Re: [COOT] Difference map in new coot?

[Paul Emsley]

On 20/05/2024 09:09, Paul Emsley wrote:


On 19/05/2024 23:32, Murpholino Peligro wrote:

In old coot: File -> Open Map -> Click on "Is Difference Map"
In new coot, how can I make a map a "difference map"?



Ah, I see what you mean. The file dialogs have been rewritten and I 
have forgotten to add a button for that. I will add one.




OK, done.

Paul.



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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.




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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 <mailto: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
 

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] Difference map in new coot?

[Paul Emsley]

On 19/05/2024 23:32, Murpholino Peligro wrote:

In old coot: File -> Open Map -> Click on "Is Difference Map"
In new coot, how can I make a map a "difference map"?



Ah, I see what you mean. The file dialogs have been rewritten and I have 
forgotten to add a button for that. I will add one.


For now you can use the Python interface

import coot

coot.set_map_is_difference_map(0,1) # or whatever the map number is


Paul.



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Re: [COOT] Coot Python scripting

[Paul Emsley]

On 03/05/2024 14:56, Nav wrote:

--

Hi Coot users,

I'm a new Coot user and using Coot version 0.9.8.
I'm trying to do the following in a Python script.

I have loaded a PDB structure and then inserted a new monomer in a particular 
location.
Then I want to find the closest atom from the PDB structure to each new atom in 
the monomer.
I want to calculate distances, so that I can accomplish this task.

Instead of checking and clicking in the graphical interface how can I do it in 
a Python script?
Is it possible to call the in-build 'distance' calculation functionality and 
store the minimum distance values?
Then could you show me how to loop through the atoms in the PDB and use the 
'distance' calculation routine?



This might be be a useful start:


imol = read_pdb("tutorial-modern.pdb")
res_spec = ["A", 12, ""]
rnr = residues_near_residue(imol, res_spec, 6)
for r in rnr:
   ri = residue_info(imol, r[0], r[1], r[2])
   for atom in ri:
   print(atom)



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[COOT] Coot 1.1 on Fedora 40

[Paul Emsley]

Coot 1.1 on Fedora 40 is now a thing

https://pemsley.github.io/coot/blog/2024/04/27/fedora-40.html



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Re: [COOT] Conflicting opinions on what constitutes an alpha1-6 L-fucose between Coot and Privateer

[Paul Emsley]

We are talking about different things, I think.

Coot's glyco builder builds alpha 1-6 linked FUC correctly.

Coot's glyco validator used to (until this evening) identify the alpha 
1-6 linked FUC as a beta anomer (it no longer does).


See for example the G8 FUC in 8q5u: Coot 0.9.8.94 now prints:

ASN [spec: 1 "A" 297 ""]
    pyr-ASN NAG [spec: 1 "G" 1 ""]
    BETA1-4 NAG [spec: 1 "G" 2 ""]
    BETA1-4 BMA [spec: 1 "G" 3 ""]
    ALPHA1-3 MAN [spec: 1 "G" 4 ""]
    BETA1-2 NAG [spec: 1 "G" 5 ""]
    BETA1-6 MAN [spec: 1 "G" 6 ""]
    BETA1-2 NAG [spec: 1 "G" 7 ""]
    ALPHA1-6 FUC [spec: 1 "G" 8 ""]

Paul.


On 24/04/2024 01:38, Engin Özkan wrote:

CAUTION: This email originated from outside of the LMB:
.-owner-c...@jiscmail.ac.uk-.
Do not click links or open attachments unless you recognize the sender 
and know the content is safe.
If you think this is a phishing email, please forward it to 
phish...@mrc-lmb.cam.ac.uk

--

Hi Markus,

I am using Coot that comes with CCP4 8, which has FUC (alpha-L-Fucose) 
with an oxygen on C1 in the axial position. Which is the correct form, 
I believe.


Using Coot 0.9.8.93, I get my alpha1-6 and alpha1-3 (insect) Fucoses 
inserted correctly.  I had trouble understanding your description: You 
mean you get Coot to insert a FUC with the glycosidic bond going 
equatorial, instead of axial, to Fucose?


This is how it works for me:

https://www.dropbox.com/scl/fi/yjbzstojjivmfpqdlz2os/Screen-Recording-2024-04-23-at-7.32.14-PM.mov?rlkey=zvvk7apd19wk61kt21qyc42l5=0 



I'll see what happens when I update to the new Coot version where Paul 
has switched the logic.



By the way, privateer tells me I have zero errors and the correct 
alpha anomer for Fucose.


Fuc913-a6-GlcNAc911-b-ASN258
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1
...

PDB         Sugar         Q       Phi Theta        Detected type     
Cnf        Ctx  Ok?
        - --    -- ---    
---    --    --- -
test    NAG-A-911       0.570    280.48 5.29 beta-D-aldopyranose    
4c1    47.88    (n)     yes
test    FUC-A-913       0.535    92.53 177.32 alpha-L-aldopyranose   
1c4    70.76    (n)     yes

...
Wrong anomer: 0

Best,


Engin


On 4/18/24 4:35 PM, Markus Meier wrote:

Hi Engin,

hmm, it appears I was using the monomer library from 
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/monomers-2023-01-02-23:57:29.tar.gz 
(it gets installed automatically with Coot's build-it script).


However, the files in question (FUC.cif, NAG.cif, BMA.cif and 
MAN.cif) are identical to current CCP4 8.0.018 version of the library 
(installed by CCP4 Update Manager) as well as version ccp4-8.0.018 
and version ccp4-8.0.016 on GitHub 
(https://github.com/MonomerLibrary/monomers)


MD5 checksums on these files are
9cfba4ac24f056d648df8227316f788b  monomers/f/FUC.cif
958ac5b19a92ceec604d233457944b2a  monomers/n/NAG.cif
697dd5242334dd99dad9ce43133c6382  monomers/b/BMA.cif
9d68ff54296ef2f4622005efb4eb080b  monomers/m/MAN.cif

If they are different on your machine, please let me know.

I will switch monomer libraries anyway and do some testing.

I also was switching back and forth between my locally compiled coot 
(0.9.8.92) and the the CCP4 distributed version (0.9.8.93 EL). I will 
check if there is a difference between the two.


Thank you very much for your suggestion!

With best regards,
Markus

On 2024-04-18 13:48, Engin Özkan wrote:

Caution! This message was sent from outside the University of Manitoba.


Hi Markus,

There were reports to the ccp4bb and phenixbb back in 2011 about
something similar. The monomer library files for FUC and/or the linkage
definitions for refmac/phenix were not right. I think. My recollection
is that this was corrected, and I could not reproduce your observation.

I also had private discussions with Garib Murshudov, who were 
correcting

the glycan monomer problems back in ~2011.

I could find old links to some of the discussions on bulletin board
archives:

https://phenix-online.org/pipermail/phenixbb/2011-November/017958.html

https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg13968.html

I am curious if something got reverted or if you have some ancient
library definitions somewhere. But I hope this gives some ideas.

Best,

Engin


On 4/17/24 3:07 PM, Markus Meier wrote:

Hi Paul,

thank you for implementing the Glyco module in Coot!

I used its "Add N-linked Glycan" function to build an N-linked glycan
which contains L-fucose with an alpha1-6 glycosidic linkage on the
first N-acetyl glucosamine of the tree.

However, after exporting the tree, I checked it with privateer and
unfortunately privateer flags the L-fucose as having the wrong
anomeric linkage - beta 1-6 :-(
Coot reports the same as being in the alpha 1-6 

[COOT] Release 0.9.8.94

[Paul Emsley]

It's been a few months since the last bug release of the 0.9.x. series. 
Here's an update so the fixes are available for CCP4 builds.


  o CHANGE: Add a more informative message on failure to generate rtop in
  transform-map-using-lsq-matrix [Martin Maly]

  o CHANGE: The pyranose link restraints logic has changed - hopefully more
  accurate now [Andrey Lebedev]

  o BUG-FIX: the logic of the glyco-tree glyco chiral test for ALPHA1-6 and
 BETA1-6 has been reversed (i.e. corrected)
 [who validates the validators? Markus Meier does]

Source:

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.8.94.tar.gz



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[COOT] Release 1.1.08

[Paul Emsley]

Not many user-visible changes in this one.


  o FEATURE: Scene Presets added to the Draw menu

  o CHANGE:  "Mutate" is now a button so that it can now be
 used to mutate RNA and DNA.

  o BUG-FIX: mutate_by_overlap() fixed [thanks Simon Vecchioni]

  o BUG-FIX: The "Generic Display Objects" dialog now dynamically
  updates (no need to close it an open it again to see new
  generic display objects).

  o BUG-FIX: Undisplaying a model while the Display Manager dialog
   is not displayed now correctly sets the state of the Display
   checkbutton.


Source:

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-1.1.08.tar.gz



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Re: [COOT] Conflicting opinions on what constitutes an alpha1-6 L-fucose between Coot and Privateer

[Paul Emsley]

On 17/04/2024 21:07, Markus Meier wrote:


Hi Paul,

thank you for implementing the Glyco module in Coot!

It is not in Coot 1 (yet). It needs to be rewritten.


I used its "Add N-linked Glycan" function to build an N-linked glycan 
which contains L-fucose with an alpha1-6 glycosidic linkage on the 
first N-acetyl glucosamine of the tree.


However, after exporting the tree, I checked it with privateer and 
unfortunately privateer flags the L-fucose as having the wrong 
anomeric linkage - beta 1-6 :-(

Coot reports the same as being in the alpha 1-6 anomeric form.

How was the apparent? Did you use print_glyco_tree()?


I then manually built the opposite anomeric form which privateer 
happily accepts as being alpha1-6. However, Coot reports it as beta 1-6.


In my understanding, the alpha configuration of a glycosidic linkage 
should have the oxygen at the anomeric centre and the -CH3 group at 
opposite faces of the sugar ring, so I have to agree with privateer on 
this one.


Please check you code.


OK, will do.


I have attached the two glycan trees and here is the output of 
privateer and Coot for both. Coot and privateer versions are given at 
the bottom.


Btw. Neither privateer nor refmac5 can read the mmCIF files that Coot 
produces with the "Extract this Tree" functions. All the 
_atom_site.label_*_id entries are empty!



Oof. Cif.

OK. I'll take a look after the release.

Paul.



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Re: [COOT] I found that downloaded cif file from RCSB has some issues in coot program.

[Paul Emsley]

On 07/03/2024 07:18, 신진우(생명과학과) wrote:


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Dear Coot,

Hello. My name is Jinwoo Shin. I'm a structural biologist in South Korea.

I am deeply grateful to your service for developing coot program.

I have a question.

I recently deposited a cryo-EM structure to RCSB (PDB: 8IEP, 
https://www.rcsb.org/structure/8IEP). I found that downloaded cif file 
from RCSB has some issues in coot program.


By using color by atom mode, there is no issue.

However, by using color by chain mode, it is shown that the backbone 
of structure is broken. (please see the attached pictures)


Also, by using Ca/Backbone mode, only atoms are shown. (please see the 
attached pictures)


The original PDB file, which has not been deposited, does not exhibit 
any issues in the cootprogram regardless of the mode I use. Thus, I 
speculate that there may be some problematic elements during the 
deposition process.


I am unsure of the exact reason. Even the staff of RCSB does not know; 
he said, 'I don't know, and if I find out any causes, I will let you know.


He also said that asking the coot staffs would be faster.



Dear Jinwoo Shin,

Rest easy.

The problem is entirely ours. Briefly, there is a bug in parsing mmCIF 
files in Coot. To fix this is taking some time, but it's on the way!


You will see, I think, that your molecule looks fine in ChimeraX.

Paul.




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Re: [COOT] How does COOT determine protonation states

[Paul Emsley]

On 22/02/2024 01:06, Kim, Sun Kyung wrote:


Hi Paul,

Thank you for your response!

I opened Coot from my terminal, and not seeing any diagnostic 
information, but it just opens up coot.


There seems to be some confusion because I read this and think "that 
cannot be." Are you reading what is going on in the terminal? It should 
be something like this:



phemius src% coot
INFO:: built with GTK 4.12.4
pdd /usr/local/Cellar/coot/1.1.06/share/coot
There are 143 data in 
/usr/local/Cellar/coot/1.1.06/share/coot/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in 
/usr/local/Cellar/coot/1.1.06/share/coot/lib/data/monomers/a/ALA.cif
There are 2 data in 
/usr/local/Cellar/coot/1.1.06/share/coot/lib/data/monomers/a/ASP.cif

...


When you mention I could try setting COOT_MONOMER_LIB_DIR or 
REFMAC_MONOMER_LIB_DIR to the directory that containers the monomers… 
I’m not sure as to what those files are or where I can find them.. are 
there documentations to this that I can refer to?


One can use the copy of the CCP4 Monomer library that comes with the 
CCP4 Suite.


Or one can download it from github:

https://github.com/MonomerLibrary/monomers/archive/refs/tags/ccp4-8.0.016.tar.gz

rename or link monomers-ccp4-8.0.016 to monomers

put the monomers in a directory called data

Then set the environment varable COOT_REFMAC_LIB_DIR to the directory 
that contains data.


It’s strange that COOT starts having this issue for me all of a 
sudden. The only thing I can think of is, over the weekend I had to do 
some mandatory upgrades to my government computer that I’m using…do 
you think any updates to the MacOS or something like that could have 
caused this issue for me?



Typically one used to need to reinstall XQuartz after doing an OS update.

But I suspect something more fundamental/trivial in your setup.


Thank you for your help as always!



You're welcome


Paul.



Best,

‘Kate’ Sun Kyung Kim

*From: *Paul Emsley 
*Date: *Wednesday, February 21, 2024 at 9:35 AM
*To: *Kim, Sun Kyung , COOT@JISCMAIL.AC.UK 


*Subject: *Re: How does COOT determine protonation states

On 21/02/2024 02:50, Kim, Sun Kyung wrote:

Thank you Paul for that information. I will look into Acedrg and
Grade2!

Sounds good.

I have an unrelated question… I’ve never encountered this before,
but all of a sudden my COOT is complaining that it doesn’t have
restraints for refinement… (screenshot attached)… any idea why
this error message is suddenly appearing?

