Re: [COOT] Phenix/Coot issue

[Paul Emsley]

On 30/04/2022 20:13, Xavier Brazzolotto wrote:

I’ve did some cleanup. Installed Phenix and CCP4-8.0 many times.
I’ve removed my Homebrew to remove all traces of my tests with Coot 
v1-pre.


I did some Phenixbb archeology and a similar issue has been reported 
in 2014 and probably solved by changing the path of Coot.


Here I’ve changed multiple times using 
/Applications/CCP4-8.0/Coot.app or 
/Applications/CCP4-8.0/Coot.app/Contents/MacOS/coot
In this case Coot starts but does not automatically open model and 
maps and in find myself in a folder not related to the Phenix projet. 
No « connected to Phenix » appears.
If I load a model and maps, then RSR is functional meaning that Coot 
has has loaded its restraints library for the residues but no ligand 
cif is injected…


If I change the path to /Applications/CCP4-8.0/bin/coot or 
/Applications/CCP4-8.0/coot_py2/bin/coot, Coot starts with the 
« connected to Phenix » tab.
Coot automatically opens model and maps and works in the Phenix 
project folder. But the residues restraints library is not loaded, RSR 
does not work (only the RSR of an injected ligand works)…



My guess is that there is (or was) an issue with the packaging of Coot 
in CCP4 8.0. I just tried to start coot from there now and it seems to 
be resolved.


I don't know about how Phenix injects Coot with restraint dictionaries 
(curious to learn though).


Paul.



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Re: [COOT] Phenix/Coot issue

[Paul Emsley]

On 28/04/2022 18:35, Georg Mlynek wrote:


Dear Xavier, for the nomenclature error there is this fix.


The "fix" is to correct the nomenclature errors.


add this to your startup-script

set_nomenclature_errors_on_read("ignore")



This tells Coot not to tell you that you have nomenclature errors. If 
you then go on to change rotamers, then you could get an erroneous 
structure (atoms in the wrong place, not just with the wrong names).



Paul




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Re: [COOT] Phenix/Coot issue

[Xavier Brazzolotto]

I’ve did some cleanup. Installed Phenix and CCP4-8.0 many times.
I’ve removed my Homebrew to remove all traces of my tests with Coot v1-pre.

I did some Phenixbb archeology and a similar issue has been reported in 2014 
and probably solved by changing the path of Coot.

Here I’ve changed multiple times using /Applications/CCP4-8.0/Coot.app or 
/Applications/CCP4-8.0/Coot.app/Contents/MacOS/coot
In this case Coot starts but does not automatically open model and maps and in 
find myself in a folder not related to the Phenix projet. No « connected to 
Phenix » appears.
If I load a model and maps, then RSR is functional meaning that Coot has has 
loaded its restraints library for the residues but no ligand cif is injected…

If I change the path to /Applications/CCP4-8.0/bin/coot or 
/Applications/CCP4-8.0/coot_py2/bin/coot, Coot starts with the « connected to 
Phenix » tab.
Coot automatically opens model and maps and works in the Phenix project folder. 
But the residues restraints library is not loaded, RSR does not work (only the 
RSR of an injected ligand works)…

The only solution I’ve found is to get back my old CCP4-7.1 folder containing 
Coot 0.9.6.
Declaring the new path /Applications/CCP4-7.1/bin/coot allowed me to get back a 
functional Coot linked to Phenix. Very strange….



> Le 28 avr. 2022 à 19:47, Xavier Brazzolotto  a écrit :
> 
> For additional informations when launching Coot from the terminal I get these 
> messages at startup. Wonder if the presence of 2 data is OK ?
> 
> INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/
> There are 244 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/list/mon_lib_list.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/a/ALA.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/a/ASP.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/a/ASN.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/c/CYS.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/g/GLN.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/g/GLY.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/g/GLU.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/p/PHE.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/h/HIS.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/i/ILE.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/l/LYS.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/l/LEU.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/m/MET.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/m/MSE.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/p/PRO.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/a/ARG.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/s/SER.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/t/THR.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/v/VAL.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/t/TRP.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/t/TYR.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/p/PO4.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/s/SO4.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/g/GOL.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/c/CIT.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/e/EDO.cif
> There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/a/A.cif
> There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/c/C.cif
> There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/g/G.cif
> There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/u/U.cif
> There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/d/DA.cif
> There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/d/DC.cif
> There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/d/DG.cif
> There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/d/DT.cif
> There are 2 data in 
> /Applications/ccp4-8.0/coot_py2/lib/data/monomers/h/HOH.cif
> There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/n/NA.cif
> Spacegroup: P 1
> (filter-fileselection-filenames-state)
> (get-active-map-drag-flag)
> (use-graphics-interface-state)
> INFO:: coot.py imported
> ...
> 
> 
>> Le 28 avr. 2022 à 19:35, Georg Mlynek > > a écrit :
>> 

Re: [COOT] Phenix/Coot issue

[Georg Mlynek]

Dear Xavier, for the nomenclature error there is this fix.

add this to your startup-script

set_nomenclature_errors_on_read("ignore")


I would be also interested to answer the first issue.

