[COOT] molecule rubber banding not working in 8.1

[Kenneth Satyshur]

After using 7.1 for a while, it was easy to 'real space refi zone' a amino 
acid. Pull on it and it will drag everything

else with it. On 8.1 when I try this, it just rips an atom away from the 
residue and does not move the whole residue.

There must be a parameter that is not set right. How do I make the 'rubber 
banding' work again. It is not useful in

its present form.

thanks



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

University of Wisconsin-Madison

Madison, Wisconsin, 53706

608-215-5207

[COOT] scroll wheel not working in 0.8.8

[Kenneth Satyshur]

The density will not scroll in 0.8.8 when using the scroll wheel on my mouse.

In v 0.7.1 it works find. How do I fix this?

Linux dingo 2.6.32-696.el6.x86_64 #1 SMP Tue Feb 21 00:53:17 EST 2017 x86_64 
x86_64 x86_64 GNU/Linux
 thanks

kas




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

Senior Scientist, Depts. Bacteriology, Bio Molecular Chemistry,

Neuroscience, Oncology, and the Carbone Cancer Center

University of Wisconsin-Madison

Madison, Wisconsin, 53706

608-215-5207

[COOT] Water do not show up at all.

[Kenneth Satyshur]

In 0.7.1 waters would display as a 3d cross. Symmetry related waters would not 
be represented at all.

Now in 0.8.8 none of the waters show up. No cross, no star. They can be 
selected and labeled, but not represented. Am i not selecting the correct 
functions?

thanks

kas

Linux dingo 2.6.32-696.el6.x86_64 #1 SMP Tue Feb 21 00:53:17 EST 2017 x86_64 
x86_64 x86_64 GNU/Linux



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

Senior Scientist, Depts. Bacteriology, Bio Molecular Chemistry,

Neuroscience, Oncology, and the Carbone Cancer Center

University of Wisconsin-Madison

Madison, Wisconsin, 53706

608-215-5207

Re: [COOT] Water do not show up at all.

[Kenneth Satyshur]

Errors go away when i delete the .coot-preferences hidden directory in my home 
directory.

Very strange. Now I have to set my preferences again. Not a problem.

kas



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

Senior Scientist, Depts. Bacteriology, Bio Molecular Chemistry,

Neuroscience, Oncology, and the Carbone Cancer Center

University of Wisconsin-Madison

Madison, Wisconsin, 53706

608-215-5207


From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Kenneth Satyshur 
Sent: Wednesday, March 22, 2017 4:50:41 PM
To: COOT@JISCMAIL.AC.UK
Subject: Water do not show up at all.


In 0.7.1 waters would display as a 3d cross. Symmetry related waters would not 
be represented at all.

Now in 0.8.8 none of the waters show up. No cross, no star. They can be 
selected and labeled, but not represented. Am i not selecting the correct 
functions?

thanks

kas

Linux dingo 2.6.32-696.el6.x86_64 #1 SMP Tue Feb 21 00:53:17 EST 2017 x86_64 
x86_64 x86_64 GNU/Linux



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

Senior Scientist, Depts. Bacteriology, Bio Molecular Chemistry,

Neuroscience, Oncology, and the Carbone Cancer Center

University of Wisconsin-Madison

Madison, Wisconsin, 53706

608-215-5207

Re: [COOT] turn off auto recentring?

[Kenneth Satyshur]

Mee too. But I can't read the reply because I don't know how to read a .scm 
file. Can you send as a pdf?

thanks



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

Senior Scientist,

Depts. Bacteriology, Bio Molecular Chemistry,

Neuroscience, Oncology, and the Carbone Cancer Center

University of Wisconsin-Madison

Madison, Wisconsin, 53706

608-215-5207


From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Paul Emsley 
Sent: Wednesday, September 6, 2017 11:49:36 AM
To: COOT@JISCMAIL.AC.UK
Subject: Re: turn off auto recentring?

On 06/09/2017 16:03, Emilia C. Arturo (Emily) wrote:
> Hello.
>
> I wonder whether there is a way to turn off recentring when moving along from 
> residue to residue within a
> single molecule? I'd like for Coot to not recentre (or ... recenter :-)) 
> automatically so that I can see
> where the breaks in the backbone occur relative to the entire structure or 
> relative to where the next built
> piece occurs. Understanding where the discontinuities in the model occur is 
> difficult to do when centring on
> the current atom is done by default once I've navigated there with the space 
> bar.

Hello Emily,

Perhaps you want to see the residue atom label advance as you step through the 
residues of a chain? Here are
some buttons in a dialog that does that - put this script in you 
$HOME/.coot-preferences directory.

Regards,

Paul.

Re: [COOT] navigating back to the ligand

[Kenneth Satyshur]

Thanks, this is great. Very helpful, but I tried to open the .scm in GIMP and 
it says unknown file type.

kas



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

Senior Scientist,

Depts. Bacteriology, Bio Molecular Chemistry,

Neuroscience, Oncology, and the Carbone Cancer Center

University of Wisconsin-Madison

Madison, Wisconsin, 53706

608-215-5207


From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Paul Emsley 
Sent: Wednesday, September 6, 2017 1:25:40 PM
To: COOT@JISCMAIL.AC.UK
Subject: Re: navigating back to the ligand

On 06/09/2017 18:22, Paul Emsley wrote:

>
>  Similar case for
>> ligands...the ligand button short cut is pretty good, but if I navigate off 
>> the ligand to look at
>> surroundings, the next click of the heteroatom /ligand center button will 
>> likely have reset to the top of
>> the list, and with cofactors in all copies that can be 16 clicks until I get 
>> back to through the cycle.
>
> :-) Yes.  This could be better.
>
> You could probably make a script for "Quick View Save" and "Go To Last View" 
> - I imagine that would do most
> of what you want.
>

Script attached.  Put it in your ~/.coot-preferences directory.

When you centre on a ligand to which you think that you might want to return, 
press Shift L.
Shift U will return you to the last saved view.  All the views can be recalled 
in the Views Panel:
Extensions -> Views -> Views Panel...

Paul.

Re: [COOT] navigating back to the ligand

[Kenneth Satyshur]

ok sorry. I should have investigated a little bit more. Great scripts.

kas



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

Senior Scientist,

Depts. Bacteriology, Bio Molecular Chemistry,

Neuroscience, Oncology, and the Carbone Cancer Center

University of Wisconsin-Madison

Madison, Wisconsin, 53706

608-215-5207


From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Paul Emsley 
Sent: Wednesday, September 6, 2017 4:30:29 PM
To: COOT@JISCMAIL.AC.UK
Subject: Re: navigating back to the ligand

On 06/09/2017 20:14, Kenneth Satyshur wrote:
> Thanks, this is great. Very helpful, but I tried to open the .scm in GIMP and 
> it says unknown file type.
>

If this is a joke, I don't get it.

If not, then I am somewhat bemused - the script I sent was for Coot, not the 
GIMP.

Regards,

Paul.

Re: [COOT] correct protonation state in His side chain

[Kenneth Satyshur]

In fitting electron density of a His residue, the orientation should depend on 
the hydrogen bonding that can be assigned to the proton(s) on the His. If there 
is clear H bond acceptor, like a carboxylate, then it is likely that the proton 
is on this N in the ring and this is the correct orientation. However, H bond 
is not always clear, especially if the His is exposed to solvent, which is 
usually water and not really easy to see because of disorder. Then the 
orientation could be 0 or 180 deg, and probably a mix of the two. Note that 
means the nitrogens can be on all 4 ring atoms of the 5 membered ring.  And, as 
explained in one of the references in this thread, both nitrogens can have a 
proton. This is because His is the only amino acid with a pK near 7. And it 
proves very useful in chelation as well as enzymatic reactions. It's the 
chemistry.

kas



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

Senior Scientist,

Depts. Bacteriology, Bio Molecular Chemistry,

Neuroscience, Oncology, Carbone Cancer Center,

and the School of Pharmacy

University of Wisconsin-Madison

Madison, Wisconsin, 53706

608-215-5207


From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Xiao Lei 
Sent: Wednesday, September 13, 2017 2:38:59 AM
To: COOT@JISCMAIL.AC.UK
Subject: Re: correct protonation state in His side chain

Dear Tim，

Thank you very much for the suggestions! Flip did the work 😀  Thank you all.