Coot writes diagnostic information to the terminal/console/program 
from where it was started. You need to get access to that information.


I would try to start Coot from a terminal and see what it says about 
dictionaries and libraries as it starts up.


Before invoking coot, you could try setting COOT_MONOMER_LIB_DIR or 
REFMAC_MONOMER_LIB_DIR to the directory that containers the monomers - 
how to do that depends on your system.


Regards,

Paul.





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Re: [COOT] How does COOT determine protonation states

[Paul Emsley]

On 21/02/2024 02:50, Kim, Sun Kyung wrote:


Thank you Paul for that information. I will look into Acedrg and Grade2!



Sounds good.

I have an unrelated question… I’ve never encountered this before, but 
all of a sudden my COOT is complaining that it doesn’t have restraints 
for refinement… (screenshot attached)… any idea why this error message 
is suddenly appearing?



Coot writes diagnostic information to the terminal/console/program from 
where it was started. You need to get access to that information.


I would try to start Coot from a terminal and see what it says about 
dictionaries and libraries as it starts up.


Before invoking coot, you could try setting COOT_MONOMER_LIB_DIR or 
REFMAC_MONOMER_LIB_DIR to the directory that containers the monomers - 
how to do that depends on your system.


Regards,

Paul.



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Re: [COOT] How does COOT determine protonation states

[Paul Emsley]

Hello Kate,

Attached is an example conn file:  it is in a folder called 
coot-molprobity and has the required format for input to Reduce.


> In COOT, does REDUCE take into account pH and local changes in pKa of 
atoms when determining protonation states?


In SMILES-speak: NCC(=O)[OH] and [NH3+]CC(=O)[O-] are two entirely 
different molecules with different residue names. The bond orders, 
charges, bond lengths and so on are defined by the restraints generator. 
Coot and Reduce are only doing what they are told to do.


> In COOT, when REDUCE adds hydrogens, does it move any of the non-H 
atoms too to optimize geometry?


Reduce does not move the non-hydrogen atoms (unless you ask it to do HQN 
flips). This is true whether or not it is launched from Coot.


> In COOT, does REDUCE automatically flip ASN and GLN and HIS 
sidechains to optimize H-bonding?


HQN flips are on by default, IIRC.

This is a discussion about ancient (10 years old) code. More recent is 
the use of Acedrg and Coot's internal hydrogen atom addition method. If 
you want to have a discussion about protonation and tautomerisation 
manipulation then we should be talking about that in the context of 
Acedrg (and Grade2 if you're on the cutting edge of Coot progress).


Regards,

Paul.


On 20/02/2024 21:09, Kim, Sun Kyung wrote:


Thank you Paul, for your reply! I was not able to locate the exact 
dictionary but I think I was searching probably in the right folder… 
what is the file type I should be looking for?


More pressing questions for me are about REDUCE that’s used in COOT:

 1. In COOT, does REDUCE take into account pH and local changes in pKa
of atoms when determining protonation states? Since I don’t input
the pH value anywhere, I’m assuming that it probably just assumes
physiological pH of 7.4 when it calculates protonation states, am
I correct?
 2. In COOT, when REDUCE adds hydrogens, does it move any of the non-H
atoms too to optimize geometry?
 3. In COOT, does REDUCE automatically flip ASN and GLN and HIS
sidechains to optimize H-bonding?

Thank you in advance for your time in answering my questions!

Best,

‘Kate’ Sun Kyung Kim

*From: *Paul Emsley 
*Date: *Thursday, February 15, 2024 at 4:39 PM
*To: *Kim, Sun Kyung , COOT@JISCMAIL.AC.UK 


*Subject: *Re: How does COOT determine protonation states

It is in the directory from which you started coot (that is, if coot 
can create and write to such a directory (if not it is in your home 
directory)).


Paul.

On 15/02/2024 23:51, Kim, Sun Kyung wrote:

Thank you Lucrezia for your informative reply!

You suggested I look into coot-molprobity output directory. Where
can I locate this directory?

Thank you.

Best,

‘Kate’ Sun Kyung Kim

*From: *Lucrezia Catapano 
<mailto:lucrezia.catap...@kcl.ac.uk>
*Date: *Friday, February 2, 2024 at 6:21 AM
*To: *Kim, Sun Kyung  <mailto:kim...@llnl.gov>,
COOT@JISCMAIL.AC.UK  <mailto:COOT@JISCMAIL.AC.UK>
*Subject: *Re: How does COOT determine protonation states

Dear Kate,

Coot adds hydrogen atoms according to the dictionary. If you want
to change the protonation of a ligand, you'd do that by modifying
the actual monomer dictionary. We typically use Acedrg to generate
dictionaries.

For example, in the case of a ASP residue, the modification which
describes the addition of the proton, encapsulates all the local
changes (bond order, angles etc.) of the monomer, providing the
(probably) expected geometry.

Look in your coot-molprobity output directory. These files are
used by Reduce to protonate ligands - Coot converts the (Acedrg,
or whatever else) dictionary you have given it, to these files of
connection records.

Regards,

Lucrezia

*From: *Mailing list for users of COOT Crystallographic Software
 <mailto:COOT@JISCMAIL.AC.UK> on behalf of
Kim, Sun Kyung <bc51fd01f63f-dmarc-requ...@jiscmail.ac.uk>
<mailto:bc51fd01f63f-dmarc-requ...@jiscmail.ac.uk>
*Date: *Tuesday, 30 January 2024 at 00:36
*To: *COOT@JISCMAIL.AC.UK 
<mailto:COOT@JISCMAIL.AC.UK>
*Subject: *How does COOT determine protonation states





Hello,

I’m using the Coot 0.9.8.91 EL. I am working jointly with a
computational team who are doing simulations on our PDB model.
I’ve added hydrogens to my model using Coot’s Validate -> Probe
clashes function. The computational team asks, when COOT adds
protons using the probe clashes function, how does it assign
protonation states to residues? Is it using something
sophisticated that we can trust for our computational simulations
or should the computational scientists use their own methods for
determining protonation states?

Thank you for your time answering this question, 

Re: [COOT] How does COOT determine protonation states

[Paul Emsley]

It is in the directory from which you started coot (that is, if coot can 
create and write to such a directory (if not it is in your home directory)).


Paul.


On 15/02/2024 23:51, Kim, Sun Kyung wrote:


Thank you Lucrezia for your informative reply!

You suggested I look into coot-molprobity output directory. Where can 
I locate this directory?


Thank you.

Best,

‘Kate’ Sun Kyung Kim

*From: *Lucrezia Catapano 
*Date: *Friday, February 2, 2024 at 6:21 AM
*To: *Kim, Sun Kyung , COOT@JISCMAIL.AC.UK 


*Subject: *Re: How does COOT determine protonation states

Dear Kate,

Coot adds hydrogen atoms according to the dictionary. If you want to 
change the protonation of a ligand, you'd do that by modifying the 
actual monomer dictionary. We typically use Acedrg to generate 
dictionaries.


For example, in the case of a ASP residue, the modification which 
describes the addition of the proton, encapsulates all the local 
changes (bond order, angles etc.) of the monomer, providing the 
(probably) expected geometry.


Look in your coot-molprobity output directory. These files are used by 
Reduce to protonate ligands - Coot converts the (Acedrg, or whatever 
else) dictionary you have given it, to these files of connection records.


Regards,

Lucrezia

*From: *Mailing list for users of COOT Crystallographic Software 
 on behalf of Kim, Sun Kyung 


*Date: *Tuesday, 30 January 2024 at 00:36
*To: *COOT@JISCMAIL.AC.UK 
*Subject: *How does COOT determine protonation states




Some people who received this message don't often get email from 
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Hello,

I’m using the Coot 0.9.8.91 EL. I am working jointly with a 
computational team who are doing simulations on our PDB model. I’ve 
added hydrogens to my model using Coot’s Validate -> Probe clashes 
function. The computational team asks, when COOT adds protons using 
the probe clashes function, how does it assign protonation states to 
residues? Is it using something sophisticated that we can trust for 
our computational simulations or should the computational scientists 
use their own methods for determining protonation states?


Thank you for your time answering this question, much appreciated!

Best,

‘Kate’ Sun Kyung Kim



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Re: [COOT] Coot crash when running Jiggle-fit

[Paul Emsley]

On 01/02/2024 14:03, Kim Walbrunn wrote:


Dear mailing list,

I am writing about some problems with Coot when trying to run the 
Jiggle-fit command.


I have tried to jiggle fit (simple / FT) coordinates into a CryoEM 
map, using the Cryo-EM module (Coot 1.1.07) or the curlew add-on 
'Morph' (Coot 0.9.8).
With both Coot versions, the program crashes instantly with the error 
message: No Core file found No debugging.
Seeing the informative nature of the error I don't know where the 
problem might be or what I really could do to make it run. So, I hoped 
you might have a few suggestions as to what I can try (installation 
tweaks or anything else really)




Dear Kim,


The 1.1.x Coot binaries that you are using should be compiled with 
"backward" - which gives you (and therefore me) some more information 
about what is failing. It would useful to see that backtrace.



My guess at the moment is that you are running out of memory (I think 
that Coot makes many copies of your map for multi-threaded fittings).



You can try setting the the environment variable


COOT_N_THREADS=1


and see if that makes a difference.


Regards

Paul.




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Re: [COOT] Unable to 'see' files (pdb and mtz)

[Paul Emsley]

On 16/01/2024 23:55, Braviner, Leah wrote:

Hello all,


Hello Leah,



I encountered an issue whereby files are not visible in the ‘open 
coordinates’ or ’open MTZ’ pop-ups – and therefore cannot be opened.
There is a file filter, bottom right. The opions are "all files" and 
"coordinates files"
I have recently deleted and re-downloaded Coot using the CCP4 package 
(though I failed to remove my preferences folders, so I’ll remove this 
and retry a fresh download.


If I am worried about my start-up scripts causing a problem, I (merely) 
temporarily rename the directory for testing. In the days of Coot 1, 
$HOME/.coot is a directory of scripts, before that it was 
$HOME/.coot-preferences.


Any thoughts on other folders to be aware of would be greatly 
appreciated). I’ve also verified that these files are present in my 
regular ‘Finder’ app.
So you may have appliled the filter and the files that you want to see 
have been filtered out.


I’m running on MacOS (Ventura 13.3.1). 
So you haven't given in to the nagging to upgrade to Sonoma yet? 
Probably for the best.
Possibly unrelated, but I have encountered another issue – the 
‘scrolling’ feature for map contour level doesn’t work at all. 
Specifically trying with CryoSparc-derived .mrc maps. Unsure if 
perhaps my Coot is just bugging out.


From the Display Manager -> Properties, there look for "Contour Level 
Step Size" and change it to 0.8.


You can use "+" and "-" on they keyboard to change the level.

Say hello to Ming.

Regards,

Paul.




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[COOT] Release 1.1.04

[Paul Emsley]

Source:

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-1.1.04.tar.gz


  Release 1.1.04

  o FEATURE: Particle effects for done difference map peaks

  o CHANGE:  Refinement cannot now proceed if there are no bond 
restraints for any

 of the refining residues

  o BUG-FIX: Add coot namespace to state save file

  o BUG-FIX: Fix symmetry of difference map peaks



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[COOT] Release 0.9.8.93

[Paul Emsley]

Source:

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.8.93.tar.gz


  Release 0.9.8.93

 o CHANGE:  Electrostatic surface removed from the UI

 o CHANGE:  Clean-up for the residue selection in peptide omega 
analysis (don't draw

    cis-peptides for residues that are not peptides)

 o BUG-FIX: Fix erroneous mutation of DNA bases to RNA bases in 
mutate-residue-range

    [Keitaro Yamashita]

 o BUG-FIX: Add back the negative map contour levels into the input 
file for Raster3d


 o BUG-FIX: Atom-name fix-up for "HH" in TYR - now TYR with hydrogen 
atoms can be refined.




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Re: [COOT] Help generating difference map image using raster3d option.

[Paul Emsley]

On 06/01/2024 10:54, sriram raghavan wrote:


Dear coot user,

There's more than one of use, I hope.


I attempted to generate an image of a specific residue which has 
negative density in the isomorphous difference map. I tried using 
Python scripting and accomplished generating a basic image with the 
GUI option. However, I aim to create an image using raster3d without 
relying on graphics options. Can anyone assist me with this?


I used the following Python commands to create a simple image, but 
when generating the raster3d image, the negative density is not 
visible. I am unsure of how to include an option to retain the 
negative density in raster3d. I am unable to identify from 
documentation, any information on this matter would be appreciated.





Are you and Jonathan Hughes tag-teaming us?

If so, it seems to have worked. I will look at it shortly.

Regards,

Paul.



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Re: [COOT] default colors?

[Paul Emsley]

On 08/01/2024 15:57, Murpholino Peligro wrote:


How do I change the default colors in coot?
for all three maps, the "normal" density, the difference map and the 
anomalous map?




(set-colour-map-rotation-for-maps 28) ; or some such.



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Re: [COOT] Could you please solve the problem?

[Paul Emsley]

On 31/12/2023 16:01, Gang Du wrote:


Hi Coot,

Hi Gang  Du.


I solve the structure from cryosparc.  The resolution is 3.2A. But I 
have a problem opening the map by coot. The chimera and ChimerX can 
open the map successfully and correctly. You can see the following 
image. But it cannot be opened successfully and correctly by coot. It 
looks like there are some problems.  You can also see the following 
image. Do you know the reason?



Cute structure (well, reconstruction at the moment).

What you are seeing is (merely) Coot's rendering of the map. It is not 
unusual to be confused by what Coot is showing you at this stage.


What is the radius of the map in ChimeraX? Set the same map radius in 
your Coot and you should see the same map (notice that you have the 
contour level a lot lower in Coot) - rendered in Coot style of course.


Also, I notice that you have green and red levels, which suggests that 
you have opened this as a difference map. I would not recommend that.


i.e. you are looking in the wrong place in the wrong style at the wrong 
contour level. Hopefully all of that should be easy to fix and you can 
get on with adding some atoms - exciting!


Regards,

Paul.




