[COOT] Minor request selection status line

[Bernhard Rupp]

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. 

Maybe this is already different in newer versions or one can fix this 

with a script line – in any case there is plenty of real estate available in
this bottom line.

 

Cheers, BR

 

--

Bernhard Rupp

k.k. Hofkristallamt

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

--

Institute of Genetic Epidemiology

Medical University Innsbruck

Schöpfstr. 41

A 6020 Innsbruck

 <mailto:bernhard.r...@i-med.ac.at> bernhard.r...@i-med.ac.at

+43 676 571 0536

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Re: [COOT] PDB vs Cif read

[Bernhard Rupp]

Thank you Johan,

these are the same results I get in Wincoot. So there is a problem with
either
the cif file itself
or
the interpretation of the (maybe malformed) cif file by coot.

original post below.

Thanks & best wishes, BR

Dear Cootiers,

Wincoot version 0.9.6

When I read the PDB format file of 7PGU downloaded from PDBe, everything is
fine.
If I convert both the archive and updated cif from PDBe to PDB format,
everything is fine.
Fine means I see chains F and N in the Go-to menu, see the Zn links , and
can display Ca/backbone normal as traces.

If I open the archive or updated cfif file, I see an empty chain A and B in
the go-to menu, the Zn links are gone, and if I display Ca/backbone, the
chain F is interpreted/displayed as single hetero atoms (also the AA images
are dislayed like ligands).

I find nothing offensive in the cif, but if I remove from the cif the
content of the (I believe correct)
loop_
_struct_asym.id...
#
then the empty A,B chains are gone, ca/backbone is displayed correctly as
backbone traces, but the Zn links are still missing.

Can someone please verify if this finding is correct and happens on other
versions?
My suspicion is that some part of the chain assignment is interpreted
incorrectly and causes the mess.

Best regards, BR

-----
Bernhard Rupp (Hofkristallrat a. D)
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org/
-
The hard part about playing chicken
is to know when to flinch
-


On Sat, Dec 18, 2021 at 2:45 PM Zeelen, Johan Philip <
j.zee...@dkfz-heidelberg.de> wrote:

> Coot 0.9.6. EL (ccp4) and Coot 0.8.9.2-pre EL (revision count 7607):
>
> pdb
>
>
>
>
> cif
>
> Johan
>
> On 18 Dec 2021, at 22:43, Bernhard Rupp  wrote:
>
> Perfect,same so far - now can you please - for the cif - select in display
> manager the option Ca/backbone  and compare that with Ca/backbone for the
> PDB?
> Thx, BR
> -
> Bernhard Rupp (Hofkristallrat a. D)
> 001 (925) 209-7429
> +43 (676) 571-0536
> b...@ruppweb.org
> hofkristall...@gmail.com
> http://www.ruppweb.org/
> -
> The hard part about playing chicken
> is to know when to flinch
> -
>
>
> On Sat, Dec 18, 2021 at 1:18 PM Zeelen, Johan Philip <
> j.zee...@dkfz-heidelberg.de> wrote:
>
>> Dear Bernhard,
>>
>> here the result from Coot 0.9.6 EL (ccp4) on Mac Catalina
>> (I get the same result with Coot 0.8.9.2-pre EL (revision count 7607) on
>> Mac Catalina)
>>
>> PDB:
>> 
>> 
>>
>> INFO:: Reading coordinate file: …./7pgu.pdb
>>  PDB file ….../7pgu.pdb has been read.
>> INFO:: Found 1 models
>>Model 1 had 8 links
>>
>>
>> CIF
>> 
>> 
>>
>> INFO:: Reading coordinate file: …../7pgu.cif
>>  mmCIF file …./7pgu.cif has been read.
>> INFO:: Found 1 models
>>Model 1 had 0 links
>>
>> Johan
>>
>> On 18 Dec 2021, at 20:48, Bernhard Rupp  wrote:
>>
>> Dear Cootiers,
>>
>> Wincoot version 0.9.6
>>
>> When I read the PDB format file of 7PGU downloaded from PDBe, everything
>> is fine.
>> If I convert both the archive and updated cif from PDBe to PDB format,
>> everything is fine.
>> Fine means I see chains F and N in the Go-to menu, see the Zn links , and
>> can display Ca/backbone normal as traces.
>>
>> If I open the archive or updated cfif file, I see an empty chain A and B
>> in the go-to menu, the Zn links are gone, and if I display Ca/backbone, the
>> chain F is interpreted/displayed as single hetero atoms (also the AA images
>> are dislayed like ligands).
>>
>> I find nothing offensive in the cif, but if I remove from the cif the
>> content of the (I believe correct)
>> loop_
>> _struct_asym.id...
>> #
>> then the empty A,B chains are gone, ca/backbone is displayed correctly as
>> backbone traces, but the Zn links are still missing.
>>
>> Can someone please verify if this finding is correct and happens on other
>> versions?
>> My suspicion is that some part of the chain assignment is interpreted
>> incorrectly and causes the mess.
>>
>> Best regards, BR
>> -
>> Bernhard Rupp (Hofkristallrat a. D)
>> 00