On Wed, Sep 13, 2017 at 12:34 AM, Tim Gruene 
mailto:tim.gru...@psi.ch>> wrote:
Dear Xiao Lei, hi Paul,

unless you have data from neutron diffraction, isn't this simply flipping
around the imidazole head by 180 degrees? That's something Coot can do.

Best regards,
Tim



On Wednesday, September 13, 2017 7:40:11 AM CEST Paul Emsley wrote:
> I don't think that that's what Xiao Lei means.
>
> I think that Xiao Lei refers to the problem of assignment of rotamer,
> tautomer and ionisation state described here:
>
> https://www.chemcomp.com/journal/proton.htm
>
> Coot can't do that
>
> (yet).
>
> Regards,
>
> Paul.
>
> On 13/09/2017 02:27, Murpholino Peligro wrote:
> > Not sure if coot, but maybe molprobity can help.
> > http://molprobity.biochem.duke.edu/help/reduce_guide/reduce_guide.html
> >
> > 2017-09-12 19:10 GMT-05:00 Xiao Lei 
> > mailto:xiaolei...@gmail.com>
>>:
> > Dear All,
> >
> > Can I correct protonation state in His side chain in Coot?
--
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
Principal Investigator
Biology and Chemistry
OFLC/104
CH-5232 Villigen PSI

Phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A

Re: [COOT] set Coot download folder path in preferences

[Kenneth Satyshur]

coot 0.8.9 crashes when reading cif file. I tried reading my G4P.cif file and 
coot crashed with the following output:


** (coot-bin:167556): WARNING **: Widget not found: 
cif_dictionary_file_selector_create_molecule_checkbutton
/home/xray/ccp4/ccp4-7.0/ccp4-7.0/bin/coot: line 288: 167556 Segmentation fault 
 (core dumped) $coot_bin "$@"
catching the crash log:
Gtk-Message: Failed to load module "canberra-gtk-module"
Gtk-Message: Failed to load module "pk-gtk-module"
coot-exe: "/home/xray/ccp4/ccp4-7.0/ccp4-7.0/libexec/coot-bin"
coot-version:
/home/xray/ccp4/ccp4-7.0/ccp4-7.0/libexec/coot-bin
platform:
/bin/uname
core: #f
No core file found.  No debugging


Appears to crash for reading any cif restraints file.

kas


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

Senior Scientist,

Depts. Bacteriology, Bio Molecular Chemistry,

Neuroscience, Oncology, Carbone Cancer Center,

and the School of Pharmacy

University of Wisconsin-Madison

Madison, Wisconsin, 53706

608-215-5207


From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Paul Emsley 
Sent: Wednesday, March 21, 2018 8:42:49 PM
To: COOT@JISCMAIL.AC.UK
Subject: Re: set Coot download folder path in preferences

On 19/03/2018 17:34, Xiao Lei wrote:
>
> I would like to change the default Coot download folder path (let's say after 
> fetch a pdb, Coot saved the
> pdb in the default download folder). I looked into the Edit--> Preferences in 
> Coot and I could not find a
> place to change the PATH.  How could I find this option in Coot?
>

You could create a link from your chosen directory to coot-download in the 
current directory before coot
creates the directory.

Alternatively, you could use the dirty hack attached - edit it to set the 
directory that you choose and put
this script in your ~/.coot-preferences directory.

Paul.

Re: [COOT] Carbohydrate torsion

[Kenneth Satyshur]

Put structure in modeling program like Maestro or Sybyl, twist, minimize, save, 
generate restraints,  refine.

Get Outlook for Android


From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Paul Emsley 
Sent: Thursday, May 9, 2019 7:21:01 AM
To: COOT@JISCMAIL.AC.UK
Subject: Re: Carbohydrate torsion

On 08/05/2019 12:17, Bernhard Rupp wrote:
Dear Fellow Cootsters,

I am trying to use the flexibility of glycans as validation of a docking model 
(no density available)
by torsioning the glycans into conformations where they do not interfere/clash 
with the models.


OK, but from that description it seems better to me to do a glyco tree 
regularization.


It seems ‘general torsion’ works only on bona fide amino acid torsions and not 
in a strict ‘general’ sense?


That shouldn't be the case.  "Torsion general" least sophisticated way of 
moving atoms by manipulation of torsion angles. FWIW, I'd prefer, if possible, 
to use Chi Angle manipulation or Multi-residue torsion.


I don't use WinCoot, so I don't know the status of these tools.

How can I do such arbitrary torsions in wincoot? For now, I can do it in ICM.



Fighting talk  :-)


Paul.




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



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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1

Re: [COOT] Carbohydrate torsion

[Kenneth Satyshur]

Rinse, and repeat.

Get Outlook for Android<https://aka.ms/ghei36>


From: Kenneth Satyshur
Sent: Thursday, May 9, 2019 8:06:45 AM
To: Paul Emsley; COOT@JISCMAIL.AC.UK
Subject: Re: Carbohydrate torsion

Put structure in modeling program like Maestro or Sybyl, twist, minimize, save, 
generate restraints,  refine.

Get Outlook for Android<https://aka.ms/ghei36>


From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Paul Emsley 
Sent: Thursday, May 9, 2019 7:21:01 AM
To: COOT@JISCMAIL.AC.UK
Subject: Re: Carbohydrate torsion

On 08/05/2019 12:17, Bernhard Rupp wrote:
Dear Fellow Cootsters,

I am trying to use the flexibility of glycans as validation of a docking model 
(no density available)
by torsioning the glycans into conformations where they do not interfere/clash 
with the models.


OK, but from that description it seems better to me to do a glyco tree 
regularization.


It seems ‘general torsion’ works only on bona fide amino acid torsions and not 
in a strict ‘general’ sense?


That shouldn't be the case.  "Torsion general" least sophisticated way of 
moving atoms by manipulation of torsion angles. FWIW, I'd prefer, if possible, 
to use Chi Angle manipulation or Multi-residue torsion.


I don't use WinCoot, so I don't know the status of these tools.

How can I do such arbitrary torsions in wincoot? For now, I can do it in ICM.



Fighting talk  :-)


Paul.




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



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

Re: [COOT] Carbohydrate torsion

[Kenneth Satyshur]

Here is a good website for ring pucker of sugars, as investigated by 
Sundaralingam et.al.


https://x3dna.org/highlights/two-slightly-different-definitions-of-sugar-pucker

3DNA Homepage -- Nucleic Acid 
Structures<https://x3dna.org/highlights/two-slightly-different-definitions-of-sugar-pucker>
x3dna.org
Homepage of the 3DNA suite of software programs for the analysis, rebuilding 
and visualization of 3-dimensional nucleic acid structures




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

Senior Scientist,

Depts. Bacteriology, Bio Molecular Chemistry,

Neuroscience, Oncology, Carbone Cancer Center,

and the School of Pharmacy

University of Wisconsin-Madison

Madison, Wisconsin, 53706

608-215-5207


From: Bernhard Rupp 
Sent: Thursday, May 9, 2019 9:14:07 AM
To: Kenneth Satyshur; COOT@JISCMAIL.AC.UK
Subject: RE: Carbohydrate torsion


Just a note to remember: This is a modelling job – no density and if a refined 
glycan tree conformation would be what is really there, we also

would see them in structures one would guess…. I envision this more to see 
whether the glycans are in the way (and to what degree I can bend them away).

I prefer the fuzzball image, some sort of a ‘volume of possible presence’….



I think this is becoming more and more important but still a long way to go….



Thanks!



Best, BR



From: Mailing list for users of COOT Crystallographic Software 
 On Behalf Of Kenneth Satyshur
Sent: Thursday, May 9, 2019 15:07
To: COOT@JISCMAIL.AC.UK
Subject: Re: Carbohydrate torsion



Put structure in modeling program like Maestro or Sybyl, twist, minimize, save, 
generate restraints,  refine.

