Dear Evgenii,

The dimple --anode option uses AnoDe [1, 2] to calculate the anomalous 
difference maps, so the anomalous map phases are in the output file anode.pha, 
not in final.mtz, which is generated by refmac. You can run the script 
anom-coot.sh to view the difference map in coot, or manually load the anode.pha 
and final.pdb yourself.

Cheers,

Richard

[1] http://shelx.uni-goettingen.de/anode.php
[2] http://scripts.iucr.org/cgi-bin/paper?fs5005
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 12:35
To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Dimple anomalous peaks

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<mailto: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<mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Eugene Osipov <e.m.osi...@gmail.com<mailto:e.m.osi...@gmail.com>>
Sent: 03 December 2019 10:22
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
<CCP4BB@JISCMAIL.AC.UK<mailto: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

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--
Evgenii Osipov
Laboratory for Biocrystallography,
Department of Pharmaceutical Sciences,
KU Leuven O&N2

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