--
Maybe something is funny with my mtz?
Dataset was processed with autoproc, then phaser and refinement
in phenix...(1.21 I think)
El lun, 20 may 2024 a la(s) 2:09 p.m., Eta Isiorho
(eisio...@gc.cuny.edu) escribió:
In old coot ™, I leave the defaults alone when opening the
2Fo-Fc and only check the box ‘assign labels…’
For the difference map, I change the amplitudes to ‘FOFC’ and
the phases to ‘PHFOFCWT’ and check the ‘assign labels’ box
again along with the ‘is a difference map’
This is the way I do it for my phenix outputs (the refmac
output is slightly different).
The only time I see greyed out blocks for SIG Fobs and
others, is when I forget to press the ‘assign labels’ button
for each map.
***
Eta A. Isiorho, Ph.D.
Research Assistant Professor
Macromolecular Crystallization Facility Manager
CUNY Advanced Science Research Center
85 Saint Nicholas Terrace, 3.352B/3.134
New York, NY 10031
eisio...@gc.cuny.edu <mailto:eisio...@gc.cuny.edu>
*From: *Mailing list for users of COOT Crystallographic
Software <COOT@JISCMAIL.AC.UK> on behalf of Murpholino
Peligro <murpholi...@gmail.com>
*Date: *Monday, May 20, 2024 at 3:30 PM
*To: *COOT@JISCMAIL.AC.UK <COOT@JISCMAIL.AC.UK>
*Subject: *Re: Updating maps
Dear Lucrezia and EE.
When I open the mtz as suggested I get:
Amplitudes: ANOM_1, 2FOFCWT, 2FOFCWT_no_fill, FOFCWT and ANOM_2
Phases: PHIF-model(+), PHIF-model(-), PHANOM_1, PH2FOFCWT,
PH2FOFCWT_no_fill, PHFOFCWT and PANOM_2*
...
Assign Labels for Structure Factor Calculation?
in new-coot: I cannot select anything (Fobs contains ANOM_1,
Sig Fobs does not have a thing, and R-free seems to have
R-free-flags(+))
in old-coot: I can select stuff but I do not have F/SIGF,
only have the labels as above (ANOM_1, 2FOFCWT,
2FOFCWT_no_fill, FOFCWT and ANOM_2), SIG Fobs is greyed out
and R-free contains R-free-flags(+))
* It really says 'PANOM_2'
phenix.mtz.dump says
phenix.mtz.dump b3x11_refine_006.mtz
Processing: b3x11_refine_006.mtz
Title:
/home/murphy/doc/phenix.refine/b3x11/truncate-unique.mtz:I(+),SIGI(+),
Space group symbol from file: P43212
Space group number from file: 96
Space group from matrices: P 43 21 2 (No. 96)
Point group symbol from file: 422
Number of crystals: 2
Number of Miller indices: 54730
Resolution range: 55.5938 1.04901
History:
Crystal 1:
Name: HKL_base
Project: HKL_base
Id: 0
Unit cell: (78.6215, 78.6215, 37.0045, 90, 90, 90)
Number of datasets: 1
Dataset 1:
Name: HKL_base
Id: 0
Wavelength: 0
Number of columns: 0
Crystal 2:
Name: crystal
Project: project
Id: 2
Unit cell: (78.6215, 78.6215, 37.0045, 90, 90, 90)
Number of datasets: 4
Dataset 1:
Name: Original-experimental-data-mapped-to-asu
Id: 1
Wavelength: 0.979
Number of columns: 9
label #valid %valid min max type
H 54730 100.00% 0.00 74.00 H: index h,k,l
K 54730 100.00% 0.00 52.00 H: index h,k,l
L 54730 100.00% 0.00 35.00 H: index h,k,l
I-obs(+) 47918 87.55% -8.88 9103.94 K: I(+) or I(-)
SIGI-obs(+) 47918 87.55% 0.19 1895.54 M: standard
deviation
I-obs(-) 44308 80.96% -13.09 7510.68 K: I(+) or I(-)
SIGI-obs(-) 44308 80.96% 0.23 1895.11 M: standard
deviation