Get Outlook for Android<https://aka.ms/ghei36>





From: Mailing list for users of COOT Crystallographic Software 
mailto:COOT@JISCMAIL.AC.UK>> on behalf of Paul Emsley 
mailto:pems...@mrc-lmb.cam.ac.uk>>
Sent: Thursday, May 9, 2019 7:21:01 AM
To: COOT@JISCMAIL.AC.UK<mailto:COOT@JISCMAIL.AC.UK>
Subject: Re: Carbohydrate torsion



On 08/05/2019 12:17, Bernhard Rupp wrote:

Dear Fellow Cootsters,



I am trying to use the flexibility of glycans as validation of a docking model 
(no density available)

by torsioning the glycans into conformations where they do not interfere/clash 
with the models.



OK, but from that description it seems better to me to do a glyco tree 
regularization.





It seems ‘general torsion’ works only on bona fide amino acid torsions and not 
in a strict ‘general’ sense?



That shouldn't be the case.  "Torsion general" least sophisticated way of 
moving atoms by manipulation of torsion angles. FWIW, I'd prefer, if possible, 
to use Chi Angle manipulation or Multi-residue torsion.



I don't use WinCoot, so I don't know the status of these tools.



How can I do such arbitrary torsions in wincoot? For now, I can do it in ICM.





Fighting talk  :-)



Paul.







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





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[COOT] Coot .9 pre does not display map in stereo

[Kenneth Satyshur]

V 0.9 Pre drops the map out of display when going from mono to stereo. This 
does not happen in 0.8 V. I have enclosed the output of coot from the run in 
stereo.
thanks
kas



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

Senior Scientist,

Department of Bacteriology: College of Ag and Life Sciences;

Departments of Bio Molecular Chemistry,

Neuroscience, Oncology, and Carbone Cancer Center:

School of Medicine and Public Health;

and the School of Pharmacy

University of Wisconsin-Madison

Madison, Wisconsin, 53706

608-215-5207



To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
(coot-bin:27193): GLib-GObject-WARNING **: g_object_set_valist: object class 
'GtkSettings' has no property named 'gtk-application-prefer-dark-theme'
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: 
/home/xray/ccp4/ccp4-7.0/lib/data/monomers/
There are 153 data in 
/home/xray/ccp4/ccp4-7.0/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/a/ALA.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/a/ASP.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/a/ASN.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/c/CYS.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/g/GLN.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/g/GLY.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/g/GLU.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/p/PHE.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/h/HIS.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/i/ILE.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/l/LYS.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/l/LEU.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/m/MET.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/m/MSE.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/p/PRO.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/a/ARG.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/s/SER.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/t/THR.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/v/VAL.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/t/TRP.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/t/TYR.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/p/PO4.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/s/SO4.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/g/GOL.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/c/CIT.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/e/EDO.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/a/A.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/c/C.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/g/G.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/u/U.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/d/DA.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/d/DC.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/d/DG.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/d/DT.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/h/HOH.cif
There are 2 data in /home/xray/ccp4/ccp4-7.0/lib/data/monomers/n/NA.cif
INFO:: Reading coordinate file: 
/home/CryoEM/ccpEM/ccpem-1.4.1/share/coot/standard-residues.pdb
 PDBINFO:: file /home/CryoEM/ccpEM/ccpem-1.4.1/share/coot/standard-residues.pdb 
has been read.
Spacegroup: P 1
initalize graphics molecules...done.
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
INFO:: coot.py imported

** (coot-bin:27193): WARNING **: Trying to register gtype 'GMountMountFlags' as 
enum when in fact it is of type 'GFlags'

** (coot-bin:27193): WARNING **: Trying to register gtype 'GDriveStartFlags' as 
enum when in fact it is of type 'GFlags'

** (coot-bin:27193): WARNING **: Trying to register gtype 'GSocketMsgFlags' as 
enum when in fact it is of type 'GFlags'
INFO:: coot_python initialized
Running python script 
/home/CryoEM/ccpEM/ccpem-1.4.1/lib/python2.7/site-packages/coot/coot_load_modules.py
Good Afternoon Person with no name, Welcome to Coot version 0.9-pre
(set-display-intro-string "Good Afternoon Person with no name, Welcome to Coot 
version 0.9-pre")
Coot Python Scripting GUI code found and loaded.
Coot Python Scripting GUI code found and loaded.
(use-graphics-interface-state)
Running python script /home/satyshur/.coot-preferences/coot_toolbuttons.py
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-grap

[COOT] Where to find coot 0.9 and demos.

[Kenneth Satyshur]

Thanks Paul for your tireless work on improving coot. It is a real gem of a 
graphics program!

I went to your web site and I see 0.8.9.2 prerelease. Is there another place to 
get coot 0.9? I know that ccpem has 0.9 in it and this is the one I am using on 
Linux RHEL7. Works great (Except maps disappear when going into stereo). I have 
the 209 May YouTube of your demo of 0.9 and in there you use several demo 
scripts, but I cannot find them either. Does anyone know another source? They 
are

demo-box-of-buttons.scm
keyboard-mutate.scm
gui-test-mol-try.scm

etc.

thanks
kas



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

Senior Scientist,

Department of Bacteriology: College of Ag and Life Sciences;

Departments of Bio Molecular Chemistry,

Neuroscience, Oncology, and Carbone Cancer Center:

School of Medicine and Public Health;

and the School of Pharmacy

University of Wisconsin-Madison

Madison, Wisconsin, 53706

608-215-5207



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Re: [COOT] Where to find coot 0.9 and demos.

[Kenneth Satyshur]

There is always a plan B. Yes

set_display_lists_for_maps(0)

does work, but not in startup.py. One only needs to start coot, display map, 
and open scripting and enter the command above. Then the map will NOT disappear 
when going into stereo. Works fine.
thanks
kas



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

Senior Scientist,

Department of Bacteriology: College of Ag and Life Sciences;

Departments of Bio Molecular Chemistry,

Neuroscience, Oncology, and Carbone Cancer Center:

School of Medicine and Public Health;

and the School of Pharmacy

University of Wisconsin-Madison

Madison, Wisconsin, 53706

608-215-5207


From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Kenneth Satyshur 
<302c79f8ddd1-dmarc-requ...@jiscmail.ac.uk>
Sent: Friday, April 3, 2020 6:18 PM
To: COOT@JISCMAIL.AC.UK 
Subject: Re: Where to find coot 0.9 and demos.

Thanks Paul for the info on 0.9 coot. I will try to recompile it.

However,
I still get maps to disappear in coot 0.9 pre from ccpem. This does not happen 
in coot 0.8.
I implemented the solution you suggested to make and entry into startup.py 
under ~/.coot-preferences

set_display_lists_for_maps(0)

but it does not work. The map still disappears when going to 3D stereo. I am 
using Centos/RHEL8.1. but everything else works, like ccp4 and pymol and 
chimera in 3D stereo. I took a screenshot of the coot window while in stereo 
and included it. Centos8 uses the Gnome display manager to do stereo, but 
because the developers are writing code for VR, stereo applies to the whole 
desktop and not just the window. In Mate desktop in centos 7.7, the stereo is 
in a window, i.e. only called by the terminal that the program is launched. VR 
requires the use of 'Composite' for X11 windowing, so that the whole desktop 
can be sent to VR headset. In Mate and 7.7, x11.org needs to disable;e 
composite in order for 3D stereo to work. I would just be happy with 3D stereo 
in coot 0.9 despite the problems with 'Desktop' stereo in the GDM. 
Unfortunately, Wayland is replacing X11 so in the future, 3D stereoscopic will 
probably be dead.
I can elaborate on this more if anyone is interested.
Thanks for your consideration.
kas


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

Senior Scientist,

Department of Bacteriology: College of Ag and Life Sciences;

Departments of Bio Molecular Chemistry,

Neuroscience, Oncology, and Carbone Cancer Center:

School of Medicine and Public Health;

and the School of Pharmacy

University of Wisconsin-Madison

Madison, Wisconsin, 53706

608-215-5207


From: Paul Emsley 
Sent: Thursday, April 2, 2020 3:39 PM
To: Kenneth Satyshur ; COOT@JISCMAIL.AC.UK 

Subject: Re: Where to find coot 0.9 and demos.