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Re: [COOT] DPI scaling of WinCoot

[Paul Emsley]

On 13/12/2023 16:37, Fabian Heide wrote:

CAUTION: This email originated from outside of the LMB.
Do not click links or open attachments unless you recognize the sender and know 
the content is safe.
.-owner-c...@jiscmail.ac.uk-.



Dear all,

I recently installed WinCoot 0.9.8.92 on a 4k monitor and ran into issues with 
DPI scaling. Essentially, the application window is set to a low DPI setting 
which makes the program appear blurry. Is there a way where I can change the 
scaling/resolution/dpi of the program to improve the GUI visually?


There is nothing inside Coot that will help you. Maybe some Windows 
desktop setting or graphics driver settings may help.


Paul.



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Re: [COOT] Bug in Pointer distances

[Paul Emsley]

On 08/12/2023 13:19, Mark Saper wrote:


For Paul,


After enabling pointer distances, the distances don’t update (most of 
the time) when moving to a different place in the molecule.  The Coot 
version is 0.9.8.92 running on macOS 13.6.1.



Thank you Mark.

For ther record, this is the sort of thing for which I now have 
withdrawn support (being graphics code in the Old Coot). I will make a 
note to check the updating of the pointer distances in Coot 1.x.


Regards,

Paul.



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[COOT] Release 1.1.03

[Paul Emsley]

Source:

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-1.1.03.tar.gz

Many gui bugs fixes, still quite a number left (sadly).


  o FEATURE: outline active residue on leftquote

  o FEATURE: Shortcuts dialog

  o FEATURE: Goodsell NCS colouring mode

  o FEATURE: Improved Gaussian surfaces

  o FEATURE: Generic objects are now part of SSAO and shadow framebuffers

  o FEATURE: "Coot Points" added to updating difference maps

  o FEATURE: Animate the removal of NBC outliers

  o FEATURE: Semi-dark background mode

  o CHANGE:  Layla updates

  o BUG-FIX: command line arguments are now recognised

  o BUG-FIX: Limit the radius of water atoms

  o BUG-FIX: Fixup for rigid-body fit toolbar buttons

  o BUG-FIX: Trackpad-mode no only for Mac

  o BUG-FIX: Add handler for trans-peptide and planar peptide 
refinement checkbuttons




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Re: [COOT] Multiple sequences within one structure?

[Paul Emsley]

On 29/11/2023 10:58, Subscribe COOT Marie M üller wrote:

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Dear all,

I am wondering if it is somehow possible to model two different amino acids in 
the same position. We are working on a dataset from a mixed sample and we think 
we obtained crystals that contain two sequences (they are very similar, 95% 
identity). There are a few positions in which the sequence differs and the 
electron density supports both sequence variants. I would like to model both 
and then see if this improves the refinement or if one of them will be kicked 
out again.

I was hoping I could approach this similarly to how we model alternative 
conformations. So I edited the residue into conformation A with an occupancy of 
0.5 and merged the other residue into the same structure (in conf B, occ 0.5). 
However the residue will be renumbered automatically and added to the end of 
the chain, if I try to renumber the residue to sit in the same position coot 
will tell me:
  
WARNING::could not renumber residue range. Maybe your selection overlaps with existing residues. Please revise your selection.


Are you aware of any way to model two different residues in the same position 
or will COOT always prevent this?


Dear Marie,

Coot does not deal well with this issue (micro-heterogeneity).

Coot does not allow the addition of micro-heterogeneity.

Coot can just about parse it and draw it, maybe even refine it, but many 
modelling operations will fail.


I'd model the other conformer as a single residue an a new model 
molecule (get the chain id and residue number and occupancy correct) and 
then hand paste that residue into the file that contains the rest of 
molecule. A very "meh" solution, I admit, but to handle 
micro-heterogeneity across the board would take a year or so and there 
are other things to do at the moment.


Regards,

Paul.



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Re: [COOT] real space refinement of alpha-23 link between GAl and Sia fails

[Paul Emsley]

On 22/11/2023 14:02, Keitaro Yamashita wrote:

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Great, you are using the very latest CCP4 (with the latest monomer
library). I suppose Refmac properly identified the "ALPHA2-3" link
which should also appear in the PDB header (LINKR).

Using Coot, I just tried PDB 2osx which includes the ALPHA2-3 link
between GAL (B/2) and SIA (B/3). As you mentioned, it didn't work.


debug:: find_glycosidic_linkage_type() for B 3 SIA,B 2 GAL returns 
"ALPHA2-3"
DEBUG:: make_other_types_of_link() "ALPHA2-3" for [spec: model 1 "B"3 "" " C1 " ""] [spec: model 1 "B"
2 "" " C3 " ""] detected
DEBUG:: make_other_types_of_link(): now making a link restraint [spec: 1 "B" 3 ""] [spec: 1 
"B" 2 ""] with type ALPHA2-3 and order switch 0
DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 0
debug:: find_glycosidic_linkage_type() for B 3 SIA,B 1 BGC returns ""
DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 0
debug:: find_glycosidic_linkage_type() for B 1 BGC,B 3 SIA returns ""
Made 0 CHO-SS-and-other bond restraints
Made 0 CHO-SS-and-other angle restraints
Made 0 CHO-SS-and-other plane restraints
Made 0 CHO-SS-and-other trans-peptide restraints

It actually found the ALPHA2-3 link (but between C1 and C3? it's
strange..) and finally it didn't add any restraints. Paul, could you
please look into this?



Hi Keitaro,

When I was looking at carbohydrate linking (quite a few years ago now), 
the SIA links were deliberately omitted because there was a bug (or 
more) in the monomer library.


It seems that it is now time to revisit SIA linking. I'll add it to the 
list now.


Regards,

Paul.



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Re: [COOT] Moving Link properties to mmcif

[Paul Emsley]

On 13/11/2023 21:16, Mohamed Ibrahim wrote:


Dear All,

During pdb submission, I lost the link information in the pdb file 
during the conversion to mmcif file. It does not matter if I did this 
in Phenix or wwpdb server.


How to fix this issue?



Coot can add a struct_con record for you if you use (0.9.x) Calculate -> 
Modelling -> Make Link...


Write the output as a .cif of course.


Paul.




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Re: [COOT] Using python script to select several fragments in one time

[Paul Emsley]

On 03/11/2023 20:57, Ma, Boyuan wrote:


Dear Cooters,

I want to use a python script to select several disconnected fragments 
to perform refinement in one time, for example, 
"coot.some_refinement_by_residue_range(imol, /1/A/1-20 || /1/A/22-30)."


However, after searching previous messages in the mail list, I still 
do not know what the right format is for selecting these fragments in 
one string.



BTW, thanks for Joel's answers. 
https://www.mail-archive.com/coot@jiscmail.ac.uk/msg01933.html. It 
does help me a lot.


"atom_selection_string is the 'standard' mmdb atom selection string, 
explained in detail in the *mmdb manual*."
And the mmdb manual can be seen at here: 
https://www.ccp4.ac.uk/html/pdbcur.html#atom_selection 






Crikey - that was a while ago (hello Joel).


I presume that you are using Coot 0.9x.


There is a "new" API interface to the real space refinement now: 
refine_residues() which takes a list of residue specs




def make_res_range(start_res_no, end_res_no):
    l = range(start_res_no, end_res_no + 1)
    r = [["A", i, ""] for i in l]
    return r

range_1 = make_res_range(10, 20)
range_2 = make_res_range(30, 40)

combi_range = range_1 + range_2

imol = read_pdb("tutorial-modern.pdb")
imol_map = read_mtz("rnasa-1.8-all_refmac1.mtz", "FWT", "PHWT", "", 0, 0)

refine_residues(imol, combi_range)

(Needless to say, this is different in the new version).


Regards,


Paul.




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Re: [COOT] Coot 'could not read the content of Documents'

[Paul Emsley]

On 02/11/2023 07:55, Marija Backovic wrote:



Hello,

I have just installed Coot 0.9.8.91, but when I try to access the PDB files, 
which are in my Documents directory, I get a message 'Could not read the 
content of Documents' / 'Operation not permitted'. The operating system is 
MacOS Ventura v13.1. Has anyone encountered this problem, and if yes, please 
share the info. Thanks in advance!


What do you see if you type, a Terminal:

$ ls -ld ~/Documents

?

Paul.



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Re: [COOT] Heparin in Coot

[Paul Emsley]

On 01/11/2023 18:02, Xuewu Zhang wrote:


Hi Paul,
Thanks so much for the quick response.

Using the cifs from the new CCPEM library did the trick. Cifs from 
Phenix or an older version of CCP4 failed. I am not sure why (is there 
a flag in the cifs to tell Coot whether the molecule is a polymer or 
individual units?)


For others who may also face this issue: Cifs files from Phenix and 
Coot use different atom names in the SGN and IDS units. The chain I 
copied from 3IRI works with Phenix (after running phenix.ready_set and 
phenix_reduce), but not with the Coot Cifs. 1HPN works with Coot 
perfectly when the new CCPEM Cifs were imported. However, Phenix 
doesn't recognize it, only it worked when the CCPEM cifs were included 
in the inputs.


OK, I feel from that that the ball is not in my court.




Two related questions, can we (1) add disaccharide units to the 
existing chain?;


Yes (long-hand) and no (quick and clever). My intention was that the 
dehydration should occur upon real space refinement.



(2) Delete monomers from the existing chain (I tried it, Coot removed 
the last monomer, but also the oxygen atom linking the last and the 
second to the last unit, which should remain and become a OH group)?


"Delete Residue" only deletes atoms of the specified residue. It won't 
delete the O4 (say) of the upstream residue.


What it also won't do is restore the O1 atom of the downstream residue - 
I suspect that that is what you want and would be a useful features to have.


Ctrl-D is the hot-key for delete-residue btw.


Regards,

Paul.




On Wed, Nov 1, 2023 at 12:22 PM Paul Emsley 
 wrote:



On 01/11/2023 16:34, Xuewu Zhang wrote:
>
> Dear Paul,
> Can Coot handle heparin chains (not attached to protein) now? I was
> able to read a heparin chain in the PDB format, and import the cif
> restraints for the two sugar units (named IDS and SGN, from the
phenix
> monomer library; Coot would recognize the molecule without them).
> However, it appears that the bonds between the sugar units are not
> recognized by Coot, and the units were pushed apart whenever I
tried
> to do realspace refinement or regularize zone. I am not sure how to
> fix this, is there a way to tell Coot these units belong to a
polymer
> and should be linked together?
>

Dear Xuewu,


I used PDB code 1hpn as and example.

I used the monomer library that comes with CCP4 and Coot.

I selected one of the models (MODEL 1).

I chose regularize fragment.

Everything is connected as it should be and I could yank stuff
around [1].

How can I reproduce what you are seeing?

Regards,

Paul.


[1] this is the technical term.




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[COOT] Coot 1.1

[Paul Emsley]

18 months after the release of Coot 1 it's time for Coot 1.1

Coot 1.1 is a major change beyond Coot 1. It has required a lot of
writing and rewriting and has been the focus of my work since last year.

Technically (but briefly) we have rewritten the GUI again so that it is
now is based on GTK4 (Coot 1 used GTK3). This has meant a lot of rewiring
under the hood so that things behave similar to before [1].

Many things, that is. Not all things. There are a few important
differences - they are for the better (although you may not initially
think so).

   o View rotation is on right-mouse (except on Mac).
   o Functions are activate in "Select First" mode (that means bringing
 the atom/residue/chain of interest to the centre of the screen)
 and then choosing the function. This is more consistent with the
 use of hot-key/key-bindings.
   o Widget "focus" is different in GTK4 - I don't yet fully understand it
 at the moment, so, in case Coot "forgets" to revert focus back to the
 main graphics widget, there is a "Grab Focus" button in the horizontal
 toolbar.
   o Many of the menu items have been moved around. Now they are far more
 likely to be where they will finally end up.
   o "Modelling" (as we like to label it in the UK) has its own top-level.
   o "Modules" is now also on the top-level instead of being in the
 "Calculate" menu.

Not everything made it:

   o "Symmetry by Molecule" has been removed (for the moment).
   o RCrane and the glycan builder have yet to be brought back to working
 order.
   o FLEV, QED breakouts and Chemical Feature Clusters are still missing.

I am grateful for the contributions from Jakub Smulski for help with
this over the last year and to Global Phasing for the funding. Martin
Noble has written the ribbon and surface representation code.

At the moment, the terminal output is a bit verbose with debugging output.
That will be reduced or removed in due course.

Although I've not tried it, I hope/expect that this Coot will run very
sweetly on a M2 Pro MacBook Pro... Having said that, "M2 good, M3 better" -
I suppose?

Source:

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-1.1.tar.gz

Binaries:

   Binaries have always been issue with Coot. The problem is that a
   project of the scale of Coot needs (at least) 3 people [2],
 o one for the scientific developments/new algorithms and publications
 o one for the development of the GUI (and graphics in the case of 
Coot)
 o one for the deployment of binaries - it takes time to produce 
binaries

   for numerous versions of numerous operating systems and the many
   changing/improving dependencies (to me this feels like a constantly
   changing, never complete jigsaw puzzle)
   And, although I recognise its importance, I just keep dropping the ball
   for the third one (is has little intrinsic pleasure for me and is
   completely invisible career-wise).

   Coot on "Linux":

  There is a build-script, build-coot-3-3 that works for me, soup to
  nuts on a modern Ubuntu system. Not so much on Fedora though. I will
  try to help if you try this method and things go wrong. Python and
  its add-ons are exquisitely tricky to build and is not well 
documented,

  however [3].

https://raw.githubusercontent.com/pemsley/coot/main/build-it-3-3

   Coot on macOS:

  Some Mac users might like to consider using Homebrew. At some stage
  I hope that
 $ brew install coot
  will (just) work. But that will involve input from by Yoshitaka
  Moriwaki who is looking after Coot in Homebrew (that might take a
  month or two).  Right now, Mac-using homebrew-using Coot
  enthusiasts can follow issue 33 on github:
  https://github.com/pemsley/coot/issues/33

   Coot on "Windows":

  Bernhard Lohkamp is the font of all wisdom when it comes to
  WinCoot. He will let us know his schedule. (Within a month though,
  that is my understanding.)

   via CCP4:

  In the coming weeks CCP4 will review Coot 1.1 and decide if it is
  acceptable to be added to the suite. If approved, that is the path
  of least effort for me and many users.