R-free-flags(+) 54730 100.00% 0.00 19.00 I: integer
R-free-flags(-) 49051 89.62% 0.00 19.00 I: integer
Dataset 2:
Name: Experimental-data-used-in-refinement
Id: 2
Wavelength: 0.979
Number of columns: 4
label #valid %valid min max type
F-obs-filtered(+) 47910 87.54% 1.97 888.48 G: F(+) or
F(-)
SIGF-obs-filtered(+) 47910 87.54% 0.58 132.14 L:
standard deviation
F-obs-filtered(-) 44300 80.94% 3.54 793.53 G: F(+) or
F(-)
SIGF-obs-filtered(-) 44300 80.94% 1.30 140.15 L:
standard deviation
Dataset 3:
Name:
Model-structure-factors-(all-solvent-and-scales-included)
Id: 3
Wavelength: 0.979
Number of columns: 4
label #valid %valid min max type
F-model(+) 47910 87.54% 0.01 1005.82 G: F(+) or F(-)
PHIF-model(+) 47910 87.54% -180.00 180.00 P: phase
angle in degrees
F-model(-) 44300 80.94% 0.09 1005.82 G: F(+) or F(-)
PHIF-model(-) 44300 80.94% -179.98 179.98 P: phase
angle in degrees
Dataset 4:
Name: Fourier-map-coefficients
Id: 4
Wavelength: 0.979
Number of columns: 10
label #valid %valid min max type
ANOM_1 42215 77.13% 0.00 103.95 F: amplitude
PHANOM_1 42215 77.13% -179.98 180.00 P: phase
angle in degrees
2FOFCWT 54718 99.98% 0.00 1559.94 F: amplitude
PH2FOFCWT 54718 99.98% -180.00 180.00 P: phase
angle in degrees
2FOFCWT_no_fill 49995 91.35% 0.00 1139.40 F: amplitude
PH2FOFCWT_no_fill 49995 91.35% -180.00 180.00 P: phase
angle in degrees
FOFCWT 49995 91.35% 0.00 845.25 F: amplitude
PHFOFCWT 49995 91.35% -180.00 180.00 P: phase
angle in degrees
ANOM_2 42215 77.13% 0.00 103.95 F: amplitude
PANOM_2 42215 77.13% -179.98 180.00 P: phase
angle in degrees
Thanks for your help
El lun, 20 may 2024 a la(s) 8:58 a.m., Lucrezia Catapano
(lucrezia.catap...@kcl.ac.uk) escribió:
Dear Murpholino,
The problem is the auto open MTZ. In your case the —auto
option does not assign F and SIGF. You need to use "open
mtz" and assign them using the option menu and the Rfree
as well.
Regards,
Lucrezia
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*From:*Mailing list for users of COOT Crystallographic
Software <COOT@JISCMAIL.AC.UK> on behalf of Murpholino
Peligro <murpholi...@gmail.com>
*Sent:* Monday, May 20, 2024 3:16:37 PM
*To:* COOT@JISCMAIL.AC.UK <COOT@JISCMAIL.AC.UK>
*Subject:* Updating maps
How to Enable "Updating Maps"???
(Like the 2023tutorial
<https://urldefense.com/v3/__https://pemsley.github.io/coot/blog/2023/05/05/coot-tutorial-in-2023.html__;!!GekbXoL5ynDpFgM!V5kQFNwo5Y8BP4zfS4-sy8wovcH3vzS_W6yG1fJi3o2hwqlBTvmAdWbz3phLJbZApjtwj4enNWkLYXslsvSzXYI$>)
I tried enabling the option "updating maps" using the MTZ
output from a |phenix.refine|job with the following commands:
|cd Refine_6/|
|coot b3x11_refine_006.pdb --auto b3x11_refine_006.mtz|
After that, I went to |Calculate -> Updating Maps|,
selected |Auto Update|, and clicked OK. The labels were
set to |2FOFCWT PH2FOFCWT, FOFCWT PHFOFCWT|. However,
nothing happened—I could add or delete atoms, but there
was no change in the electron density maps.
It works perfectly when usingthe tutorial"data". Why? Do
I need something else?
PS. Trying in 'old-coot', but it would be good to know
how to do this in 'new-coot'.
Thanks again!