On 02/04/2020 18:23, Kenneth Satyshur wrote:
Thanks Paul for your tireless work on improving coot. It is a real gem of a 
graphics program!


Thank you.


I went to your web site and I see 0.8.9.2 prerelease.


The source code for 0.9 is in the release directory. I was too tired to make 
binaries. My plan is to do that today.


Is there another place to get coot 0.9?
I know that ccpem has 0.9 in it and this is the one I am using on Linux RHEL7.


CCPEM have 0.9-pre. They are pretty up to date - they don't have up-to-date 
tests, improper dihedrals or the new splash screen. But I guess that you can 
live without those for now.



Works great (Except maps disappear when going into stereo).


We discussed a fix for that on this list a week or so ago. Maybe it was 
CCP4BB.. Hmm.


add this to ~/.coot-preferences/startup.py

set_display_lists_for_maps(0)


I have the 2019 May YouTube of your demo of 0.9 and in there you use several 
demo scripts, but I cannot find them either. Does anyone know another source? 
They are



Keyboard mutate is in curlew


demo-box-of-buttons-madrid.tar.gz is in the Files folder on the web site.


gui-test-mol-tris.scm is secret/experimental :-) I doubt that CCPEM have that 
enabled. FWIW, I am completely rewriting the molecular triangles from scratch. 
Maps and licorice models have made good progress, but I have not yet been able 
to get ribbons integrated.


I will be adding blog posts and I've just downloaded kdenlive so there will be 
official YouTube videos (the SBGrid one (I think that's the one you meant) was 
only for the attendees at the meeting in March last year :-))


Paul




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Re: [COOT] Multithreading in 0.9

[Kenneth Satyshur]

There is a difference between cores and threads. Think of cores as physical and 
threads, always 2x cores, as virtual.  Some cores are not hyperthreading.  Some 
linux report cores in use, not threads. 2400 x 2 is 48 threads.

Get Outlook for Android


From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Clemens Grimm 

Sent: Tuesday, June 9, 2020 7:30:17 AM
To: COOT@JISCMAIL.AC.UK 
Subject: Re: Multithreading in 0.9

Zitat von Paul Emsley :

>
> By default, coot will try to use as many cores as you have. I have
> not been able to get the refinement past about 60% occupancy however
> (I have seen 2400% in a 48 core machine).

Indeed, doing a chain refine, I see 1500% ...


> With 80 cores, you should be able to move around (i.e. quickly
> recontour) multiple large maps with ease.

... and 2500% when spinning a bunch of large maps

>
>> I wonder if this is a configurable limit?
>
> It is. The environment variable COOT_N_THREADS can be used to set
> the maxium number of threads.

COOT_N_THREADS was not set for this test, setting it to 80 does not
change anything.

Clemens

>
> Paul.
>
> 
>
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
>
> This message was issued to members of 
> www.jiscmail.ac.uk/COOT, a
> mailing list hosted by www.jiscmail.ac.uk, terms & 
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--
Dr. Clemens Grimm
Institut für Biochemie
Biozentrum der Universität Würzburg
Am Hubland
D-97074 Würzburg
Germany
e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de
phone : +49 0931 31 84031
-



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Re: [COOT] Nature this week

[Kenneth Satyshur]

Hydrogen atoms should always be included in an X-ray model. They are half of 
the atoms in a protein. They are not refined except in a 'ridding' position, 
connected to the heavy atom. Molprobity will add hydrogens before any 
structural analysis and you can't do dynamics or MD without them. Only the 
orientation of the OH in Tyr, Ser and Thr are in question, but that is the 
importance of the H bond scheme in any structure. Students should be taught how 
to add them in any molecular modelling class and to examine the H-bonding. They 
may even help your R value if the structure is high resolution.
Just sayin.
kas



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

Senior Scientist,

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


From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Paul Emsley 
Sent: Thursday, November 5, 2020 3:41 AM
To: COOT@JISCMAIL.AC.UK 
Subject: Re: Nature this week

They are indeed in the direct map. Yes, you are right, hydrogen atoms are more 
readily seen in a cryo-EM
reconstruction than a map from x-ray data (given the same resolution of the 
data). "Atomic resolution" of
course doesn't refer the the data resolution required to resolve a hydrogen 
atom and the atom to which it is
bonded.


On 05/11/2020 09:11, Tim Gruene wrote:
>
>
> Do you know why the hydrogen atoms only show up in the difference map,
> but not in the direct map?

They are indeed in the direct map.

> The signal strength of hydrogens relative to
> C, N, O is quite strong, much stronger than for X-rays.

Yes, you are right, hydrogen atoms are more readily seen in a cryo-EM 
reconstruction than a map from x-ray
data (given the same resolution of the data).

> The large blobs
> that you illustrate in the difference map just disappear in the direct
> map. Is this expected? After the hydrogens are modelled, they seem to
> totally disappear...
>

This sounds like you've done some refinement of this dataset yourself. Is that 
what you mean?
EMD-11638/7a4m.

Paul.



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Re: [COOT] Current state of VR support

[Kenneth Satyshur]

Thanks Paul for this information. I too am interested in VR. Our labs have 
Nvidia 3D stereo which we have used for a decade and we are  happy with it. I 
have yet to be able to do any useful work with VR sets, but that may change. 
Chimera folks are also into VR.

This is not their web site but still way cool.
https://www.chimera-vr.com/
Chimera VR - Out of this world entertainment for ages 8+ - Welcome to Chimera 
VR - Chimera VR
Prison Break We visited Chimera VR in Fleet on the 31st October 2020 in a group 
of 6 adults. We played the 'Prison' escape room and what a fantastic experience 
it was. We had done escape rooms before, but the addition of... read more read 
less
www.chimera-vr.com
The Chimera I use is from USCF and is chimeraX.

https://www.cgl.ucsf.edu/chimerax/docs/user/vr.html

ChimeraX Virtual Reality
Any models displayed in ChimeraX can be shown in virtual reality headsets 
supported by SteamVR, such as HTC Vive, Oculus Rift and Samsung Odyssey.Most 
descriptions here are for Vive hand controllers, but other systems have 
hand-controller buttons that are generally similar in position and function.
www.cgl.ucsf.edu
Tom Goddard gave a nice VR demo at an SBGrid seminar.
https://www.youtube.com/watch?v=yOMKwCbXl0g

But please do not forget about those of us with legacy systems. We still use 
Nvidia 3D and "stereo in a window"
as opposed to "stereo in a desktop". We are still using our old clunkers that 
are 10 years old and are happy with them. I recently used 4.9.1 and putting the 
sequence in the display window was nice, but going into hardware stereo caused 
the sequence to go into stereo. Maybe there can be versions for us old timers 
that work for VR and 3D?

thanks
p.s. please feel free to contact me on how to get 3D stereo working in linux.


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

Senior Scientist,

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


From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Paul Emsley 
Sent: Tuesday, March 23, 2021 12:04 AM
To: COOT@JISCMAIL.AC.UK 
Subject: Re: Current state of VR support



On 23/03/2021 04:18, G ökhan Tolun wrote:

Dear COOT developers and experts,



Now that there are VR headsets with high-enough resolution (such as the HP 
Reverb G2) that allow reading smaller text and finer details in VR, I hope that 
the molecular visualization and modelling software will start providing 
easy-to-use support for these devices.

that is a worthy hope.



I see that COOT has some work done in this space,

Yes, some work.

but I could not find detailed-enough information; so, I have a few questions:


  *   Does COOT currently have built-in support for VR, or is this feature 
available only in some internal development versions?

the code is published, but you hardware setup needs to be "just so" to get it 
to work using the software as it stands.


  *   Do both Windows and Linux versions have VR support?