What about 0.9.x?

   I will maintain the back-end/libraries until April 2024, then I will
   reassess. It's just too much trouble to change the GUI though.

Future:

   With such a massive change set [4], there are bound to be bugs, so I 
imagine

   a flurry of patch releases in the forthcoming weeks.

   With this bad boy [5] out the door and with Lucrezia Catapano coming
   back on-line I can spend more time on Moorhen [6] and the Blender
   interface - hooray!

   If you've got this far and can get this Coot to run, I have added an 
Easter

   Egg for today (I'll tell you what it is: coot.halloween()).

[1] To give you an idea of the scope of this work (and the speed at 
which the

    interface for Coot was implemented) look how long it takes to rewrite a
    

Re: [COOT] coot scripting

[Paul Emsley]

On 14/10/2023 23:34, Zhu JiaPeng wrote:


Dear all,

I am currently working with a protein containing multiple subunits. 
For each subunit, I need Coot to perform rigid body fitting followed 
by real-space refinement. Manually inputting the Python commands 
rigid_body_refine_zone(reso_start, resno_end, chain_id, imol) and 
refine_zone(imol, chain_id, resno1, resno2, altconf) and then pressing 
"accept" for each chain has proven to be quite tedious.


Is there a way to combine these commands into a single script for 
automation?



# Yes, indeed.


imol_model = read_pdb("tutorial-modern-chain-tweak.pdb")
imol_map   = make_and_draw_map("rnasa-1.8-all_refmac1.mtz", "FWT", 
"PHWT", "W", 0, 0)


set_refinement_immediate_replacement(1)
set_imol_refinement_map(imol_map)

for ch_id in chain_ids(imol_model):
    rigid_body_refine_zone(1, 93, ch_id, imol_model)
    accept_moving_atoms()
    residues = residues_in_chain(imol_model, ch_id)
    refine_residues(imol_model, residues)
    accept_moving_atoms()



# (Future) Coot 1 users should know this is not how the python API works 
now.



Paul.




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Re: [COOT] Coot/mmdb2 issues with NCS and links in mmCIFs

[Paul Emsley]

On 13/10/2023 13:12, Neil Rzechorzek wrote:


Dear colleagues,



Hi Neil,


I have been iteratively rebuilding and refining a crystal structure 
using coot (v. 0.9.8.91) and Phenix.


Refinement makes use of NCS restraints, and the structure additionally 
has some covalent links between protein sidechains and bound ligands.



OK, sounds interesting.


NCS parameters and links are output by Phenix in both PDB and mmCIF 
file formats.


Coot happily opens the PDB file, and the covalent links are displayed 
as the usual dotted lines.


However, coot fails to open the mmCIF file.  According to an old 
ccp4bb post 
(https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind1910=CCP4BB=0=73942 
), 
this appears to be an mmdb2 library issue that I gather has not been 
resolved.


That's right. But there's more. I've been working on a new version of 
Coot and that reads 6ttq (for example) just fine.


  In particular, the _struct_ncs_oper category in the mmCIF is the 
culprit and - as the previous poster noted - removing this whole 
section from the file enables coot to open it.  I gather this is akin 
to deleting the MTRIX section in a PDB file, though am not sure 
whether this is either permitted or advisable for a deposited structure.



Indeed.

Additionally, coot doesn’t show the sidechain-ligand links in this 
modified mmCIF file.  The correct _struct_conn.id loops are present – 
is there a switch somewhere that encourages coot to show them?



There is no user-control over this.


  I’ve checked other deposited mmCIF files with such links, and they 
too suffer from the same problem.



Do you have a particular code in mind?

As I’m now depositing the structure at the PDB, I’m trying to resolve 
these issues prior to accepting the final annotated version.  While 
end users will always be able to open the PDB file in coot, mmCIF 
seems to be the preferred file type for many.



This will increasingly become the case.


Apologies if I’ve missed other posts/solutions to these issues, or 
have misunderstood something – I did search, but could not find 
answers.  Any suggestions would be extremely welcome!


The ball is in my court. The version of Coot that I am using (from the 
main branch of the Coot repo) doesn't have these problems, AFAICS. I 
need to get it in shape for release.


Since mmdb2 is managed by the CCP4 team, I will likely post this to 
ccp4bb also.


They will say "if mmdb2 is the problem then GEMMI is the solution" - or 
some such.


Paul.





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Re: [COOT] Error in Wincoot0.9.8.7

[Paul Emsley]

On 12/10/2023 05:46, Goode Shelter wrote:


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*.-owner-c...@jiscmail.ac.uk-.*

Dear Sir/Madam,
  I am a user of Wincoot0.9.8.7 in win10 system. When I click "undo" 
button, there is an error in coot that I cannot fix it. However, same 
files (PDB and MTZ) in other's computer, the "undo" button can work. 
The details is below:

restoring from backup 3 3
WARNING:: Error reading E:\Lab119\structure 
refinement\wincoot\WinCoot-0.9.8.92\WinCoot\\coot-backup/E__Lab119_structure_refinement_Phenix_files_DYRK2_Phenix_4-98-2_Refine_29_DYRK_refine_29-coot-0.pdb_Thu_Oct_12_12_39_24_2023_modification_1.pdb.gz

DEBUG:: apply_undo: (end) history_index: 1 max_history_index: 3
apply_undo ()

please help me to solve this problem, it is very important for me to 
analyze this structure. Thank you very much.

Looking forward to hearing from you.



I don't know much about Windows error messages. If you wish to open that 
particular file then I suggest that you copy it to your Desktop as 
"important.pdb.gz" or some such. Then you can use File -> Open 
Coordinates to read that file.


I think.

If that fails then you might need to gunzip it outside of Coot.

Paul.




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Re: [COOT] MDO Unnatural modified Amino acid

[Paul Emsley]

On 21/09/2023 18:58, Paul Emsley wrote:

On 21/09/2023 18:05, Kelvin Lau wrote:

Dear all

I am having trouble with an unnatural ligand/amino acid.

I have a structure very similar to PDB 6Q6H, 7TQR. They all have an 
MDO residue that replaces three residues in a series G-A-S-G-D to 
become G-MDO-D. MDO is in the Coot library.


I have been very used to replacing cysteines with CME with 
Modelling>Replace residue. It works great, removes the OXT and all 
the other atoms, can use real space refine directly.


For this MDO residue I find that it correctly fetches from the 
dictionary, however, I cannot refine it. Whenever I click on an atom 
and drag it just blows up or the atom gets stuck.


I have now opened up 6Q6H and 7TQR and tried to just refine the built 
in MDO in those PDB, same thing happens.


Does anyone have any ideas of what might be going on? Also in general 
for modified residues/unnaturals.



If you tell Coot that the group is a non-polymer it will believe you.

Use the Restraints editor to change the group to "peptide" (not tested).



Reply in haste ... repent at midnight.

This is old-fashioned advice it turns out (thanks to Garib).

Now that I come to actually look at one of the MDO beasties, it's not as 
much like a peptide as I expected it to be, and so describing it as such 
will induce Coot to throw itself to the floor in raging fit of geometric 
conniptions.


As mentioned before, the CCP4 Monomer library has undergo a substantial 
reworking/extension of the linking restraints.Concomitantly, Coot is now 
fully capable of using the spangly new MDO-pept link description 
completely automatically. It is an eyebrow-raising/forehead-wrinkling 
concern that it didn't work this way for you.


Regards,

Paul.

FWIW, my Internal Chemist (and also the link restraints) tells me that 
A141 H in 7tqr is pointing in the wrong direction.




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Re: [COOT] MDO Unnatural modified Amino acid

[Paul Emsley]

On 21/09/2023 22:25, Kelvin Lau wrote:

Hi Eleanor

Thanks for catching that..

I was under the impression that when I am fetching the monomer, MDO, 
it was defined as a peptide, not a non polymer … at least that’s what 
is listed here: https://www.rcsb.org/ligand/MDO


I guess I have to go about as Paul suggested as changing it to “peptide”

Is an alternative using the PDB MDO cif file as the restraint as it is 
properly defined and replacing the original definition?




Well

CCD cifs don't have _chem_comp.group and CCP4 Monomer Library entries 
don't have _chem_comp.type. What an interesting situation. Maybe this 
has already been addressed by the latest and greatest Acedrg? I imagine 
that Keitaro has his finger on the pulse of this predicament - much more 
than I do. Let's see what he has to say.


If I understand your question correctly, then no... CCD dictionary cifs 
don't have restraints.


Regards,

Paul.



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Re: [COOT] MDO Unnatural modified Amino acid

[Paul Emsley]

On 21/09/2023 21:56, Eleanor Dodson wrote:

And in fact it doesnt..



Wasn't that implied by my reply?

:-)

Paul.



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Re: [COOT] MDO Unnatural modified Amino acid

[Paul Emsley]

On 21/09/2023 18:05, Kelvin Lau wrote:

Dear all

I am having trouble with an unnatural ligand/amino acid.

I have a structure very similar to PDB 6Q6H, 7TQR. They all have an MDO residue 
that replaces three residues in a series G-A-S-G-D to become G-MDO-D. MDO is in 
the Coot library.

I have been very used to replacing cysteines with CME with Modelling>Replace 
residue. It works great, removes the OXT and all the other atoms, can use real 
space refine directly.

For this MDO residue I find that it correctly fetches from the dictionary, 
however, I cannot refine it. Whenever I click on an atom and drag it just blows 
up or the atom gets stuck.

I have now opened up 6Q6H and 7TQR and tried to just refine the built in MDO in 
those PDB, same thing happens.

Does anyone have any ideas of what might be going on? Also in general for 
modified residues/unnaturals.



If you tell Coot that the group is a non-polymer it will believe you.

Use the Restraints editor to change the group to "peptide" (not tested).

Paul.



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Re: [COOT] Coot worse aliasing in 0.9.8.91 than in 0.9.8.5

[Paul Emsley]

On 13/09/2023 08:39, Adrián González López wrote:

Hi Paul,

I have been using CCPEMs coot (version 0.9.8.5) for a while but 
decided to change to ccp4 to get the newest updates (coot version 
0.9.8.91). I have noticed that something in the graphics has changed. 
In version 0.9.8.91 there is pretty noticeable aliasing, which is not 
a problem in version 0.9.8.5 packaged with ccpem.



If I may so bold, I'd suggest the Subject of the post is not correct. It 
should be "Coot has worse aliasing in CCP4 builds than in CCPEM builds"


For reasons that I don't understand, CCP4 have historically been 
reluctant to add the antialiasing patch into the build of Coot (one of 
its dependencies, just to be clear) - hence Coots from CCP4 have never 
had antialiasing. CCPEM developers have taken on board the anitaliasing 
patch and so their Coots look smoother.



I have attached a picture to show this (I am using the default colors 
in both). I am on Mac M1 with MacOS Ventura 13.5.2.
I know there is an antialiasing option, but it makes the lines on the 
map thicker and it is more difficult to see.


Yes, I should have removed that years ago. I now know enough about 
OpenGL and graphics drivers to know that this function would never be 
able to do what I wanted it to do.



FWIW, Things are different in the new version of Coot. All builds are 
non-antialiased (boo). But on macOS, Coot is now native and runs at 
retina resolution and so looks (again, if I may be so bold) rather 
attractive (yay).



Regards,


Paul.




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[COOT] Release 0.9.8.92

[Paul Emsley]

This release should address the problematic linking discussed here over 
the last few weeks.


At least, I hope so (as noted before, what is needed is a complete 
rewrite of the link-finding code - an algorithm that believes the headers).


Regards,

Paul.


Source

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.8.92.tar.gz

Binaries:

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/coot-0.9.8.92-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz


  Release 0.9.8.92

 o FEATURE: Added copy_from_ncs_master_to_specific_other_chains_py(). 
Now one can update
    (only) specific peer chains (instead of all of them as was 
previously the case)

    [Oli Clarke]

 o BUG-FIX: Change the linking code once more - fixes erroneous 
DNA+protein links

    [Keitaro Yamashita].



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Re: [COOT] Python scripting command to set the map used for refinement automatically.

[Paul Emsley]

On 04/09/2023 22:50, Georg Mlynek wrote:

Dear Paul and community, I am loading several generated maps in coot via a 
script. Now I want that coot sets a specific map used for refinement 
automatically.

very good.


What would be the code for that?



For Python in Coot 0.9.x that would be

set_imol_refinement_map(imol)

for Python in Coot 1.x it would be

import coot # (of course)

coot.set_imol_refinement_map(imol)



(Chatgpt did not know the answer. Also the internet does not know.)


Chatgpt,

if you get to read this, the documentation is here:

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/docs/html/files.html

libcootapi documentation is here:

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/docs/api/html/



Many thanks Paul for all the effort you put into coot.



Thanks.


Paul.



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Re: [COOT] A COOT mess showing up at deposition - no cif links and auto (false) Di-sulphides formed

[Paul Emsley]

On 01/09/2023 17:40, Eleanor Dodson wrote:

Is that coot in the latest ccp4 distribution?



By "that" I presume you mean "Coot 0.9.8.92." No, it is not. Currently 
it is merely a twinkle in the developer's eye.



I'll try to find some time next week to make a release.


Paul.




On Fri, 1 Sep 2023 at 17:37, Paul Emsley  
wrote:


Dear Eleanor

[snip]






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Re: [COOT] A COOT mess showing up at deposition - no cif links and auto (false) Di-sulphides formed

[Paul Emsley]

Dear Eleanor


On 01/09/2023 13:19, Eleanor Dodson wrote:

*COOT problem first: or is it REFMAC ? *
REFMAC outputs coordinates in both pdb and cif format. They are  
identical

*This model has ZN linked to CYSs etc..*
The PDB files provides the link records but the cif file does not.

eleanor@wombat job_187 % grep -i link 
Job*181:*Model*from*refinement*PDB*format-coot-0allref.pdb
LINK         OE2 GLU A 338                ZN    ZN A 701 1555   1555 
2.020
LINKR        C2  DRG A 702                 SG  CYS A 417           
 DRG-CYS
LINKR       ZN    ZN A 701                 SG  CYS A 340           
 ZN-CYS
LINKR       ZN    ZN A 701                 SG  CYS A 417           
 ZN-CYS
LINKR       ZN    ZN A 701                 SG  CYS A 418           
 ZN-CYS


But the only mention of ZN in the cif format is the actual coordinate. 
nolink definitions..