Br, Georg.


Am 28.04.2022 um 19:22 schrieb Xavier Brazzolotto:

Dear Phenix and Coot users and developers

I've recently observed a kind of conflict between Phenix and Coot.

I am using Phenix v1.20.1-4487 and Coot 0.9.8.1 from thee CCP4 8.0 
suite under macOS Monterey (v12.3.1).


If I launch Coot through Phenix via the « Open in Coot » tab (the path 
to Coot has been defined in Phenix preferences), Coot opens correctly 
and displays the structure with the « Connected to Phenix tab". 
However if I wand to do some RSR then, I get this error message.



In parallel if I use Coot by itself (launched through the terminal), 
RSR works well… but upon opening Coot states that there is some 
"Nomenclature errors ».



I wonder if there would be some conflict between residue libraries 
between Phenix and Coot ?


Just to leet you know I’ve also recently tried to install/comlplie the 
Coot v1 pre-version to have a loot at it and I do also have libccp4 
installed in my Homebrew. Maybe everything comes from that ?


Xavier





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Re: [COOT] Phenix/Coot issue

[Xavier Brazzolotto]

For additional informations when launching Coot from the terminal I get these 
messages at startup. Wonder if the presence of 2 data is OK ?

INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: 
/Applications/ccp4-8.0/coot_py2/lib/data/monomers/
There are 244 data in 
/Applications/ccp4-8.0/coot_py2/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/a/ALA.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/a/ASP.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/a/ASN.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/c/CYS.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/g/GLN.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/g/GLY.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/g/GLU.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/p/PHE.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/h/HIS.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/i/ILE.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/l/LYS.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/l/LEU.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/m/MET.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/m/MSE.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/p/PRO.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/a/ARG.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/s/SER.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/t/THR.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/v/VAL.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/t/TRP.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/t/TYR.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/p/PO4.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/s/SO4.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/g/GOL.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/c/CIT.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/e/EDO.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/a/A.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/c/C.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/g/G.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/u/U.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/d/DA.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/d/DC.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/d/DG.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/d/DT.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/h/HOH.cif
There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/n/NA.cif
Spacegroup: P 1
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
INFO:: coot.py imported
...


> Le 28 avr. 2022 à 19:35, Georg Mlynek  a écrit :
> 
> Dear Xavier, for the nomenclature error there is this fix.
> 
> add this to your startup-script
> 
> set_nomenclature_errors_on_read("ignore")
> 
> 
> I would be also interested to answer the first issue.
> 
> Br, Georg.
> 
> 
> 
> Am 28.04.2022 um 19:22 schrieb Xavier Brazzolotto:
>> Dear Phenix and Coot users and developers
>> 
>> I've recently observed a kind of conflict between Phenix and Coot.
>> 
>> I am using Phenix v1.20.1-4487 and Coot 0.9.8.1 from thee CCP4 8.0 suite 
>> under macOS Monterey (v12.3.1).
>> 
>> If I launch Coot through Phenix via the « Open in Coot » tab (the path to 
>> Coot has been defined in Phenix preferences), Coot opens correctly and 
>> displays the structure with the « Connected to Phenix tab". However if I 
>> wand to do some RSR then, I get this error message.
>> 
>> 
>> 
>> In parallel if I use Coot by itself (launched through the terminal), RSR 
>> works well… but upon opening Coot states that there is some "Nomenclature 
>> errors ».
>> 
>> 
>> 
>> I wonder if there would be some conflict between residue libraries between 
>> Phenix and Coot ?
>> 
>> Just to leet you know I’ve also recently tried to install/comlplie the Coot 
>> v1 pre-version to have a loot at it and I do also have libccp4 installed in 
>> my Homebrew. Maybe everything comes from that ?
>> 
>> Xavier
>> 
>> 
>> 
>> To unsubscribe from the COOT list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 
>>