Re: [COOT] Updating maps

[Paul Emsley]

On 21/05/2024 15:29, Murpholino Peligro wrote:



--

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. :)


Cool.

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?


That is exactly what it is for. There is an coot api function the 
multiply B-factors of a particular residue. It is, if I may be so bold, 
interesting/fun/educational to see the difference map and Coot Points 
change as the B-factor varies.


( I guess at the end of the day a phenix.refine jobs is still 
needed...right?)



So you have something to look at in the morning, yes.




PS. Is there any documentation on 'update maps'? what's the difference 
with a phenix.refine job?


I don't have a good answer. That would make a popular blog article (or 
journal article, maybe). The map generated in Coot is created by Clipper 
algorithms (and uses bulk solvent modelling). I know less about 
phenix.refine sadly (we're all about the servalcat these days).


Paul.




To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [COOT] Updating maps

[Murpholino Peligro]

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, 

Re: [COOT] Updating maps

[Paul Emsley]

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  on behalf of Murpholino
Peligro 
*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, 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
    

Re: [COOT] Updating maps

[Murpholino Peligro]

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, 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  %validmin max type
>> H54730 100.00%   0.00   74.00 H: index h,k,l
>> K54730 100.00%   0.00   52.00 H: index h,k,l
>> L54730 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  minmax 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%

Re: [COOT] Updating maps

[Paul Emsley]

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
 on behalf of Murpholino Peligro

*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, 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(-)  

Re: [COOT] Updating maps

[Murpholino Peligro]

Maybe something is funny with my mtz?
Dataset was processed with autoproc, then phaser and refinement in
phenix...(1.21 I think)
[image: image.png]


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
>
> ** This email originates from a sender outside of CUNY. Verify the sender
> before replying or clicking on links and attachments. **
>
> 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  %validmin max type
> H54730 100.00%   0.00   74.00 H: index h,k,l
> K54730 100.00%   0.00   52.00 H: index h,k,l
> L54730 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  minmax 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 

Re: [COOT] Updating maps

[Murpholino Peligro]

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  %validmin max type
H54730 100.00%   0.00   74.00 H: index h,k,l
K54730 100.00%   0.00   52.00 H: index h,k,l
L54730 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  minmax 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
2FOFCWT54718 99.98%0.00 1559.94 F: amplitude
PH2FOFCWT  54718 99.98% -180.00  180.00 P: phase angle in
degrees
2FOFCWT_no_fill49995 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_242215 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 
> --
> *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 
> *Subject:* Updating maps
>
> You don't often get email from murpholi...@gmail.com. Learn why this is
> important 
>
> How to Enable "Updating Maps"???
>
> (Like the 2023 tutorial
> 
> )
>
> I tried enabling the option "updating 

Re: [COOT] Updating maps

[Lucrezia Catapano]

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

From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Murpholino Peligro 
Sent: Monday, May 20, 2024 3:16:37 PM
To: COOT@JISCMAIL.AC.UK 
Subject: Updating maps

You don't often get email from murpholi...@gmail.com. Learn why this is 
important

How to Enable "Updating Maps"???

(Like the 2023 
tutorial)

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!



To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1



To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[COOT] Updating maps

[Murpholino Peligro]

How to Enable "Updating Maps"???

(Like the 2023 tutorial
)

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!



To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/