No. The Windows client needs to be run in Firefox and the server needs to be 
run on Linux. It's a bit of a mishmash.


  *   Does COOT support only a specific headset/controller combination (e.g., 
HTC Vive),

Currently yes.

  *   or does it work with a variety of these (e.g., also with WMR headsets and 
controllers)?

No, but it shouldn't take much work, I think.

  *   Is there a recommended minimum system spec for getting high-enough frame 
rates with large models? (I know that usually we look at only a very small part 
of a structure, but still…)

Last year's CPUs and last year's graphics cards should be fine. Say a Ryzen 
3700x and a RTX 2070 Super.


  *   Is there documentation on how to launch a COOT VR session?

Um Not that I've written.

  *   Are both consumer or professional line GPUs supported? (This is related 
to the need for a Quadro card supporting QuadBuffered stereo for a 3DVision 
system [3D monitor and 3D glasses, which is our current setup]).

Highly likely - not tested. QuadBuffered stereo doesn't make different in VR.

  *   Is there a difference between using either (i.e., would one be 
recommended over the other for any reason)?

Not that I can see.



We are planning to put together a new system soon for molecular visualization 
and modelling, and answers to these will guide us in our effort.



Ah, OK. Well, I'd encourage you not to be thinking about VR with Coot at the 
moment. Or this year. As Coot is pretty good at using multiple cores now, if I 
were speccing a PC, I'd choose a CPU with a high core count, say a  Ryzen 5900x 
or 5950x or a Threadripper and a RTX 3080 (or a Quadro RTX 6000 for stereo if 
that fits your budget). The grap

Re: [COOT] on centos instll

[Kenneth Satyshur]

Centos 8 is newer than what was used to compile coot. It will be missing some 
libraries that are installed with a a centos7 or 6 system. Usually, 8 has an 
upgraded version of a module and the compiled version is looking for the old 
one. You can install the older version and have then newer and older installed 
at the same time. This is probably what is happening with fft. On the other 
hand, "canberra-gtk-module" may be missing since a n 8 system is going to be 
cleaner than 7. try

sudo yum install  canberra-gtk

You probably need to have 'extended packages for enterprise level 8' in your

/etc/yum.repo.d

These packages will install some older packages that are not standard install 
with 8.

kas


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

Senior Scientist,

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


From: Mailing list for users of COOT Crystallographic Software 
 on behalf of 
0459ef8548d5-dmarc-requ...@jiscmail.ac.uk 
<0459ef8548d5-dmarc-requ...@jiscmail.ac.uk>
Sent: Saturday, April 10, 2021 3:45 AM
To: COOT@JISCMAIL.AC.UK 
Subject: on centos instll

Dear All,

In Centos 8 system I have downloaded 
"coot-0.9.5-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz ". By 
"tar -xzvf 
coot-0.9.5-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz ", in 
the automatically created directory there was no "README" file for 
installation, but it looks as in have been installed. In the automatically 
created directory I "cd bin", and input "./coot", and click "enter" its first 
error message was "Gtk-Message: XX:XX:XX.XXX: Failed to load module 
"canberra-gtk-module". Will you please let me know whether 
"canberra-gtk-module" was necessary for coot? If necessary, is it possible and 
how to install "canberra-gtk-module" in centos 8?

The second error message was "error while loading shared libraries: 
libsrfftw.so.2: cannot open shared object file: No such file or directory". 
Will you please let me how to solve this error, i.e., how to install 
ibsrfftw.so.2?

Best wishes,

Smith






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[COOT] coot crash.

[Kenneth Satyshur]

I installed 0.9.5 on RHEL7.9 and it does not work. Just crashes. Enclosed is 
the txt file of the output.
kas



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

Senior Scientist,

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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CLIBD_MON not set using COOT_REFMAC_LIB_DIR

(coot-bin:8598): GLib-GObject-WARNING **: 16:39:59.063: 
g_object_set_is_valid_property: object class 'GtkSettings' has no property 
named 'gtk-application-prefer-dark-theme'
There are 143 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/a/ALA.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/a/ASP.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/a/ASN.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/c/CYS.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/g/GLN.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/g/GLY.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/g/GLU.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/p/PHE.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/h/HIS.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/i/ILE.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/l/LYS.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/l/LEU.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/m/MET.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/m/MSE.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/p/PRO.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/a/ARG.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/s/SER.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/t/THR.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/v/VAL.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/t/TRP.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/t/TYR.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/p/PO4.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/s/SO4.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/g/GOL.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/c/CIT.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/e/EDO.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/a/A.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/c/C.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/g/G.cif
There are 2 data in 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/li

Re: [COOT] on centos instll

[Kenneth Satyshur]

Unfortunately, I only use 7 although I have a Centos 8 system for testing. It 
is best to ask this of the developers.
kas



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

Senior Scientist,

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


From: smith_lee...@yahoo.com 
Sent: Sunday, April 11, 2021 2:08 AM
To: coot@jiscmail.ac.uk ; Kenneth Satyshur 

Subject: Re: on centos instll

Dear All,

Then is any way which can install coot 0.95 successfully in centos 8? And if 
there is the way, will you please share me with the step by step installation 
method?

Best wishes,

Smith

On Saturday, April 10, 2021, 10:20:51 PM GMT+8, Kenneth Satyshur 
<302c79f8ddd1-dmarc-requ...@jiscmail.ac.uk> wrote:


Centos 8 is newer than what was used to compile coot. It will be missing some 
libraries that are installed with a a centos7 or 6 system. Usually, 8 has an 
upgraded version of a module and the compiled version is looking for the old 
one. You can install the older version and have then newer and older installed 
at the same time. This is probably what is happening with fft. On the other 
hand, "canberra-gtk-module" may be missing since a n 8 system is going to be 
cleaner than 7. try

sudo yum install  canberra-gtk

You probably need to have 'extended packages for enterprise level 8' in your

/etc/yum.repo.d

These packages will install some older packages that are not standard install 
with 8.

kas


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

Senior Scientist,

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


From: Mailing list for users of COOT Crystallographic Software 
 on behalf of 
0459ef8548d5-dmarc-requ...@jiscmail.ac.uk 
<0459ef8548d5-dmarc-requ...@jiscmail.ac.uk>
Sent: Saturday, April 10, 2021 3:45 AM
To: COOT@JISCMAIL.AC.UK 
Subject: on centos instll

Dear All,

In Centos 8 system I have downloaded 
"coot-0.9.5-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz ". By 
"tar -xzvf 
coot-0.9.5-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz ", in 
the automatically created directory there was no "README" file for 
installation, but it looks as in have been installed. In the automatically 
created directory I "cd bin", and input "./coot", and click "enter" its first 
error message was "Gtk-Message: XX:XX:XX.XXX: Failed to load module 
"canberra-gtk-module". Will you please let me know whether 
"canberra-gtk-module" was necessary for coot? If necessary, is it possible and 
how to install "canberra-gtk-module" in centos 8?

The second error message was "error while loading shared libraries: 
libsrfftw.so.2: cannot open shared object file: No such file or directory". 
Will you please let me how to solve this error, i.e., how to install 
ibsrfftw.so.2?

Best wishes,

Smith






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Re: [COOT] Feature suggestion: Check/Delete Waters, toggle hydrogens on/off

[Kenneth Satyshur]

WOW. thanks Paul. If there is a category of 'super scientist' you certainly are 
one.
kas



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

Senior Scientist,

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


From: Mailing list for users of COOT Crystallographic Software 
 on behalf of CRAIG A BINGMAN 
<21371e2fba31-dmarc-requ...@jiscmail.ac.uk>
Sent: Tuesday, June 8, 2021 9:55 AM
To: COOT@JISCMAIL.AC.UK 
Subject: Re: Feature suggestion: Check/Delete Waters, toggle hydrogens on/off

Paul,

Thank you so much!