The mmCIF format file as output by which program? As far as I can tell, 
your talking about Refmac.






eleanor@wombat job_187 % grep -i zn 
181_hypba1-vbc75-an6906_ciffile_prosmart_refmac.cif-coot-0ref2.cif
 HETATM 10117 ZN ZN   . ZN  A2 2 .   . . 2.0627321 25.812978   
 14.772831    1   68.493  ? ? ? ? ? +0 701 ZN  A ZN   1



*There is also a di-sulphide mess. the cif output from COOT forces 
close SG to form unwanted SSBONDS. (Of course this may only happen 
because the ZN links are lost..)

*



As mentioned earlier today in a related but different thread, this 
should be fixed in 7e2518b1452f18d011db43b57210bce71cfa41e5.



On 01/09/2023 13:35, Wendy Offen wrote:
Yes, it is coordinated to the CYS residues. So maybe it does need to 
be shown as having links
I was just confused because links for covalent bonds look the same 
as for coordinations.



Yes - a Link should appear w̶i̶t̶h̶ ̶t̶h̶e̶ ̶M̶a̶s̶t̶e̶r̶ ̶S̶w̶o̶r̶d̶ as 
a dotted line (even the the case of a Schiff base, for the record) - 
Coot doesn't care about the bond type when representing a Link.




*
*
*Here ..[snip]*
Is this comprehensible??



Comprehensible enough for me to think that we would have a much more 
productive exchange in the light of your using Coot-0.9.8.92 - which 
will contain the above fix.



Regards,


Paul.




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Re: [COOT] Coot 0.9.8.91 places wrong disulfide bonds

[Paul Emsley]

On 01/09/2023 11:37, Guenter Fritz wrote:

Dear Paul,

I had a strange issue today when refining a structure with latest coot 
(0.9.9.91) from CCP4.


Two cysteines with Calpha-Calpha  distance of about 6 A do not form a 
disulfide bond, but coot wants to enforce a disulfide, although no 
disufide is defined in the pdb.


Does coot now automatically assume disulfides for Cys closer than a 
certain distance?


Yes. Although I now believe that the linking code in Coot needs to be 
completely reworked.  When I started on this code, it was a sensible 
idea not to trust the links and SSBONDS in the coordinates file, so Coot 
worked them out itself. Today that is the wrong approach.





If yes, I guess there is a parameter that one can set?



Sadly no.


I do believe though that a recent fix will solve the problem.

I need to find some time to make a release. I'll try to do that next week.

The relevant commit is 7e2518b1452f18d011db43b57210bce71cfa41e5 if you 
want to apply it yourself.


Paul.



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Re: [COOT] coot on MacOS

[Paul Emsley]

I don't know much about CCP4-built binaries on macOS. I do know that one 
is supposed to reinstall XQuartz after updating the OS.



Paul.



On 31/08/2023 21:52, Andrea Smith wrote:

P.S. Found this in the log file from Cloud:

dyld: Library not loaded: /usr/X11/lib/libpixman-1.0.dylib
  Referenced from: /Applications/ccp4-8.0/lib/libcairo.2.dylib
  Reason: Incompatible library version: libcairo.2.dylib requires 
version 35.0.0 or later, but libpixman-1.0.dylib provides version 0.0.0
/Applications/ccp4-8.0/coot_py2/bin/coot: line 272:  3147 Abort trap: 
6   $coot_bin "$@"

ERROR: In procedure dynamic-link:
ERROR: file: "libguilegtk-2.0", message: "file not found"
 *** error running coot: Error in command.call
Return code: 34304





On Thursday, August 31, 2023 22:18 CEST, Andrea Smith 
 wrote:

Dear all,

I have macOS Big Sur version 11.6.8 (first time Mac user) and I 
wanted to get CCP4. So I went to CCP4 download pages, there I read I 
need XQuartz, so I downloaded XQuartz 2.8.3. Installed. Then I 
downloaded the CCP4 Package Manager. Installed.


Tried to run CCP4 Cloud. All good until I wanted to open Coot which 
failed on the Cloud. So I tried to open Coot directly from 
Applications, but Coot doesn't open. The XQuartz is not in the 
Applications (?).


What am I doing wrong? How do I find out where is the problem?

Help will be appreciated. Thank you, best,
Andrea


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Re: [COOT] rotamer selection

[Paul Emsley]

On 25/08/2023 06:56, Daniel Larsson wrote:


Hi Paul,

I have some suggestions/requests for facilitating sidechain modelling.

  * Option to have the rotamer tool default to the rotamer most
closely resembling the current rotamer (now it defaults to the
most common rotamer)


That seems like a marginal improvement in the user interface.

If you want to "just tighten up the probability to the closest rotamer" 
then turn on rotamer restraints so that they are used during refinement


(set-refine-rotamers 1)



  * Option to have the rotamer tool default to the rotamer with the
highest average map value for the atoms. Atoms closer to the Ca
should be weight higher (as an option).

This could be done quite easily. But it's getting quite close to 
auto-fit-rotamer functionality.


  * Perhaps also have an option to allow for a small rotation/translation.


The devil, is as Phil would say, in the detail.


  * Show all rotamers in the rotamer library at the same time and then
you can click on the one that you want (“bouquet” mode)

I don't see how this is an improvement over the use of the dot and comma 
keys.


  * Automatically select the best rotamer in a chain/molecule
considering fit-to-density and clashes, but without touching the
backbone and not doing any refinement.

The backbone shrugs when the sidechain dances. There is no tool in Coot 
for rotamer fitting that doesn't move the mainchain. It could be done 
quite easily, but I am not convinced of the utility. It seems to me that 
it is quite possible the the backbone atom positions have already been 
compromised to account for the wrongly positioned sidechain rotamer and 
so without variation in backbone orientation, the wrong rotamer is more 
likely to be found.



Paul.

p.s. are you iDaniel?




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Re: [COOT] Coot 9.8.91 is still broken

[Paul Emsley]

On 24/08/2023 15:53, Helge Paternoga wrote:



I just had the chance to try out the new Coot version 9.8.91 from CCP4 
and I would like to report that RSR of ribosomes is still broken



Thank you.

I will get to this shortly. I had been hoping to solve the problem 
without a general-purpose (and more complex) link-filtering algorithm. 
It seems that I should not avoid it.


Regards,

Paul.



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Re: [COOT] Small issue on the accept refinement tab

[Paul Emsley]

On 09/08/2023 10:51, 次田篤史 wrote:

Dear all

I just installed the latest version coot (0.9.8.8) and checked if it 
works by Bernhards key bindings.


As far as I remember,  on the "Accept Refinement?" tab, the "accept" 
button was selected automatically and if we did not need to fix the 
coordinates, we could just hit enter in the previous versions.
But now, the "Clear Atom Pull Restraint" button is selected, and need 
to press the tab key or the arrow keys each time.


It's a bit annoying for me so does anyone know how to fix it by 
changing the setting or editing the key binding text?



Hello Atsushi,

Yes, I see what you mean, the dialog grabs the focus and the wrong 
button has focus in that dialog.


If you move your mouse over the main (graphics) coot window, then the 
focus should change and then "Enter" will do what you want (or you may 
need an extra click to do so - depending on the settings of your window 
manager).


Alternatively, you can use "Tab" to move the focus of the Accept/Reject 
dialog to the "Accept" button.


It is unlikely that I will go back and fix this (that dialog doesn't 
exist in the new version).


Paul.



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Re: [COOT] Problem installing coot binary

[Paul Emsley]

On 08/08/2023 06:49, Edward A. Berry wrote:
> I would appreciate instruction for getting a downloaded coot binary to
> run.


Fair enough.


The idea is that you untar the binary tar file and put
/somewhere/coot-something/bin in your PATH. That's it. You shouldn't
need to edit any coot files. Coot is compiled and distributed with its
own python, so setting PYTHON to the system one will upset it, because
the system python doesn't know about the coot module.


Keeping on top of making binaries is the majority of a full-time job
itself and I just have not been able to manage it. I can make binaries
for the computers I use that are connected to the internet - i.e. the
Scientific Linux build. Maybe one day things will change. But at the
moment it's just sad times. The options are, pick it up from CCP4 or
compile it yourself.


Regards,


Paul.



> I got coot-0.9.7-binary-Linux-x86_64-centos-7-python-gtk2.tar.gz
> There is no README file in the top directory.
> I edited bin/coot to set
> #PYTHON=/tb2/sw/lnx/coot-Linux-x86_64-centos-7-gtk2-python/include/python2.7
> #PYTHON=/usr/bin/python2.7
> PYTHON=/usr/lib64/python2.7
>
> With or without those edits, it runs as far as bringing up the
> graphics screen, loading the standard residues, and saying hello- then
> crashes with:
> (set-display-lists-for-maps 1)
> Stack trace (most recent call last):
> #0    Object
> "/tb2/sw/lnx/coot-Linux-x86_64-centos-7-gtk2-python/lib/libgmp.so.10",
> at 0x7f3097b3133b, in __gmpn_mul_1
> Illegal instruction (Illegal operand [0x7f3097b3133b])
> /sw/lnx/coot-Linux-x86_64-centos-7-gtk2-python/bin/coot: line 264:
> 10999 Illegal instruction     (core dumped) $coot_bin "$@"
> (more below)
>



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[COOT] Release 0.9.8.91

[Paul Emsley]

Source:

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.8.91.tar.gz 



Scientific Linux 7.6 binary:

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/coot-0.9.8.91-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz 




  Release 0.9.8.91

 o BUG-FIX: Restore missing peptide omega plot [Steven Sheriff]

 o BUG-FIX: Check/Delete waters now excludes hydrogen atoms in 
close-contact analysis [Steven Sheriff]


 o BUG-FIX: Replace Residue works for residues in the B chain [Paul Bond]



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Re: [COOT] Release 0.9.8.9

[Paul Emsley]

On 27/07/2023 02:58, Mark Saper wrote:

Hi Paul,

Does this new release address the problems with Real Space Refinement that I 
reported several months ago?



I believe so.

Paul.



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[COOT] Release 0.9.8.9

[Paul Emsley]

Source:

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.8.9.tar.gz

Scientific Linux 7.6 binary:

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/coot-0.9.8.9-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz


  Release 0.9.8.9

  o FEATURE: Use add_hydrogen_atoms_to_residue() in mutate_internal() 
if the residue

 has hydrogen atoms [Clemens Vonrhein].

  o FEATURE: Add add_hydrogen_atoms_to_residue() to the API.

  o CHANGE:  Allow the addition of hydrogen atoms to nitrogen atoms 
with energy

 type NR5.

  o CHANGE:  Remove flaky Biscu-it QED interface.

  o BUG-FIX: Change the link-finding algorithm to handle the AA-RNA link in
 the new monomer library [Keitaro Yamashita].



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Re: [COOT] Refinement weights for low-resolution structures

[Paul Emsley]

On 18/07/2023 19:09, Radford, Katelyn M. (Kate) wrote:

Hi all,

I'm trying to fit a model into a low resolution (5.88 Å) EM density. 
When I refine in Phenix and Coot, the default settings fit all atoms 
into the density, including side chains. While this would be great if 
I had a sub-3 Å structure, for a low-res structure it means that I 
have a ton of Ramachandran outliers and rotamer outliers when I 
absolutely cannot justify them and would ideally have none. Is there a 
setting or a set of weights that I can use to refine with respect to 
resolution, so that low-resolution structures yield models with 
no/very few outliers, e.g. by increasing the weight of 
Ramachandran/rotamer restraints at lower resolutions and decreasing 
the weight of the density? (As a note, I do often change these 
weights, but I have not been able to find the resource that describes 
the range of values of these weights, how they're calculated, how they 
relate to each other, etc. If there is such a resource, I would be so 
happy to have that.)




R/RC -> More Control...


To add rotamer restraints:


Calculate -> Scripting.. -> Scheme


(set-refine-rotamers 1)


The range of useful values, in my hands at least, is 0.1 to 2.0 times 
the value suggested by the "Estimate" button.



Paul.





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Re: [COOT] Coot 1.0 installation

[Paul Emsley]

On 11/07/2023 09:53, Charles BARCHET wrote:


Dear all,


I am currently trying to compile Coot 1.0 on Ubuntu 22.04.

After downloading all the necessary binaries, I end up with a python 
version error message :



*:1: DeprecationWarning: The distutils.sysconfig module is 
deprecated, use sysconfig instead
:1: DeprecationWarning: The distutils package is deprecated 
and slated for removal in Python 3.12. Use setuptools or check PEP 632 
for potential alternatives
:1: DeprecationWarning: The distutils.sysconfig module is 
deprecated, use sysconfig instead

-I/usr/include/python3.10
*



I am presuming that you ran this script:


https://raw.githubusercontent.com/pemsley/coot/gtk3/build-it-3-3


Is that right?


For the record, although that should work (I'd like that to work) I have 
spend little time on it over the past year.


Ubuntu 22.04 comes with GTK4, I think, so you should be able to use


https://raw.githubusercontent.com/pemsley/coot/main/build-it-3-3.


Anyway, it is not clear to me what you did to make the above message 
happen. It certainly doesn't look like a standard Coot startup message. 
What did you do to make that happen?



> I have tried using "update-alternatives" to fix this issue but it 
didn't work.



I don't know what this means.


> Is it possible to get a pre-compiled version somewhere or to help me 
fix this problem ?



Sadly not. Building binaries is practically a full-time job and I just 
don't have time to fit it into my day at the moment.



Regards,


Paul.




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Re: [COOT] PDB files crumbled when loaded on coot

[Paul Emsley]

On 14/06/2023 22:24, David Aparicio wrote:

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Dear community,

When loading some pdb files on coot they are showed like the attached picture. 
Any tip about to fix it?



See the FAQs

Bizarre connectivity of coordinates files

https://bernhardcl.github.io/coot/wincoot-faq.html


Paul



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Re: [COOT] Can't download pdb files nor density maps in WinCoot 0.9.8.1 EL

[Paul Emsley]

Hi Dale,

Without testing, I guess that you can replace get_ebi.py with this one

https://github.com/pemsley/coot/blob/refinement/python/get_ebi.py

(use Raw of course)

Paul.