[COOT] PDB vs Cif read

[Bernhard Rupp]

Dear Cootiers,

Wincoot version 0.9.6

When I read the PDB format file of 7PGU downloaded from PDBe, everything is
fine.
If I convert both the archive and updated cif from PDBe to PDB format,
everything is fine.
Fine means I see chains F and N in the Go-to menu, see the Zn links , and
can display Ca/backbone normal as traces.

If I open the archive or updated cfif file, I see an empty chain A and B in
the go-to menu, the Zn links are gone, and if I display Ca/backbone, the
chain F is interpreted/displayed as single hetero atoms (also the AA images
are dislayed like ligands).

I find nothing offensive in the cif, but if I remove from the cif the
content of the (I believe correct)
loop_
_struct_asym.id...
#
then the empty A,B chains are gone, ca/backbone is displayed correctly as
backbone traces, but the Zn links are still missing.

Can someone please verify if this finding is correct and happens on other
versions?
My suspicion is that some part of the chain assignment is interpreted
incorrectly and causes the mess.

Best regards, BR
-
Bernhard Rupp (Hofkristallrat a. D)
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org/
-
The hard part about playing chicken
is to know when to flinch
-



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[COOT] Jigglefit

[Bernhard Rupp]

.at the risk of looking really stupid here.where do I find the jigglefit in
wincoot 9.4.1? 

 

Cheers, BR

 

--

Bernhard Rupp

http://www.hofkristallamt.org/

b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Hope is a mistake.

--

 




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Re: [COOT] Link residues in different chains

[Bernhard Rupp]

*   Why not rename chains and if necessary renumber

 

Sure, that is how I had to do it. But with many chain fragments and residues in 
the high thousands and 

medium to low resolution this becomes cumbersome. Many domain/motif/helix 
connections are initially exploratory and 

determine the residue numbers/sequence based on side chain fit. Then everything 
changes 

again when you correct. 

 

I don’t think anything is unrealistic about the link per se – the chain 
assignment or residue numbers are unrealistic 

in the beginning.

 

Best, BR

 

From: Mailing list for users of COOT Crystallographic Software 
 On Behalf Of Eleanor Dodson
Sent: Wednesday, March 31, 2021 23:43
To: COOT@JISCMAIL.AC.UK
Subject: Re: Link residues in different chains

 

Why not rename chains and if necessary renumber residues to make a sensible 
single chain? Very easy with the edit options and much simpler than creating an 
unrealistic link?? 

I find myself going that often after an build molecule run. 

Eleanor 

 

On Thu, 1 Apr 2021 at 00:40, Paul Emsley mailto:pems...@mrc-lmb.cam.ac.uk> > wrote:

On Wed, 2021-03-31 at 16:34 -0700, Kevin Jude wrote:
> Just want to note that it's not that esoteric - it's not uncommon to
> find (or engineer) disulfide bonds between chains, eg 6WDQ, 6BJ8, and
> others that I have worked on. Being able to RSR those links would be
> quite useful!
> 
> --
> Kevin Jude, PhD (he/him/his)
> Structural Biology Research Specialist, Garcia Lab
> Howard Hughes Medical Institute
> Stanford University School of Medicine
> Beckman B177, 279 Campus Drive, Stanford CA 94305
> Phone: (650) 723-6431
> 
> 
> On Wed, Mar 31, 2021 at 3:04 PM Paul Emsley <
> pems...@mrc-lmb.cam.ac.uk <mailto:pems...@mrc-lmb.cam.ac.uk> > wrote:
> > On 31/03/2021 22:08, Bernhard Rupp wrote:
> > > 
> > > I spectacularly fail trying to link for real space refine 2
> > different chains with the modelling/make link 
> > > command.
> > 
> > The bonding in Coot's RSR only works within the chain - including
> > links. (You can make links between chains, 
> > but RSR won't use them.)
> > 
> > > How can I do that short of renaming my chains?
> > 
> > If I understand what you are trying to do (sounds a bit esoteric)
> > then I don't think that there is a way.
> > 
> > Paul.
> > 

OK, interesting. I've made a note.