Craig

> On Jun 8, 2021, at 9:48 AM, Paul Emsley  wrote:
>
> On Fri, 2021-06-04 at 18:45 +, CRAIG A BINGMAN wrote:
>> The "Check/Delete Water" function under “Validate" would be more useful to 
>> me if it were possible to ignore hydrogen
>> atoms in the distance calculations. There seems to be no distance window 
>> that works simultaneously for water O-O
>> distances, where riding hydrogens are almost never present, and water 
>> O-protein distances, where the protein almost
>> always carries riding hydrogens.
>>
>
> I managed to find a useful PDB file on an old laptop. The fix to ignore water 
> hydrogen atoms has now been published and
> will be available in 0.9.6.
>
> Paul.
>
> 
>
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[COOT] 0.9.5 crashes on RHEL7.9

[Kenneth Satyshur]

Here is the error:

Coot Scheme Scripting GUI code found and loaded.
Good afternoon Ken Satyshur. Welcome to Coot 0.9.5.
(set-display-intro-string "Good afternoon Ken. Welcome to Coot 0.9.5")
(set-display-lists-for-maps 1)
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/bin/coot: 
line 264:  9276 Illegal instruction (core dumped) $coot_bin "$@"
. -- Coot crashed - trying to diagnose -
ldd -r on guile gives:
linux-vdso.so.1 =>  (0x7ffed2b4a000)
libguile.so.17 => 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/lib/libguile.so.17
 (0x7fd88d27a000)
libgmp.so.10 => 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/lib/libgmp.so.10
 (0x7fd88d005000)
libcrypt.so.1 => /lib64/libcrypt.so.1 (0x7fd88cdce000)
libm.so.6 => /lib64/libm.so.6 (0x7fd88cacc000)
libltdl.so.3 => 
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/lib/libltdl.so.3
 (0x7fd88c8c4000)
libdl.so.2 => /lib64/libdl.so.2 (0x7fd88c6c)
libpthread.so.0 => /lib64/libpthread.so.0 (0x7fd88c4a4000)
libc.so.6 => /lib64/libc.so.6 (0x7fd88c0d6000)
/lib64/ld-linux-x86-64.so.2 (0x7fd88d56f000)
libfreebl3.so => /lib64/libfreebl3.so (0x7fd88bed3000)
Guile 1.8.8
Copyright (c) 1995, 1996, 1997, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 
2008 Free Software Foundation
Guile may be distributed under the terms of the GNU General Public Licence;
certain other uses are permitted as well.  For details, see the file
`COPYING', which is included in the Guile distribution.
There is no warranty, to the extent permitted by law.
catching the crash log:
coot-exe: 
"/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/libexec/coot-bin"
/usr/bin/ls
coot-version:
/home/xray/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/libexec/coot-bin
platform:
/usr/bin/uname
core: #f
No core file found.  No debugging


How do I fix this?
thanks
kas



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

Senior Scientist,

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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Re: [COOT] 0.9.5 crashes on RHEL7.9

[Kenneth Satyshur]

[satyshur@dingo ~]$ lscpu
Architecture:  x86_64
CPU op-mode(s):32-bit, 64-bit
Byte Order:Little Endian
CPU(s):16
On-line CPU(s) list:   0-15
Thread(s) per core:2
Core(s) per socket:4
Socket(s): 2
NUMA node(s):  2
Vendor ID: GenuineIntel
CPU family:6
Model: 26
Model name:
Stepping:  5
CPU MHz:   1600.000
CPU max MHz:   2668.
CPU min MHz:   1600.
BogoMIPS:  5333.63
Virtualization:VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache:  256K
L3 cache:  8192K
NUMA node0 CPU(s): 0-3,8-11
NUMA node1 CPU(s): 4-7,12-15
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca 
cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx 
rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology 
nonstop_tsc aperfmperf eagerfpu pni dtes64 monitor ds_cpl vmx est tm2 ssse3 
cx16 xtpr pdcm dca sse4_1 sse4_2 popcnt lahf_lm ssbd ibrs ibpb stibp tpr_shadow 
vnmi flexpriority ept vpid dtherm ida spec_ctrl intel_stibp flush_l1d
[satyshur@dingo ~]$


all of my systems are legacy. I can go back to using the older version of 
sbgrid if recommended.

kas
Launch Date Q1'09

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

Senior Scientist,

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


From: Jason Key 
Sent: Friday, June 25, 2021 6:26 PM
To: Kenneth Satyshur 
Cc: COOT@jiscmail.ac.uk 
Subject: Re: 0.9.5 crashes on RHEL7.9

Hi Kenneth,

Illegal instruction errors usually mean the binary you are executing was 
compiled on a CPU that has a different (newer) instruction set than the one 
you're using. What generation of CPU are you using? Usually the only way to fix 
this is to recompile the code for the older CPU microarchitecture.

Best,
Jason



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Re: [COOT] removing dotted lines

[Kenneth Satyshur]

Yes. Thanks.  Get confused sometimes with so many versions. I will upgrade all 
6 computers. We greatly appreciate all the teams efforts!

Sent from my Verizon, Samsung Galaxy smartphone
Get Outlook for Android<https://aka.ms/AAb9ysg>

From: Mailing list for users of COOT Crystallographic Software 
 on behalf of pems...@mrc-lmb.cam.ac.uk 

Sent: Monday, November 8, 2021 3:47:37 PM
To: COOT@JISCMAIL.AC.UK 
Subject: Re: removing dotted lines

Did you read the blog post mentioned by Murpholino Peligro?

Paul

On 08/11/2021 19:16, Kenneth Satyshur wrote:
>
>
> Kenneth A. Satyshur, M.S., Ph.D.
>
> Senior Scientist,
>
> 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
>
> 
> *From:* murpholi...@gmail.com 
> *Sent:* Monday, November 8, 2021 1:05 PM
> *To:* Kenneth Satyshur ; COOT@jiscmail.ac.uk 
> 
> *Subject:* Re: removing dotted lines
> Dear Kenneth.
> For this to work you need to do:
> Calculate->Scripting -> Python
> and then write
> set_draw_missing_residues_loops(0)
> (in the window that emerges)
> and then press enter.
>
> I am attaching your message below and adding this to the coot mailing list 
> just in case someone else does
> not find the python scripting window.
> PS I guess you can put this line in the configuration file for coot.
>
>  >>>
> coot >> set_draw_missing_residues_loops(0)
> BL WARNING:: Python error!
> (Or you attempted to use an invalid guile command...)
> Python error:
> name 'set_draw_missing_residues_loops' is not defined
> 
> coot >>
> Does not work.
> kas
>
> Kenneth A. Satyshur, M.S., Ph.D.
>
> Senior Scientist,
>
> 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
>
> <<<
>
>
> El lun, 8 de nov. de 2021 a la(s) 12:46, Kenneth Satyshur 
> (kenneth.satys...@wisc.edu
> <mailto:kenneth.satys...@wisc.edu>) escribió:
>
> coot >> set_draw_missing_residues_loops(0)
> BL WARNING:: Python error!
> (Or you attempted to use an invalid guile command...)
> Python error:
> name 'set_draw_missing_residues_loops' is not defined
> 
> coot >>
> Does not work.
> kas
>
> Kenneth A. Satyshur, M.S., Ph.D.
>
> Senior Scientist,
>
> 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
>
> 
> 
> *From:* Mailing list for users of COOT Crystallographic Software 
>  <mailto:COOT@JISCMAIL.AC.UK>> on behalf of murpholi...@gmail.com 
> <mailto:murpholi...@gmail.com>
> mailto:murpholi...@gmail.com>>
> *Sent:* Wednesday, November 3, 2021 10:41 AM
> *To:* COOT@JISCMAIL.AC.UK <mailto:COOT@JISCMAIL.AC.UK> 
> mailto:COOT@JISCMAIL.AC.UK>>
> *Subject:* Re: removing dotted lines
>
> https://pemsley.github.io/coot/blog/2020/06/25/turn-off-missing-loops.html
> 
> <https://pemsley.github.io/coot/blog/2020/06/25/turn-off-missing-loops.html>
>
> |set_draw_missing_residues_loops(0)|
>
>
>
> El mié, 3 de nov. de 2021 a la(s) 09:18, Thomas, Leonard M. 
> (lmtho...@ou.edu <mailto:lmtho...@ou.edu>)
> escribió:
>
> Hello,
>
> Just a quick question, is there an easy way to toggle off and on the 
> lines showing the end and start
> of a chain were there are missing residues?  I have one initial 
> structure that has a bunch of
> fragments and the lines go all over the place making any possible 
> analysis next to impossible.
>
> Thanks,
> Len Thomas
>
>