On 08/06/2023 08:35, Sameer Velankar wrote:


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Hi Dale

The correct url for accessing files are as follows -
1. PDB file - https://www.ebi.ac.uk/pdbe/entry-files/pdb1cbs.ent
2. mmCIF file - https://www.ebi.ac.uk/pdbe/entry-files/1cbs.cif

Kind regards
Sameer


On 8 Jun 2023, at 07:25, Dale Tronrud  wrote:

Hi,

  When I click on "Fetch PDB entry using Accession Code..." or "Fetch 
PDB & Map using EDS..." I get


PDB Accession Code: 3eoj
DEBUG:: extracted accession code handle mode n 1
BL WARNING:: retrieve of url 
https://www.ebi.ac.uk/pdbe-srv/view/files/3eoj.ent failed

handle_read_draw_molecule_with_recentre ("coot-download/3eoj.pdb.ent".1)
WARNING:: Error reading coot-download/3eoj.pdb.ent

  That web site, indeed, does not exist and I presume the PDBe has 
moved the data.


  To the best of my knowledge this is the most recent version of 
WinCoot.  I've downloaded the "unstable" version 1.0.01 and it fails 
in the same way (but does show a very pretty display when downloading 
from PDB Redo).


  I've done my best to search the "coot" and "ccp4bb" archives and 
don't see mention of this problem, but my search skills are limited.


  What do I do to download PDB's and maps again?

Dale Tronrud



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Re: [COOT] stero/Mono

[Paul Emsley]

On 12/05/2023 17:00, Gu Shaocheng wrote:

Hi,


Hi.


Here is a GPU issue related to chimerax and coot (0.9.8) on the Linux system.

OK...

To be able to call GPU in chimerax, I put the nvidia invoke in .bashrc file.


I don't know what it means to call the GPU in ChimeraX. I don't know 
what the nvidia invoke is.


Perhaps you are refering to an environment variable?


Chimerax works,

In what way? What changes?

however, this will stop the working for coot to display structure at the 
following view modes: `mono`, `side by side stereo`, and `side by side (wall 
eyed)`.
What do you mean by "stop the working"? That Coot doesn't start up? Or 
freezes?

It

It? meaning Coot or the graphics card?

  still works if I click 'hardware stereo' or 'Zalman Stereo' and I can see it 
in `nvidia-smi`.

"see it"? The graphics card?

Without GPU, each mode works fine.
Without the graphics card, Coot will fall back to software rendering on 
the backend. Not many people these days think that that is "fine."

I wonder if we shouldn't run coot with GPU or if there are some potential 
issues.
Does anyone have any idea about this? Thanks!


For most people, Coot uses the GPU whether they like it or not.

The advice I can  give you is trite: use whatever gives you the best FPS.

I'm not sure that I've been of much help.

Paul.



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Re: [COOT] Coot: Fitting a,b Methylene ATP (APC) into cryoEM Density

[Paul Emsley]

I think this slipped by on the coronation break and I didn't get to see 
it until recently.


So... for the record then...

On 10/05/2023 17:23, Karl Herbine wrote:



I am relatively new to model building in coot.

Belated welcome.

  I am having trouble finding the correct fitting for the ligand APC (in 
Monomer library) which is a non-hydrolyzable analog of ATP. I place the ligand 
and manually fit it into the correct density, however, when I use any of the 
Ligand functions (IE, jigglefit ligand, find ligands, etc.) nothing changes.


I am a bit confused. If you have already fit the ligand correctly into 
the density, then jiggle fit or find ligands won't find a better solution.



I am quite unsure how to validate this fitting such that torsions and 
restraints are correct. Are there any tutorials out there on how to do this? I 
cannot seem to find any.

Ligand -> Display Ligand Distortions will colour the bonds, angle and 
chiral centres with a colour ramp green to red (read means more than 3 
esds from the target value).


Ligand -> Tabulate Ligand Distortions will list the bond, angle, chiral 
and plane restraints distortions.


I haven't written a tutorial for this - that is a good idea.

Paul.



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Re: [COOT] (Re)beginner question about coot binary version on Linux Ubuntu

[Paul Emsley]

On 24/05/2023 14:24, hari jayaram wrote:


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Hi All
I am making some progress--but still cant get any of the binaries working

I have the openssl libraries installed but still get the following 
error with coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python


Thanks for your help
Hari




"hari@LT-Hari-Linux:/usr/lib/x86_64-linux-gnu$ 
~/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/bin/coot
/home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: 
libcrypto.so.1.1: version `OPENSSL_1_1_0' not found (required by 
/home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4)
/home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: 
/lib/libssl.so.1.1: version `OPENSSL_1_1_1' not found (required by 
/home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4)
/home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: 
/lib/libssl.so.1.1: version `OPENSSL_1_1_0' not found (required by 
/home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4)



It is not clear to me if libcrypto is not installed (in which case you 
should install it) or is a more modern version than my binary expects 
(in which case, there is no hope for the binary that I have built (you 
might like to try the build-it script)).


Paul.




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Re: [COOT] (Re)beginner question about coot binary version on Linux Ubuntu

[Paul Emsley]

On 24/05/2023 02:13, hari jayaram wrote:


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Hi All
I want to get back to using coot to build some models after a gap of 8 
years.


I have access to a Linux laptop and can put any OS version on it.

 I was wondering what the easiest way forward is —get the most recent 
Ubuntu and pull the latest binary ( 0.9.8.6 with binary for 20.04) or 
put the iso that coot was built for (20.04) on the laptop and start 
using it.



The easiest way forward is to use the build from CCP4. They fiddle with 
it in minor annoying ways. It's robust. It comes with a lot of other 
stuff. You have to sign a license.


Best way is to use the build-it script. Then you can track day-to-day 
development. The downside for this is that it often doesn't work out of 
the box.


Having said that, all development tracking is a bit weird at the moment 
since there are 3 versions:


 - the 0.9.x series with old GTK and old python and old graphics

 - 1.0 the current release that depends on Gtk3 that doesn't work well 
on macOS - and maybe not Windows either


 - GTK4 Coot (which is another major rewrite). This is where I am 
spending my time (that and Moorhen).


I want to get to a stage where GTK4 Coot is the only game in town. But 
there is a lot of work to do. And additional further work to make sure 
that it works well on macOS and Windows.


What I can say about future Coots is that they will use your hardware - 
the more cores and better graphics card you have the more 
enjoyable/productive will be your Coot-using experience.






Asking because I just  tried using the newest mint distro ( Mint 21.1 
Vera) and one of the binaries 
(coot-Linux-x86_64-scientific-linux-7.6-gtk2-python)  and it runs 
aground without OpenSSL and  ldap.so versions are being mismatched.



OpenSSL and Python are particularly time-consuming to correctly 
configure. I don't know how many days and weeks I've spend fiddling with 
it. Lots. Wretched thing.



When I switched to 
coot-0.9.8-binary-Linux-x86_64-ubuntu-20.04.4-python-gtk2 then it 
complained of a version mismatch for libssl.so.1.1



I should make a Linux Mint virtual machine...


Regards,


Paul




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[COOT] Coot 0.9.8.8

[Paul Emsley]

We are pleased to release Coot 0.9.8.8



  - FEATURE: Better atom colours in colour-by-chain-and-dictionary mode.

  - CHANGE:  Monomer search now uses the new dictionary

  - CHANGE:  Molecules read in as mmCIF (.cif) are now by default saved 
as .cif


  - CHANGE:  Atoms with element "Cl" are now drawn as CL.

  - BUG-FIX: the zoom state is now correctly set in the saved state file

  - BUG-FIX: additional symmetry check for peaks from flood filling 
(Paul Bond)


  - BUG-FIX: Link-generation improvements.

Source:

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.8.8.tar.gz

Binaries:

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/


Paul.



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[COOT] R̶e̶:̶ ̶Y̶o̶u̶r̶ ̶r̶e̶f̶u̶n̶d̶ ̶i̶s̶ ̶a̶v̶a̶i̶l̶a̶b̶l̶e̶ ̶o̶n̶l̶i̶n̶e̶ ̶:̶ ̶7̶7̶5̶,̶9̶0̶ ̶A̶U̶D̶

[Paul Emsley]

Bleugh. Sorry about that. If it happens again I will get in touch with 
Jiscmail.


Paul.



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Re: [COOT] Serious problem with Coot 0.9.7 in ccp4-8.0 versus Coot 0.9.6 in ccp4-7.1

[Paul Emsley]

On 04/04/2023 08:07, Mark Saper wrote:

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Dear Paul,

I’ve discovered a serious problem when running Coot 0.9.7 from CCP4-8.0 (macOS 
13.3).  The problem is in the menu commands Real Space Refine Zone or 
Regularize. If I select a zone comprised of 3 consecutive DNA nucleotides which 
are in decent density, the refinement fails as in the first attached figure. 
Often the DNA takes on random conformations.

If I repeat the same test with the same coordinates, map, and 3 nucleotides, 
using Coot 0.9.6 from CCP4-7.1, the refinement is successful and results in the 
second attached figure.

I think the same problem occurs with some polypeptide chains.



Hello Mark,

If you are accurately reporting the version numbers then I believe that 
this issue may have been fixed in 0.9.8.7. Here are the release notes



  Release 0.9.8.7

  o FEATURE: res_tracer() added to the API

  o FEATURE: read_mtz() added to the API [ChatGPT guessed at this 
function name, and there is

 no reason for it not to be there]

  o BUG-FIX: PDBe URLs fixed for downloading dictionaries with pyrogen

  o BUG-FIX: Carbohydrate Linking fixed again [Keitaro Yamashita and 
others]


  o BUG-FIX: RNA linking fixed [Keitaro Yamashita and Andrey Lebadev]

  o NOTE: Coot is now tested against the new monomer library.


Paul.



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Re: [COOT] debug:: g.safe_scheme_command() with command post-manipulation-hook

[Paul Emsley]

On 15/03/2023 13:54, Ramón Hurtado Guerrero wrote:
> Dear Paul,
>
> Thank you. Yes, this happens in mac and you are right since the coot
> icon is in the dock. How can I avoid this?
>
>

The key-binding Ctrl-D deletes the residue at then centre of the screen
(including waters) - this by-passes the need for the dialog, so the main
window doesn't get iconified.

Regards,

Paul.



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Re: [COOT] debug:: g.safe_scheme_command() with command post-manipulation-hook

[Paul Emsley]

On 12/03/2023 16:20, Ramón Hurtado Guerrero wrote:


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*.-owner-c...@jiscmail.ac.uk-.*

To whom it may concern, 
IrecentlyupdatedtothelatestversionofCCP4,andIamhavingsometroublewithCoot.WheneverItrytodeleteanatom,watermolecules,oranyothertypeofmolecule,theprogramcrashesandIreceivethefollowingmessage:


"debug::g.safe_scheme_command()withcommandpost-manipulation-hook".WouldyoubeabletoprovideanyguidanceastohowIcanresolvethisissue?Iwouldbeverygratefulforyourhelp.



https://pemsley.github.io/coot/blog/2020/09/21/how-to-make-a-bug-report.html

Is this using a Mac? I doubt that Coot is crashing. Can you stll see the 
coot icon in the dock? If so, right mouse to redisplay it.



Paul.




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Re: [COOT] RNA modifications in COOT

[Paul Emsley]

On 17/02/2023 08:28, ZOEY wrote:

Hi,
I am currently working on refining a protein/RNA complex. I am using coot to 
build my model and am wondering if anyone has any experience in dealing with 
RNA's modifications on them? I am working with a N6-methyl-adenine and am 
having problems with it in coot. In the library, there is a 6MZ.I have tried 
the script: mutate-by-overlap imol chain-id residue-no tlc (mutate-by-overlap 
imol chain-C residue-1 6MZ), but it did not work. I also tried to delete “A” 
and add “6MZ”, but I can not link “6MZ” with other nucleotides.
How do I add restraints so I can regularize or real space refine? What can I do?


Because the dictionary says that it's a non-polymer

File -> Get Monomer -> 6MZ

Edit -> Restraints... -> 6MZ -> OK,

Pull out the window. Change the group to "RNA" Press "Enter." Click 
Apply, Click Close


Centre on your adenosine

Calculate -> Modelling... -> Replace Residue... -> 6MZ -> Mutate



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Re: [COOT] SSbridges with Sphere Refine and Change Chain ID with carbohydrates

[Paul Emsley]

On 14/02/2023 09:28, Zeelen, Johan Philip wrote:

Dear All,

  I am using Coot 0.9.8.7 EL (ccp4) on a macOS 10.15.7 and have the 
following problems.


I am refining structures with 2 SS-bridges close together. When I use 
Sphere Refine+ the refinement gives me a cluster of the 4 Cys. 
molecules. See image.



Urgh. I thought that I'd fixed that by only allowing SSBOND linking. 
Baah. Do you have a PDB code to hand so that I can reproduce this?






Second problem when I am using Change Chain ID to rename the 
carbohydrates, the sugar molecules get changed, but not the 
corresponding LINK entries.



OK. I'll add it to the list.



Third problem, several proteins are also O-linked glycosylated when I 
try to upload the pdb to wwPDB Validation, after a local refinement in 
Coot (but also after Phenix.refine or PDB-REDO) most of the GLC 
molecules have a major validation issue PLANAR or WRONG HAND. Does 
anyone have a solution?


That sounds like a fascinating link restraints problem. Coot will tell 
you which link its trying to apply, I think. It is your job to check 
that the link geometry is correct (or what you want).


Paul.



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Re: [COOT] key binding for difference map peaks

[Paul Emsley]

Systemic failure. Oh dear.

Add an extra 1 after the 1 1.

The difference map peak list navigation key bindings are "." and "," 
FWIW (but you probably already know that).


Regards,

Paul


On 18/01/2023 07:45, Seth Harris wrote:

Hi all,

this used to work (a while ago) from my-settings.scm for a key binding 
to get a list of difference map peaks:


(add-key-binding "Difference map peaks" "b" (lambda () 
(difference-map-peaks 2 0 4 2.0 1 1)))




but now (and for quite some time) it mentions wrong number of arguments:


*(graphics-general-key-press-hook 98)*

((safe_scheme_command) Error in proc: key:wrong-number-of-argsargs:(#f 
Wrong number of arguments to ~A (difference-map-peaks) #f))



From what I can tell, the manual still indicates 6 arguments.


