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