Re: [COOT] Centos issues

[Kenneth Satyshur]

Already reported by Me. upgrade to 0.9.6 or 0.9.7. Although it still does not 
work correctly in 3D, since the windows are connected to 3D and the text is 
grabled. Centos 7 with Mate desktop works in 3D because stereo is associated 
with a window (stereo-in-a-window) which the Gnome desktop does 
stereo-in-a-desktop, so everything on the desktop is affected.

set_sequence_view_is_docked(0)
kas



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

Senior Scientist,

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


From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Hruza, Alan 
<5e71eea46e75-dmarc-requ...@jiscmail.ac.uk>
Sent: Tuesday, February 15, 2022 2:53 PM
To: COOT@JISCMAIL.AC.UK 
Subject: Centos issues


Hi all,



Recently we (IT) tried to upgrade our Linux box to a newer version of Centos7 
and it seemed to break the graphics.

By breaking, I mean when Coot is launched, there are no errors (except for a 
library that was missing and was installed now)

But as I use Coot the display ( Sequence ) gets garbled and is not viable.  
Anyone else come across this issue before.



Thanks for any help.

Alan



PS we are running:

   Coot 0.9.4

  Operating System: CentOS Linux 7 (Core)

  CPE OS Name: cpe:/o:centos:centos:7

  Kernel: Linux 3.10.0-1160.45.1.el7.x86_64

  Architecture: x86-64

+-+

| NVIDIA-SMI 470.82.00Driver Version: 470.82.00CUDA Version: 11.4 |

|---+--+--+

| GPU  NamePersistence-M| Bus-IdDisp.A | Volatile Uncorr. ECC |

| Fan  Temp  Perf  Pwr:Usage/Cap| Memory-Usage | GPU-Util  Compute M. |

|   |  |   MIG M. |

|===+==+==|

|   0  Quadro P4000Off  | :18:00.0  On |  N/A |

| 46%   34CP8 7W / 105W |170MiB /  8119MiB |  0%  Default |

|   |  |  N/A |

+---+--+--+



+-+

| Processes:  |

|  GPU   GI   CIPID   Type   Process name  GPU Memory |

|ID   ID   Usage  |

|=|

|0   N/A  N/A  1837  G   /usr/bin/X138MiB |

|0   N/A  N/A 25781  G   ...A= --shared-files   29MiB |

+-+

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Re: [COOT] Recent communication

[Kenneth Satyshur]

You deserve a medal, award, or something for the enormous effort in the 
programming.  Without your effort I don't know where we would all be now. 
Thanks.
kas
p.s I have been working in this area for more than 50 years.


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

Senior Scientist,

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


From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Paul Emsley 
Sent: Friday, April 8, 2022 4:50 AM
To: COOT@JISCMAIL.AC.UK 
Subject: Recent communication

Please forgive me if it takes a few days to get back to you, I'm swamped.


Paul.



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Re: [COOT] Recent communication

[Kenneth Satyshur]

You are not old unless you remember using pennies to shove onto Plexiglas 
sheets with electron density sharpie contours.
Or a Richards Box.
kas



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

Senior Scientist,

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


From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Artem Evdokimov 
Sent: Tuesday, April 12, 2022 11:50 AM
To: COOT@JISCMAIL.AC.UK 
Subject: Re: Recent communication

Let's not go back to Evans & Sutherland please.

Yes, I used E&S. I guess that dates me a bit.

When O came out it felt like the skies opened and it rained chocolate lab 
puppies.

Then Quanta came out and it felt pretty good, but pricey.

Then finally Coot came out and it rained doggie noses and ice cream again. 
Thank you, Paul.

Artem


On Tue, Apr 12, 2022, 12:33 PM Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk<mailto:176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>>
 wrote:
Hear Hear - hard to remember life pre-COOT
Eleanor

On Tue, 12 Apr 2022 at 16:16, Kenneth Satyshur 
<302c79f8ddd1-dmarc-requ...@jiscmail.ac.uk<mailto:302c79f8ddd1-dmarc-requ...@jiscmail.ac.uk>>
 wrote:
You deserve a medal, award, or something for the enormous effort in the 
programming.  Without your effort I don't know where we would all be now. 
Thanks.
kas
p.s I have been working in this area for more than 50 years.


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

Senior Scientist,

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


From: Mailing list for users of COOT Crystallographic Software 
mailto:COOT@JISCMAIL.AC.UK>> on behalf of Paul Emsley 
mailto:pems...@mrc-lmb.cam.ac.uk>>
Sent: Friday, April 8, 2022 4:50 AM
To: COOT@JISCMAIL.AC.UK<mailto:COOT@JISCMAIL.AC.UK> 
mailto:COOT@JISCMAIL.AC.UK>>
Subject: Recent communication

Please forgive me if it takes a few days to get back to you, I'm swamped.


Paul.



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[COOT] H-bonding in sphere refine

[Kenneth Satyshur]

I use the sphere refine in coot all the time. It's great. And when I turn on  
'Environmental Distances'. I can see the H-bonding to the residue. Great. I 
have recently been using Isolde in ChimeraX to fit 3 A CryoEM density. When I 
select a residue, turn on H-bonding, it shows all the nearest H-bonding. And 
when I run the MD to fix up the problems, the H-bonds move in real time with 
the MD. Thus I can see where the H-bonds of a neighbor may in fact be messing 
up the phi/psi in question.  Sometimes it is a sidechain that decides to pick a 
fight with the backbone. Pulling on the offending group can resolve the 
phi/psi. This is especially true of beta sheets with its alternating peptide 
bonds.
My question is, can coot display the H bonds within a 'sphere refine' radius so 
I can see all the H-bonding, and watch it more in real time. Is there a 
'radius' parameter for 'environmental distances'?
thanks
kas
p.s. coot is so powerful I keep learning new things the more I use it. Thanks 
Paul.


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

Senior Scientist,

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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[COOT] disulfide bond breaks in coot 0.9.6

[Kenneth Satyshur]

I have a disulfide bond defined in the pdb as SSBOND. It shows up in coot as a 
link between the sulfur atoms. But when I use 'sphere refine' the link is 
broken and there is no disulfide bond. The same happens for my CYS  to ZN 
ligands. They are defined with a 'LINK' line in the pdb. How do I tell 'sphere 
refine' to not break these links? Do I need to define a restraint explicitly?
thanks


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

Senior Scientist,

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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Re: [COOT] Missing Restrains for standard amino acids

[Kenneth Satyshur]

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.
kas



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

Senior Scientist, Retired 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


From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Cryo EM 
Sent: Sunday, August 7, 2022 12:58 AM
To: COOT@JISCMAIL.AC.UK 
Subject: Missing Restrains for standard amino acids

Hi everyone,

I am using Coot 0.9.8.3 EL (ccp4) on my iMac M1 with MacOS Monterey. The phenix 
version I am using is 1.20.1-4487.

At the end of validation run or real space refinement for my cryo-EM map, I 
want to fix the problems in the model interactively by the "open in coot" 
button displayed in phenix. As soon as I click on the problems list in phenix, 
coot takes me to that atom but I am not able to do any local real space 
refinement in coot since it complains about the missing restrains for even 
standard amino acids and nucleotides (screenshot attached).

Please note that coot alone (when not connected to phenix) works for me 
flawlessly. I guess it has something to do with missing monomer library path in 
coot when connected to phenix but I am unable to fix this. Can someone please 
redirect me to the solution?

Regards and thanks!


[Mailtrack] 

  Sender notified by
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 07.08.22, 07:51:32




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[COOT] coot does not save hydrogens.

