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
>>> *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,
