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 <[email protected]> on behalf of Eugene Osipov
<[email protected]>
Sent: 03 December 2019 10:22
To: [email protected] <[email protected]>
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
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