-mail and any attachments may contain confidential, copyright and or >> privileged material, and are for the use of the intended addressee only. If >> you are not the intended addressee or an authorised recipient of the >> addressee please notify us of receipt by returning the e-mail and do not >> use, copy, retain, distribute or disclose the information in or attached to >> the e-mail. >> Any opinions expressed within this e-mail are those of the individual and >> not necessarily of Diamond Light Source Ltd. >> Diamond Light Source Ltd. cannot guarantee that this e-mail or any >> attachments are free from viruses and we cannot accept liability for any >> damage which you may sustain as a result of software viruses which may be >> transmitted in or with the message. >> Diamond Light Source Limited (company no. 4375679). Registered in England >> and Wales with its registered office at Diamond House, Harwell Science and >> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom >> >> >> >> ________________________________ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > -- > Evgenii Osipov > Laboratory for Biocrystallography, > Department of Pharmaceutical Sciences, > KU Leuven O&N2 > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