Paul.



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[COOT] Link residues in different chains

[Bernhard Rupp]

Dear Cootiers,

 

I spectacularly fail trying to link for real space refine 2 different chains
with the modelling/make link command.

 

How can I do that short of renaming my chains (which I'd hate to do at
intermediate stages)

 

Thx, BR

 

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

-

Doors and corners - that's where they get you

-

 

 




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[COOT] add_module_for cryo() ?

[Bernhard Rupp]

Hi Fellows,

 

could someone please share what's the secret handshake to

get the Cryo-EM module up into the menu bar?

Such as

add_module_carbohydrate() for the Glyco

would be

add_module_?() for the Cryo-EM ?

 

Where does one find these addable modules list?

 

Similar, I'd like the modelling up there in the menu bar instead in the
Calculate pull-down?

Doable?

 

Many thanx, BR

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

-

Doors and corners - that's where they get you

-

 

 




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[COOT] Copy fragment with instertion

[Bernhard Rupp]

Hi Fellows,

 

wincoot 9.4.1

 

when I try to copy a fragment with insertions, say 855 to 855M, only the
first residue gets copied

 

Is there a different copy option I could/should use?

 

Many thx, BR

 

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

-

Doors and corners - that's where they get you

-

 

 




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[COOT] visual mask editor - why

[Bernhard Rupp]

Maybe I should explain an example: Say coot detects an unmodelled blob
(maybe a ligand). Now, I would like to do

a number of things without biasing towards a model. Like comparing these map
regions, excluding

intrusion of a solvent mask, etc.

 

Now could coot for example just generate a mask around what it already knows
are blobs?  

Possible useful items could be a solvent mask not including that regions, or
a density map

that includes only features with a certain boundary around that blob.

 

I pilfered some kludges together from different sources, but let's just say
inelegant would be a compliment.

 

Best, BR



Brief question: Does something like a visual density mask editor exist?

Thx, BR

--

Bernhard Rupp

http://www.hofkristallamt.org/

b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> 

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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Re: [COOT] List of preference functions

[Bernhard Rupp]

Example.. just dump it into .coot-preferences

 

Best, BR

 

From: Mailing list for users of COOT Crystallographic Software 
 On Behalf Of Daniel Asarnow
Sent: Wednesday, May 13, 2020 16:01
To: COOT@JISCMAIL.AC.UK
Subject: List of preference functions

 

Hi Paul,

Is there a list of functions that can be used in the preferences file? Are 
there other files besides coot.py that define them? I'd like to change the 
default map display properties and map parameters in more detail.

 

Thanks,

-da

 

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set_graphics_window_size (1200,700)
set_default_initial_contour_level_for_map (0.8)
set_default_initial_contour_level_for_difference_map (2.5)
set_show_environment_distances(1)
set_show_symmetry_master(1)
set_symmetry_size(20)
add_module_carbohydrate()
set_do_anti_aliasing (1)
brighten_maps
brighten_maps



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[COOT] fail on simple ligand task - disregard

[Bernhard Rupp]

Please disregard - got it to work in 9.0 by "import Cif dictionary"

--

Hi Fellows,

 

I fail on a trivial task in COOT (all version, not  COOT problem):

I have already a ligand PDB, whatever.pdb, and a corresponding whatever.cif.

Let the 3-letter ligand be LIG.

When I load whatever.pdb, COOT complains correctly about missing restraints
for LIG when I try to fit.

However, if I load whatever.cif (with coordinates) nothing is displayed  and
the display manager shows no molecule.

Still no restrains.

 

Could someone please post me a link to the answer (this got to be trivial,
like a hidden 'load restraints' or so.). 

I am aware that 'LIG' has a monomer cif - feel free to invent anything else 

 

Sorry for the brainblock, 

probably the virus, BR

 

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> 

+1 925 209 7429

+43 676 571 0536

--

Real knowledge is to know 

the extent of one's ignorance 

--

 

 




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[COOT] fail on simple ligand task

[Bernhard Rupp]

Hi Fellows,

 

I fail on a trivial task in COOT (all version, not  COOT problem):

I have already a ligand PDB, whatever.pdb, and a corresponding whatever.cif.

Let the 3-letter ligand be LIG.

When I load whatever.pdb, COOT complains correctly about missing restraints
for LIG when I try to fit.

