Dear Paul
I re-refined using phenix.refine (same job as before, but without using the
anomalous intensities). So I got the proper labels.
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
F-obs 50005 91.37% 2.72 873.74 F: amplitude
SIGF-obs 50005 91.37% 0.83 149.33 Q: standard deviation
R-free-flags 54730 100.00% 0.00 19.00 I: integer
Now I can use "update maps" in Coot. :)
Here's the thing... A few days ago, I noticed some waters with green
density in my difference map. Changing the element ID (Na+, Cl-, etc.),
then doing a refinement, and then looking at the maps was quite a burden (I
have turned on optimize_xyz and optimize_adp in phenix and my let's say my
computer is not a supercomputer). In the end, it turned out to be Cl- with
low occupancy (although checkmyblob wasn't very happy about it). I thought
that "update maps" would be perfect for this kind of task, i.e., to get an
'idea' of the element ID, and/or occupancy/b-factor, right? ( I guess at
the end of the day a phenix.refine jobs is still needed...right?)
Please, correct me if I am wrong.
PS. Is there any documentation on 'update maps'? what's the difference with
a phenix.refine job?
Thanks again!!
El lun, 20 may 2024 a la(s) 5:25 p.m., Paul Emsley (
pems...@mrc-lmb.cam.ac.uk) escribió:
>
> Not quite what I mean.
>
> I meant that, for Updating Maps to work, Coot (just) needs Fobs, SIGFobs
> and Rfree to be in the mtz file - you don't need to use them for refinement
> outside of Coot.
>
>
> Paul.
>
>
> On 20/05/2024 23:59, Murpholino Peligro wrote:
>
>
> --
> So... I should rerefine using IMEAN,SIGIMEAN, instead of I(+),SIGI(+),
> I(-),SIGI(-).
>
> Thanks Paul
>
> El lun, 20 may 2024 a la(s) 4:56 p.m., Paul Emsley (
> pems...@mrc-lmb.cam.ac.uk) escribió:
>
>>
>> The "Updating Map" feature in Coot expects (plain old) Fobs, SIGFobs,
>> Rfree columns - you have lots of exciting columns in your mtz file but not
>> those ones.
>>
>> It would be cool if Coot could handle anomalous intensities, but at the
>> moment it doesn't. I'll add it to the list.
>>
>> Regards,
>>
>> Paul
>>
>>
>> On 20/05/2024 22:50, Murpholino Peligro wrote:
>>
>>
>> --
>> 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
>>>
>>>
>>>
>>>
>>>
>>> *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
>>>
>>>
>>>
>>> Sent from Outlook for iOS
>>> <https://urldefense.com/v3/__https://aka.ms/o0ukef__;!!GekbXoL5ynDpFgM!V5kQFNwo5Y8BP4zfS4-sy8wovcH3vzS_W6yG1fJi3o2hwqlBTvmAdWbz3phLJbZApjtwj4enNWkLYXslO79Fy0g$>
>>> ------------------------------
>>>
>>> *From:* Mailing list for users of COOT Crystallographic Software <
>>> COOT@JISCMAIL.AC.UK> on behalf of Murpholino Peligro <
>>> murpholi...@gmail.com>
>>> *Sent:* Monday, May 20, 2024 3:16:37 PM
>>> *To:* COOT@JISCMAIL.AC.UK <COOT@JISCMAIL.AC.UK>
>>> *Subject:* Updating maps
>>>
>>>
>>>
>>>
>>>
>>> How to Enable "Updating Maps"???
>>>
>>> (Like the 2023 tutorial
>>> <https://urldefense.com/v3/__https://pemsley.github.io/coot/blog/2023/05/05/coot-tutorial-in-2023.html__;!!GekbXoL5ynDpFgM!V5kQFNwo5Y8BP4zfS4-sy8wovcH3vzS_W6yG1fJi3o2hwqlBTvmAdWbz3phLJbZApjtwj4enNWkLYXslsvSzXYI$>
>>> )
>>>
>>> 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 using the 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!
>>>
>>>
>>>
>>>
>>
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