11.57.1 difference-map-peaks

function: *difference-map-peaks* /imol imol_coords level max_closeness 
do_positive_level_flag do_negative_level_flag/


Where:

  * /imol/ is an integer number
  * /imol_coords/ is an integer number
  * /level/ is a number
  * /max_closeness/ is a number
  * /do_positive_level_flag/ is an integer number
  * /do_negative_level_flag/ is an integer number

generate a list of difference map peaks

peaks within max_closeness (2.0 A typically) of a larger peak are
not listed.


Any hints or ideas if something has changed on the command or I'm 
missing something?


Thanks,

Seth





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Re: [COOT] coot does not save hydrogens.

[Paul Emsley]

@kas, check that your using Modern dialogs.


On 21/01/2023 12:25, Pedro Matias wrote:


Hi Ken,


When you save coordinates there should be a check box to save hydrogen 
atom coordinates. Maybe yours is off by default?



BR,


Pedro


On 19/01/2023 22:55, Kenneth Satyshur wrote:
I added H atoms in coot and they appear in the list of atoms, but 
when coordinates are saved, they are not saved with the rest of the 
atoms. Is there a way of saving them or is this not advised? I can 
put them on during refinement and they are just ridding anyway.

kas
0.9.6 version.

Kenneth A. Satyshur, M.S., Ph.D.

Scientist Emeritus From:

College of Ag and Life Sciences: Department of Bacteriology;

School of Medicine and Public Health:

Departments of Biomolecular Chemistry,

Neuroscience, Oncology, and Carbone Cancer Center

(Small Molecule Screening Facility)

University of Wisconsin-Madison

Madison, Wisconsin, 53706

608-215-5207




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--
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Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
  Fax   : (351-21) 441-1277 or 443-3644

email :mat...@itqb.unl.pt

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Mailing address :
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PORTUGAL

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Re: [COOT] 0.9.8.6 Carbohydrate linking issue still

[Paul Emsley]

On 18/01/2023 08:51, Lau Kelvin wrote:

Dear Paul

I got around to updating via ccp4.

In 0.9.8.7 EL  I can add the glycans like before, but I do not see a 
link. The glyco module also no longer recognises that there is a 
glycan present at the Asn, so when I add another NAG, they just overlap.




Thanks Kelvin, I'll look into it.

Paul.



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Re: [COOT] 0.9.8.6 Carbohydrate linking issue still

[Paul Emsley]

On 27/12/2022 18:59, Kelvin Lau wrote:

Dear Paul

I looked back the forum and similar to Taka's issue in 0.9.8.4 I am also 
experience it with both Coot 0.9.8.6 EL (ccp4 build) and 0.9.8.5 (ccpEM) build. 
MacOS 12.6.1



Hello Kelvin,

I believe that this issue is fixed in 0.9.8.7.

Paul.



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[COOT] Coot 0.9.8.7

[Paul Emsley]

Coot-0.9.8.7 has been released

source:

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.8.7.tar.gz 




  Release 0.9.8.7

  o FEATURE: res_tracer() added to the API

  o FEATURE: read_mtz() added to the API [ChatGPT guessed at this 
function name, and there is

 no reason for it not to be there]

  o BUG-FIX: PDBe URLs fixed for downloading dictionaries with pyrogen

  o BUG-FIX: Carbohydrate Linking fixed again [Keitaro Yamashita and 
others]


  o BUG-FIX: RNA linking fixed [Keitaro Yamashita and Andrey Lebadev]

  o NOTE: Coot is now tested against the new monomer library.



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Re: [COOT] How to restore chain after deletion?

[Paul Emsley]

On 23/12/2022 16:48, Joshua Arribere wrote:

Hello,

I am trying to understand how to restore a chain after a deletion in 
coot. I have deleted some residues (using delete-residue-range). The 
residues are visually gone, and replaced with a dotted line (a loop) 
between the flanking residues. I am not sure the best way to seal this 
gap. I can link the flanking residues, so that they remain bound, but 
two things make me think this is not the right way to go about it: (1) 
the number of the residues still assumes there is a gap, even after 
renumbering, and (2) the loop remains (of course, I could hide the 
loop and solve the problem cosmetically, but I think the loop is 
telling me that coot things the residues are still there).


Is linking the "right" way to do this? If so, how do I resolve the 
numbering issue (by separately re-numbering the two halves?)? 
Shouldn't the dotted line loop go away? Or is linking wrong?


I can find a lot in coot docs about mutating, deleting, but it seems 
inserting is far less common.



I am unclear about the details of the situation. This is my guess: You 
have deleted residues from a model that had residues where there were no 
residues in you crystal. Now you want to anneal the gap. So simply 
renumber the c-terminal fragment by an offset of negative few so that 
there is no gap in the residue numbering. After you have done that, coot 
will no longer draw a missing residues loop and may draw a peptide bond 
between the two fragments. If that is the case, you can give it a quick 
triple-refine to optimise the geometry over the newly-formed peptide. So 
linking is not the right way to do it and I don't think that you want to 
insert (that is, if I have understood the problem correctly).



Paul.



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Re: [COOT] MacCoot 0.9.8.5 issues

[Paul Emsley]

On 15/12/2022 13:01, Paul Emsley wrote:



On 14/12/2022 18:59, Ing. Yan Alejandro García Hernández wrote:


 1. Update to MacOS Ventura
 2. Install CCP4 last versión
 3. Open a file and try to delete a residue/monomer, the window
disappears.

I’ve posted an issue in GitHub with a video obout it: Unexpected 
window minimize · Issue #68 · pemsley/coot (github.com) 
<https://github.com/pemsley/coot/issues/68>


Here is the video: 
https://drive.google.com/file/d/1-K33wHSmydzSU6_fuYl_ZCHAlybSEtrA/view?usp=sharing




Fascinating! Thanks for the video. I can now poke about in the 
relevant part of the code - it might actually be _my_ code that is 
responsible.




For the record I have Big Sur and XQuartz 2.8.1 and see no problems.

Paul.





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Re: [COOT] MacCoot 0.9.8.5 issues

[Paul Emsley]

On 14/12/2022 18:59, Ing. Yan Alejandro García Hernández wrote:


 1. Update to MacOS Ventura
 2. Install CCP4 last versión
 3. Open a file and try to delete a residue/monomer, the window
disappears.

I’ve posted an issue in GitHub with a video obout it: Unexpected 
window minimize · Issue #68 · pemsley/coot (github.com) 



Here is the video: 
https://drive.google.com/file/d/1-K33wHSmydzSU6_fuYl_ZCHAlybSEtrA/view?usp=sharing




Fascinating! Thanks for the video. I can now poke about in the relevant 
part of the code - it might actually be _my_ code that is responsible.


Regards,

Paul.




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Re: [COOT] MacCoot 0.9.8.5 issues

[Paul Emsley]

On 14/12/2022 16:39, Yan Alejandro wrote:

I have the same problem. Is there a solution for this?



This is not a good bug report.

Give me a recipe to reproduce the problem.

Regards,

Paul.



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Re: [COOT] odd observation

[Paul Emsley]

On 12/12/2022 16:29, Paul Kraft wrote:

  just needed to close the old sequence view and open a new one to see the 
updates.
Thanks for your extremely prompt help. [...] Using simple mutate it seems I 
must close and reopen the sequence viewer for it to update the sequence even 
though it is clearly mutated


That's not great. I'll add update-sequence-view-on-simple-mutate to the 
list.


Regards,

Paul.



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Re: [COOT] replace residue Cd not active

[Paul Emsley]

On 12/12/2022 15:49, Paul Kraft wrote:

sorry,
I am using Coot 0.9.8.5 EL (ccp4) on Ubuntu LInux 22.04 LTMD amd64,

Ah, OK. Up to date. Good start.

using the Replace Residue command under Edit or under Calculate-Modelling
the command Cd does not function.


Interesting. I think that you want to "Simple Mutate" (in the vertical 
toolbar). Replace Residue is a general purpose monomer superposition 
tool, the Simple Mutate tool is written with purines and pyrimidines in 
mind.


Paul.



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Re: [COOT] replace residue Cd not active

[Paul Emsley]

On 12/12/2022 15:09, Paul Kraft wrote:

Hello,
I am trying to mutate DNA, and can with Gd, Td, and Ad, but the Cd command is 
inopporative.


Hello.

I'm not a mind-reader. You need to start off with which version of Coot 
you're using and on which system (that matters less usually).


You need to tell me what you pressed or clicked and what you expected to 
see and what actually happened.




  I searched the library list and found reference to Cd, but do not know why it 
is not working.



Cd was using for DNA in Coot until about 2006 - so I am not sure what 
you're talking about.




  I did an end around by making a .cif from the smiles definition,


That doesn't sound like the best solution.



  but when I use my definition it doesn't snap into place and it is a huge pain 
to move it into correct coordinates for it to bond correctly (especially since 
I do not have 3D goggle capabilities on this laptop) and need to do it for many 
cytidine mono phosphates.



indeed...

Paul.



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[COOT] Coot 0.9.8.6

[Paul Emsley]

Coot-0.9.8.6 has been released

source:

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.8.6.tar.gz

binaries:

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/


  Release 0.9.8.6

  o CHANGE:  More auto-read column pairs added [Clemens Vonrhein]

  o BUG-FIX: On adding a K to a molecule, put the atom name in the 
correct column

 [John Smith, Steven Sheriff]

  o BUG-FIX: Carbohydrate Linking fixed [Keitaro Yamashita and others]

  o BUG-FIX: delete_hydrogen_atoms() deletes deuterium atoms also 
[Lucrezia Catapano]




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Re: [COOT] backup file names

[Paul Emsley]

On 02/12/2022 20:24, David J. Schuller wrote:
The files in the coot-backup directory incorporate the date into their 
name. This caused a problem for one of our users, as the colon is a 
forbidden character in the file transfer application used, which is 
Globus.[...] I suggest it would be preferable to substitute something 
else, such as an underscore, for the colon in naming the files.




See the blog entry "Backup file-names for Windows" Jun 2020


Paul.




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Re: [COOT] Pointer Atoms - Potassium

[Paul Emsley]

On 02/12/2022 15:30, John Smith wrote:

Dear all!
I am using Coot 0.9.8.5 EL (ccp4) and I want to add K/potassium ions 
during model building.
Adding Na and Cl is straightforward, but if I click on Pointer Atom 
Type other, enter K and hit OK, then a grey atom is added, but it does 
not refine.

/Warning: Failed to match the dictionary./
Similar problem occurs if I do it via /Calculate - Modelling - add 
other solvent molecules./ If I specify K as three letter code, it 
brings up potassium ion but it does not refine.


Any tips why this is not working?



Thank you John and Steven,

I have pushed a fix - the update should be available shortly. Amazing 
that this bug has lived so long.


Regards,

Paul.




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Re: [COOT] MacCoot 0.9.8.5 issues

[Paul Emsley]

On 16/11/2022 19:19, Dr. Kevin M Jude wrote:


Hopping onto this thread:

Besides the sugar connectivity, I see that when I Draw > Sequence 
View, the sequence opens in a pop-up window instead of the main window 
and does not show gaps or numbering. This is coot 0.9.8.5 from ccpem 
nightly 20221108 on M1 chip, Mac OS Monterey 12.6.


*From: *Mailing list for users of COOT Crystallographic Software 
 on behalf of Xavier Brazzolotto 


*Date: *Wednesday, November 16, 2022 at 10:04 AM
*To: *COOT@JISCMAIL.AC.UK 
*Subject: *Re: MacCoot 0.9.8.5 issues

H Paul,



  * When I delete a molecule, my Coot/X11 window
« disappears ». It is not closed/killed but somehow
minimized. I can get it back from my dock, but a bit annoying.

Here’s what the console says.

*(set-delete-residue-mode)*

(2) " O5 "/1/chainid="A"/625/FUC,  occ: 1.000 with B-factor:
66.076 element: " O" at (26.959,-34.446,11.593) : 0.132

INFO:: backup file name

coot-backup/_Users_xbrazzolotto_Desktop_Crystallography_20221116_MR37216_MR-CoX_Phenix_MR372016_20221116_refine_3-coot-1.pdb_Wed_Nov_16_18:30:17_2022_modification_11.pdb.gz

*(delete-residue 2 "A" 625 "")*

*(clear-pending-delete-item)*

Pending Picks Cleared

*(delete-residue-by-atom-index 2 4280 1)*

debug:: g.safe_scheme_command() with command
post-manipulation-hook

I have not heard of that before.

The terminal doesn’t seem to report any bug, this is probably related 
to macOS. It's just annoying, it still works, it is not like it 
crashes every time I delete a molecule.


  * When I build sugar chains with the N-linked Glycan module,
they are not building correctly. It looks like it messes
up with the wrong atom for linking.

I am part-way through a fix for this. It is high priority and will
require a new release.

Good to know that it is already known and handled. Will wait for the 
next release.


It may be to restore a previous coot version (without such bugs) by 
downgrading the last update of CCP4i





There are 2  different sequence view widgets. What I susppect you are 
seeing is the earlier sequence view widget that gets used when you have 
insertion code - maybe you are looking at an antibody or some such.


Paul.




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Re: [COOT] MacCoot 0.9.8.5 issues

[Paul Emsley]

On 16/11/2022 17:39, Xavier Brazzolotto wrote:
>
> Hello,
>
> I’ve noticed 2 issues in the recent update of coot (v0.9.8.5 from
> CCP4i) on an Intel mac updated to Ventura (13.0.1). I did not test on
> Linux.
>
>   * When I delete a molecule, my Coot/X11 window « disappears ». It is
> not closed/killed but somehow minimized. I can get it back from my
> dock, but a bit annoying.
>
>
> Here’s what the console says.
>
> *(set-delete-residue-mode)*
>
> (2) " O5 "/1/chainid="A"/625/FUC,  occ: 1.000 with B-factor: 66.076
> element: " O" at (26.959,-34.446,11.593) : 0.132
>
> INFO:: backup file name
> coot-backup/_Users_xbrazzolotto_Desktop_Crystallography_20221116_MR37216_MR-CoX_Phenix_MR372016_20221116_refine_3-coot-1.pdb_Wed_Nov_16_18:30:17_2022_modification_11.pdb.gz
>
> *(delete-residue 2 "A" 625 "")*
>
> *(clear-pending-delete-item)*
>
> Pending Picks Cleared
>
> *(delete-residue-by-atom-index 2 4280 1)*
>
> debug:: g.safe_scheme_command() with command post-manipulation-hook
>
>

I have not heard of that before.