However, if I load whatever.cif (with coordinates) nothing is displayed  and
the display manager shows no molecule.

Still no restrains.

 

Could someone please post me a link to the answer (this got to be trivial,
like a hidden 'load restraints' or so.). 

I am aware that 'LIG' has a monomer cif - feel free to invent anything else 

 

Sorry for the brainblock, 

probably the virus, BR

 

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Real knowledge is to know 

the extent of one's ignorance 

--

 

 




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[COOT] Startup Message 9.0 Ubuntu 16.04

[Bernhard Rupp]

Hi Fellows, 

 

not sure if this means anything or what the consequences might be (haven't
found a problem as of yet)

 

on Coot 0.9 EL Marina bay under Ubuntu 16.04 LTS I get following startup
message:

 

Gtk-Message: Failed to load module "overlay-scrollbar"

Gtk-Message: Failed to load module "gail"

Gtk-Message: Failed to load module "atk-bridge"

Gtk-Message: Failed to load module "unity-gtk-module"

Gtk-Message: Failed to load module "canberra-gtk-module"

.

(coot-bin:2312): GLib-GObject-WARNING **: g_object_set_valist: object class
'GtkSettings' has no property named 'gtk-application-prefer-dark-theme'

.

** (coot-bin:2312): WARNING **: Trying to register gtype 'GMountMountFlags'
as enum when in fact it is of type 'GFlags'

** (coot-bin:2312): WARNING **: Trying to register gtype 'GDriveStartFlags'
as enum when in fact it is of type 'GFlags'

** (coot-bin:2312): WARNING **: Trying to register gtype 'GSocketMsgFlags'
as enum when in fact it is of type 'GFlags'

 

and it does not like my (win) carbohydrate module

File "", line 1, in 

  File "/home/ubuntu/.coot-preferences/br_preferences.py", line 7, in


add_module_carbohydrate()

NameError: name 'add_module_carbohydrate' is not defined

 

rest ok and operative.

 

Best, BR

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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Re: [COOT] Wincoot 0.9

[Bernhard Rupp]

Not sure what you are asking for – in principle it works, just unzip the file 
in a directory, and execute the batch file in the /bin directory.

 

I was able to load local coordinates and maps.

 

Fetch from PDB failed, but the link it has is correct 

 

DEBUG:: extracted accession code handle mode n 1

BL WARNING:: retrieve of url https://www.ebi.ac.uk/pdbe-srv/view/files/6fak.ent 
failed

handle_read_draw_molecule_with_recentre ("coot-download/6fak.pdb.ent", 1)

WARNING:: Error reading coot-download/6fak.pdb.ent

 

Is that your problem? I haven’t gone through the rest yet, obviously….

 

Cheers, BR

From: Daniel Asarnow  
Sent: Friday, April 24, 2020 18:59
To: b...@hofkristallamt.org
Cc: COOT@jiscmail.ac.uk
Subject: Re: Wincoot 0.9

 

If you get it to run, please let us know how!

 

Good luck,

-da

 

On Fri, Apr 24, 2020 at 5:31 PM Bernhard Rupp mailto:hofkristall...@gmail.com> > wrote:

Yes I found the beta release now thx!

 

From: Mailing list for users of COOT Crystallographic Software 
mailto:COOT@JISCMAIL.AC.UK> > On Behalf Of Daniel Asarnow
Sent: Friday, April 24, 2020 16:57
To: COOT@JISCMAIL.AC.UK <mailto:COOT@JISCMAIL.AC.UK> 
Subject: Re: Wincoot 0.9

 

My apologies for the confusion!

 

It was posted by Bernhard Lohkamp 12 days ago: 
https://github.com/bernhardcl/coot/releases

 

Best,

-da

 

 

On Fri, Apr 24, 2020 at 4:49 PM Bernhard Rupp mailto:hofkristall...@gmail.com> > wrote:

If you could reveal where you got wincoot 0.9.x from, one could perhaps assist…

See no message to this effect maybe got lost…

 

Cheers, BR

 

From: Mailing list for users of COOT Crystallographic Software 
mailto:COOT@JISCMAIL.AC.UK> > On Behalf Of Daniel Asarnow
Sent: Friday, April 24, 2020 14:48
To: COOT@JISCMAIL.AC.UK <mailto:COOT@JISCMAIL.AC.UK> 
Subject: Wincoot 0.9

 

Hi all,

Bernhard kindly posted a Wincoot build based on 0.9 recently. I was wondering 
if anyone was using it, and what is the correct way to use the package (with 
just /bin, /include, /lib provided).

