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