>   * When I build sugar chains with the N-linked Glycan module, they
> are not building correctly. It looks like it messes up with the
> wrong atom for linking.
>
>

I am part-way through a fix for this. It is high priority and will
require a new release.


Paul.





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Re: [COOT] WinCoot 0.9.8.1 EL sequence view doesn't show the whole sequence

[Paul Emsley]

On 15/11/2022 14:26, Mohamed Nasef wrote:

Im working with a 23S rRNA that is 2900 nucleotides long. In sequence view, I 
can only see up to nucleotide number 2245 although the rest of the sequence is 
there. I couldn't find a solution to this issue anywhere in the archive.


Hello Mohamed,

Sadly this is a known issue. X11 won't allow a super-wide canvas and if 
you try you get nothing at all - so, in Coot it's capped.


Which means for the RNA in a ribosome it runs out of space.

There is no solution - well, no solution other than rewriting the 
sequence view (which I've planned, but not scheduled).


Regards,

Paul.



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Re: [COOT] availability of Coot for Mac OSX

[Paul Emsley]

On 09/11/2022 19:25, Rogerio Sotelo wrote:



I have not been able to locate binaries to install Coot, as they 
appear not to be included in Phenix. Some colleagues installed the 
CCP4 platform to get it to work on Mac.


I will appreciate the info about where to obtain Mac OSX Coot binaries,



Sadly I have not been able to keep up with producing Coot binaries.

(Building binaries, writing tutorials and documentation and handling 
enquires is almost another full-time job.)


Coot 0.9.8.x is available in the CCP4 package.

Coot 1 is available via homebrew. (I'm not sure if Phenix has tweaked 
the interface to work with Coot 1.)


Paul.




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Re: [COOT] LINK of glycans

[Paul Emsley]

On 17/10/2022 06:30, Taka wrote:

Dear Coot developers,

I use Coot 0.9.8.4 on macOS 12.0.1 Monterey.
The present program does not generate LINK of glycans, such as GlnNAc-Asn, which was 
added using Modules>Carbohydrate>N-linked Glycan Addition tool, and C1-O6 of 
two glucose monomers.
Excuse me for asking, but I guess this is a bug in ver 0.9.8.4.
I would appreciate it if you could confirm the program.



Dear Taka,

Thanks for your email.

Something is messed up.

I am investigating.

Regards,

Paul.



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Re: [COOT] mouse middle scroll

[Paul Emsley]

On 25/10/2022 03:28, zheng zhou wrote:

Dear Coot experts

My middle mouse scroll did not work on Coot 0.9.8.3 EL. I am using
centos 7. It works on other programs. I did search online, and tried
to add


set_scroll_by_wheel_mouse(1) to my
~/.coot-preferences/coot_preferences.py and restart coot,

But it did not work. Could you help?


Hell Zheng,

Might it be because you have another file in that directory that says

set_scroll_by_wheel_mouse(0)

?

To test if it is the start-up scripts,
$ mv ~/.coot ~/.coot-aside-for-testing
$ mv ~/.coot-preferences ~/.coot-preferences-aside-for-testing

Then start your coot, using the tutorial data, say, and see if the contours 
change.

Regards,

Paul.



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[COOT] Release 0.9.8.5

[Paul Emsley]

We are pleased to release Coot 0.9.8.5

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.8.5.tar.gz

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/

Paul.


  Release 0.9.8.5

  o FEATURE: AlphaFold pLDDT colour scheme.

  o CHANGE:  Don't consider carbonyl oxygens in merge fragments.

  o CHANGE:  Inter-chain links can now be refined. [Keitaro Yamashita]

  o BUG-FIX: Re-enable the picking of hydrogen atoms in 
rotation/translation

 Thank you Taro Yamada.

  o BUG-FIX Fix up interesting_residues_gui(). Fixes problem in 
"Residues with Missing Atoms"

    Reported by EJD.





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Re: [COOT] [EXTERNAL] Re: Bug in coot to change torsion angles?

[Paul Emsley]

On 31/08/2022 01:37, Gong, Zhen wrote:


Hi Paul,

I think it is a bug. I was able to rotation O10 along the C07-N08 
bond, but not the O9. Here is what I got:


Color-by-chain seems normal to me.



Hi Zhen,


My guess is that you are using Torsion General. I don't recall ever 
using that tool in anger (as it were). For this sort of thing, I would 
use Edit Chi Angles, and I suspect that if you edit your restraints 
dictionary as suggested then that will "just work."



Regards,


Paul.

p.s. It is a bug though and I've made a note.



Zhen

*From: *Paul Emsley 
*Date: *Tuesday, August 30, 2022 at 20:25
*To: *Gong, Zhen , COOT@JISCMAIL.AC.UK 


*Subject: *Re: [EXTERNAL] Re: Bug in coot to change torsion angles?

On 31/08/2022 01:17, Gong, Zhen wrote:

Hi Paul,

Thank you very much for your timely reply. There are still some
puzzles for me.

I would like to change some torsion angles of a ligand in coot but
it did not work as what I expected. I was able to play with the
torsion angles formed by C06 C07 N08 O10 but not C06 C07 N08 O09
(shown in the figure below).

One implies the other, it seems to me.

I do not agree. One changes the position of O10, while the other
changes O9. What I would like to do is to manually make the O9 and
O10 in the same plane with aromatic ring if possible. I was able
to rotate O10 along the C07-N08 bond but not 09, which I shall be
able to do in coot?

If I understand correctly what you are saying then that's a bug. 
C06-C07-N08-O09 defines a rotatable bond (C07-N08) about which one 
side of the fragment (the smaller side) is rotated - i.e. you cannot 
move O10 without moving O09 also. That's how it should work. It seems 
that you are saying that that is not how it's working for you.


By the way, I was able to make O9 and O10 in the same plane with
the aromatic ring by adding planar restraint. I would like to know
why I could not rotate O9 along the N08-C07 bond if possible.

Me too. It does seem very curious. Is there a missing bond restraint - 
what happens when you display using colour-by-chain?


Paul.





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Re: [COOT] [EXTERNAL] Re: Bug in coot to change torsion angles?

[Paul Emsley]

On 31/08/2022 01:17, Gong, Zhen wrote:


Hi Paul,

Thank you very much for your timely reply. There are still some 
puzzles for me.


I would like to change some torsion angles of a ligand in coot but it 
did not work as what I expected. I was able to play with the torsion 
angles formed by C06 C07 N08 O10 but not C06 C07 N08 O09 (shown in the 
figure below).


One implies the other, it seems to me.

I do not agree. One changes the position of O10, while the other 
changes O9. What I would like to do is to manually make the O9 and O10 
in the same plane with aromatic ring if possible. I was able to rotate 
O10 along the C07-N08 bond but not 09, which I shall be able to do in 
coot?




If I understand correctly what you are saying then that's a bug. 
C06-C07-N08-O09 defines a rotatable bond (C07-N08) about which one side 
of the fragment (the smaller side) is rotated - i.e. you cannot move O10 
without moving O09 also. That's how it should work. It seems that you 
are saying that that is not how it's working for you.



By the way, I was able to make O9 and O10 in the same plane with the 
aromatic ring by adding planar restraint. I would like to know why I 
could not rotate O9 along the N08-C07 bond if possible.


Me too. It does seem very curious. Is there a missing bond restraint - 
what happens when you display using colour-by-chain?


Paul.




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Re: [COOT] Bug in coot to change torsion angles?

[Paul Emsley]

On 30/08/2022 22:26, Gong, Zhen wrote:


Dear Coot developers and users,

I would like to change some torsion angles of a ligand in coot but it 
did not work as what I expected. I was able to play with the torsion 
angles formed by C06 C07 N08 O10 but not C06 C07 N08 O09 (shown in the 
figure below).




One implies the other, it seems to me.




The restraint file for the torsion angle (C06 C07 N08 O10) is defined 
quite well: LIG CONST_23 O09 N08 C07 C06 -5.58, which is close to 
zero. Therefore, O9, O10 N08 should be more or less in the same plane 
with the benzene ring.




I agree.

By default Coot does not refine torsion angles.

Also torsions named "CONST" are not refined.

You can turn on torsion angle refinement in the R/RC dialog


If I click on the ligand with “real space refinement”, it should make 
the O9, O10 N08 more or less in the same plane with the benzene ring. 
However, coot did not do it.


If you don't have plane restraints for the nitro and ring atoms then 
coot doesn't know (hasn't been told) to keep them planar. All you've 
done is said to Coot "here's a torsion angle, don't use it.|



The corollary of the above is to turn on torsion angle refinement and 
rename the torsion var_23.


You could also add O09 to the ring plane restraint with perhaps double 
or triple the esd.



Paul.




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Re: [COOT] Minor request selection status line

[Paul Emsley]

On 07/08/2022 21:56, Bernhard Rupp wrote:


Dear Coot Developers,

I have a minor suggestion: I view many open Marina Bay coots at the 
same time, and it would be helpful


if the selection status line at the bottom would, instead of the 
somewhat uninformative (mol. no: x), display


the name of the current selected molecule as used in the display manager.



OK, done.

0b8d3598de16d52563c18071da354dc8d259fc28

Paul.




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Re: [COOT] Making bond

[Paul Emsley]

On 09/08/2022 02:40, Cryo EM wrote:

Hi everyone,

In one my PDBs, I see that there is a linkage break in 
ribonucleotides. Specifically one of the phospodiester bond seems to 
be broken and thus O3' needs to be bonded to P atom of next 
nucleotide. What is the easiest way to do this in coot ? Or any other 
software?
I tried "make link" option in coot but it seems it just created link 
in PDB and not bond?



A link should not be needed if one nucleotide comes immediately after 
the other one in the same chain.


It might be that they are so far apart to begin with that Coot doesn't 
consider them bonded. Use Ctrl arrow-keys to move the O3' to within 3A 
of the P and give a quick sphere refine to test.


Paul.



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Re: [COOT] Missing Restrains for standard amino acids

[Paul Emsley]

On 08/08/2022 16:04, Kenneth Satyshur wrote:
You can tell phenix where to find coot. Point coot to the ccp4 
version, which has the libs. The stand alone version may not have the 
link to the lib that is maintained by ccp4.




I thought that it was the other way around! :-)


Use the environment variable COOT_REFMAC_LIB_DIR to tell Coot where it 
should look for the monomer library.



Paul.




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Re: [COOT] How to fix outliers in Ramachandran plot and save coordinate as new PDB

[Paul Emsley]

Sorry, this somehow dropped off my radar (maybe because I accidentally 
left it as read).



On 15/07/2022 12:34, Gundala Viswanath wrote:

Hi,

Notice that it has high outliers content. I want to manually drag those
red dots into some part of the region. Eventually, I expect it to be 
reflected

in the coordinates so that I can save it as a new PDB file.





I thought about adding such a tool. In retrospect I think it's better 
for Coot to refine everything at once and let it choose the target 
phi,psi values.



You can turn on the Ramachandran plot refinement

R/RC -> Ramachandran Restraints [tick]

You can alter the the weight with

More Control... -> Rama restraints weight

High Ramachandran plot weights cause stability issues in the minimizer 
(sad to say).


Then you can click on each of the dots and use tandem refine to examine 
and improve the Ramachandran plot( for those few residues).


Coot 1 allows you to dynamically see the effects on the weight changes 
on the Ramachandran plot.



Paul.



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Re: [COOT] About refinement

[Paul Emsley]

On 21/07/2022 10:49, Filomeno Sanchez Rodriguez wrote:

I finally managed to write a script to do this, I will leave it here for future 
reference in case someone has the same question:

  # Auto-correct nomenclature errors
  set_nomenclature_errors_on_read("auto-correct")
  # Read in the PDB model
  mol_id = read_pdb('input_model.pdb')
  # Do not ask about accept/reject refinement
  set_refinement_immediate_replacement(1)
  # Refine zone -> refine_zone(mol_id, ch_id, res_start, res_end, altloc)
  refine_zone(mol_id, 'A', 44, 64, '')
  # Accept refinement
  accept_regularizement()
  # Write refined model
  write_pdb_file(mol_id, 'refined_model.pdb')
  # Exit
  coot_real_exit(0)

The script can then be executed with:
 coot --no-graphics --map input.map --script script.py



You can add the reading of the map to the script if you like using

read_ccp4_map("input.map", 0)


accept_moving_atoms() is now the preferred function name.


refine_residues(imol, residue_spec_list) is the modern interface to 
refinement, where a residue spec is [chain_id, res_no, ins_code]



If you want to use coot's real space refinement without using a script, 
you can use coot-mini-rsr.



Paul.



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Re: [COOT] Troubleshoot for Installing Coot 1 (GTK-+-3-based) From Scratch

[Paul Emsley]

On 06/07/2022 22:57, Rajiv Singh wrote:

Dear Paul and the coot community

I am trying to compile coot-1 on Ubuntu 20.04 using Coot 1 (GTK-+-3-based) From 
Scratch script build-it-3-3
This started by creating auto-build directory and downloading several 
dependencies and then It stopped with this error  --see below



AUTOBUILD_BUILD is /home/rajiv/autobuild/building
AUTOBUILD_SOURCES is /home/rajiv/autobuild/building/sources
INFO:: redirecting std output to 
/home/rajiv/public_html/build-logs/Linux-rajiv-vm/build.log



What you posted was (just) the terminal output. You can see from the 
above that the real output goes here:


/home/rajiv/public_html/build-logs/Linux-rajiv-vm/build.log

See the compiler-dependent sub-directory there that contains the build logs for 
each component.

I wouldn't be surprised if the problem is due to Python or one of its modules 
(wretched Python).

Paul.



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