[Kenneth Satyshur]

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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coot@jiscmail.ac.uk

[Kenneth Satyshur]

Harware stereo. A complicated issue. I have been using it for a long time. The 
SGI computers used crystal eyes glasses and was displaying fine for the 90's, 
but went away with the end of SGI. So we switched to linux. For a while 
(2000's) 3D stereo was not useable, except on old SGI. Then Nvidia decided to 
take over the 3D gaming market with it's Nvidia 3D Vision system and GPUs. 
Wonderful, until they quit in 2019. Now all is WR, which is basically useless 
for molecular modelling density fitting. But I have gotten many a 3D hardware 
systems running on Linux. SBGrid has a web page explaining how to do this that 
still works.

https://www.sbgrid.org/wiki/usage/stereo

I don't know of any systems other than RHEL 7 and centos 7 that will do 3D. I 
have not tried them. Two issues need to be addressed: 1. hardware 2. Software


  1.  Hardware:  You need an Nvidia graphics card that will do 3D stereo. I am 
using quadro cards, like K4000 and P5000. They will need an extra plugin 
connection to the card that will send a signal to a backplane 3DIN plus. This 
plug connects to the emitter back side. You only need this for Linux. Not 
needed for Windows. You also need a 3D ready 120 Hz monitor or better. However 
some gaming monitors will not work. And of course, the Nvidia 3D vision kit of 
glasses and emitter only sold on Ebay (used).
  2.  The OS should be Centos 7, Centos 8 will not work well. Also, the Gnome 
desktop no longer supports 3D Vision system. Use the mate Desktop. With the 
implementation of Wayland that replaces X11, gone are the 'no-compositing' 
options. VR uses composition, 3D Vision does not. This is changed in the 
xorg.conf file if you are still using X11. However, no-compositing will kill 
other graphics programs. I have not tried Ubuntu. Also, install the Nvidia 
drivers for your card.

Section "Extensions"
Option "COMPOSITE" "Disable"
EndSection

https://docs.nvidia.com/drive/drive_os_5.1.6.1L/nvvib_docs/index.html#page/DRIVE_OS_Linux_SDK_Development_Guide/Windows%20Systems/window_system_wayland.html

if you want to find out about Wayland.

and for the Geeks, check out the new Linix OS to replace Centos 7 since it is 
dead.
https://wiki.archlinux.org/title/arch_compared_to_other_distributions


I have checked the following programs for 3D stereo on my system (Centos 7, 
Mate desktop, K4000 Quadro, Acer GN24hl monitor) and they all do hardware 
stereo using Nvidia K4000 and 3D Vision system.

coot 0.9.6
pymol all versions
chimerax ver. 1.3 (Isolde does not do 3D stereo correctly).
vmd 1.9.2 for 3D display of MD.

I realize this is a lot of non-specific info, but if you contact me I can maybe 
walk you thru it.
kas
https://users.csc.calpoly.edu/~zwood/teaching/csc572/final11/rsomers/

https://pymolwiki.org/index.php/Stereo_3D_Display_Options

https://wiki.uni-konstanz.de/ccp4/index.php?title=Stereo&mobileaction=toggle_view_desktop

enough?


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


From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Paul Emsley 
Sent: Wednesday, May 24, 2023 11:47 PM
To: COOT@JISCMAIL.AC.UK 
Subject: Re: stero/Mono&GPU

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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coot@jiscmail.ac.uk

[Kenneth Satyshur]

Curse of Nouvea. Must blacklist it then install Nvidia driver. Lots of web help 
on that. You need to be a geek for that.

Sent from my Verizon, Samsung Galaxy smartphone
Get Outlook for Android<https://aka.ms/AAb9ysg>

From: Mailing list for users of COOT Crystallographic Software 
 on behalf of David Bhella 
Sent: Friday, May 26, 2023 8:56:23 AM
To: COOT@JISCMAIL.AC.UK 
Subject: Re: stero/Mono&GPU

Hi all

There is another element to this I think - that NVIDIA have not supported 3D 
vision in their GPU drivers since 2019 - so you need to download and install a 
legacy driver I think 425 was the last release with 3Dvision support.

I am away from my lab now so can’t check which version I am running on our 
CentOS 7 machine.

D

Professor of Structural Virology
Associate Director - MRC-University of Glasgow Centre for Virus Research
Director - Scottish Centre for Macromolecular Imaging

Sir Michael Stoker Building
Garscube Campus
464 Bearsden Road
Glasgow G61 1QH
Scotland (UK)

Telephone: 0141-330-3685
Skype: d.bhella

On 26 May 2023, at 14:45, Colin Gauvin  wrote:

 We are running openSUSE Leap, but have also gotten hardware stereo working on 
other systems.

Once you have a 3D vision capable GPU, display, and glasses kit, there are 
three tricky components I've discovered:

The first is the Nvidia driver. I suspect the original emailer ran into issues 
here. There are two Nvidia drivers generally available: Nouvea, which is an 
open source driver, and Nvidia's own proprietary driver. You must use Nvidia's 
driver in my experience. Most distributions package this, but if not, it can be 
found on Nvidia's website. However, Nouveau likes to reinstall itself when 
updating some systems. I recommend using the package manager to lock the 
Nouveau after uninstalling it, so that it cannot be reinstalled. If nvidia-smi 
isn't working, this could be why.

The next issue is the display manager/windowing system. This must be X11, not 
Wayland in my experience. A number of newer distributions such as Fedora use 
Wayland by default. Additionally, window compositing must be off. KDE desktop 
allows compositing to be switched off. Mate desktop + LightDM doesn't use 
compositing. I'm not sure about GNOME.

3rd is the X11 config file. X11 can have multiple configuration files. I can be 
tricky to figure out which one is actually in use. So if you make changes to 
one that don't work, start searching your system for others. Perhaps there's a 
rhyme or reason to this, but I've never checked. Make the changes to the Stereo 
type as listed on the SBGrid site (linked earlier in this thread). That should 
get hardware stereo working.

Best,
Colin Gauvin
Cryo-EM Facility Assistant Manager
Montana State University


May 26, 2023 2:00:39 AM Dirk Kostrewa :

Hi Kenneth & other 3D stereo users,


what Kenneth writes overlaps with my experience, except for RHEL 8, which works 
fine in 3D stereo using the standard Gnome 3 desktop without any modifications 
(including composite). To my knowledge, this is the only distribution (and the 
underlying development version Fedora) which works in 3D stereo using the Gnome 
3 shell. Upon switching to 3D stereo it takes about 1-2 seconds or so, until a 
message pops up telling you about enabling 3D stereo, and it also takes the 
same time to disable 3D stereo, again with a popup window. Interestingly, it 
appears to me that only the active 3D window switches to 3D stereo, not the 
whole desktop. How this is done by Fedora/RHEL 8 under the hood, I really do 
not know. The advantage of this window-switching is, that you can still use 
Coot's windows for scrolling through residues, rotamers, etc with clear 
readability. The disadvantage is, that you have to get the active 3D window 
into the foreground (by minimizing/maximizing or clicking its icon on the 
panel) to get rid of a sometimes flickering background. And you don't need to 
disable composite, neither in the xorg.conf file nor in the desktop settings.


Best,


Dirk


On 25.05.23 17:49, Kenneth Satyshur wrote:
Harware stereo. A complicated issue. I have been using it for a long time. The 
SGI computers used crystal eyes glasses and was displaying fine for the 90's, 
but went away with the end of SGI. So we switched to linux. For a while 
(2000's) 3D stereo was not useable, except on old SGI. Then Nvidia decided to 
take over the 3D gaming market with it's Nvidia 3D Vision system and GPUs. 
Wonderful, until they quit in 2019. Now all is WR, which is basically useless 
for molecular modelling density fitting. But I have gotten many a 3D hardware 
systems running on Linux. SBGrid has a web page explaining how to do this that 
still works.

https://www.sbgrid.org/wiki/usage/stereo

I don't know of any systems other than RHEL 7 and centos 7 that will do 3D. I 
have not tried them. Two issues need to be addressed: 1. h