 

Thanks & best,

-da

 

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Re: [COOT] Wincoot 0.9

[Bernhard Rupp]

Yes I found the beta release now thx!

 

From: Mailing list for users of COOT Crystallographic Software 
 On Behalf Of Daniel Asarnow
Sent: Friday, April 24, 2020 16:57
To: COOT@JISCMAIL.AC.UK
Subject: Re: Wincoot 0.9

 

My apologies for the confusion!

 

It was posted by Bernhard Lohkamp 12 days ago: 
https://github.com/bernhardcl/coot/releases

 

Best,

-da

 

 

On Fri, Apr 24, 2020 at 4:49 PM Bernhard Rupp mailto:hofkristall...@gmail.com> > wrote:

If you could reveal where you got wincoot 0.9.x from, one could perhaps assist…

See no message to this effect maybe got lost…

 

Cheers, BR

 

From: Mailing list for users of COOT Crystallographic Software 
mailto:COOT@JISCMAIL.AC.UK> > On Behalf Of Daniel Asarnow
Sent: Friday, April 24, 2020 14:48
To: COOT@JISCMAIL.AC.UK <mailto:COOT@JISCMAIL.AC.UK> 
Subject: Wincoot 0.9

 

Hi all,

Bernhard kindly posted a Wincoot build based on 0.9 recently. I was wondering 
if anyone was using it, and what is the correct way to use the package (with 
just /bin, /include, /lib provided).

 

Thanks & best,

-da

 

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Re: [COOT] Carbohydrate torsion

[Bernhard Rupp]

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.

 

 

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[COOT] Carbohydrate torsion

[Bernhard Rupp]

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.

 

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

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

 

Cheers, BR

 

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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Re: [COOT] How to display the console in Coot?

[Bernhard Rupp]

I do not really understand the question. If I open wincoot, the console appears 
in a sperate window and includes exactly that info

on SSM DMC ready for copy and paste?

 

Best, BR

 

From: Mailing list for users of COOT Crystallographic Software 
 On Behalf Of Eleanor Dodson
Sent: Friday, April 12, 2019 10:13 AM
To: COOT@JISCMAIL.AC.UK
Subject: Re: How to display the console in Coot?

 

Paul - what about a useful log file? Not recording centred on A 237 but 
including potentially useful info like SSM matrices (in orthogonal and 
fractional system) - difference map peaks with the map they come from, etc etc..

 

Eleanor

 

On Fri, 12 Apr 2019 at 17:13, Ahmad Khalifa mailto:underoath...@gmail.com> > wrote:

I want to copy the output matrices of SSM, how to display the console window? 

 

Regards. 

 

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Re: [COOT] glassy map

[Bernhard Rupp]

Bingo! That is of course the one menu I did not check….

 

Many thanks, BR

 

From: Jessica Bruhn  
Sent: Thursday, March 21, 2019 6:58 PM
To: b...@hofkristallamt.org; Bernhard Rupp 
Cc: COOT@JISCMAIL.AC.UK
Subject: Re: glassy map

 

Hi Bernhard, 

 

In Display Manager click on “properties" for your map. Then in displayed map 
style select “Solid/Transparent” or perhaps “Cut-Glass”.

 

Best,

Jessica

 

Jessica Bruhn, PhD
Postdoctoral Fellow
Lyumkis Lab
The Salk Institute for Biological Studies

 

On Mar 21, 2019, at 6:10 PM, Bernhard Rupp mailto:hofkristall...@gmail.com> > wrote:

 

Dear Fellows of the Coot,

 

with senility extending its merciless grip on a daily basis…I remember a 
feature to make a glassy map

(or similar name) that gave a semi-transparent shading of the contour surface.  
Does anybody

remember where it is because I did not find it under the usual suspects….

 

Many thx, BR

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 

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[COOT] glassy map

[Bernhard Rupp]

Dear Fellows of the Coot,

 

with senility extending its merciless grip on a daily basis.I remember a
feature to make a glassy map

(or similar name) that gave a semi-transparent shading of the contour
surface.  Does anybody

remember where it is because I did not find it under the usual suspects..

 

Many thx, BR

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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Re: [COOT] Calculating sigma value

[Bernhard Rupp]

A key difference perhaps is that on one situation (all mice, all electron 
density values) we are dealing with the entire population. There is no doubt 
about what the
rmsd is, no expectations and uncertainty. Of that population 'sigma' is per 
definition the same. Whether it is a good idea to call it standard 
error/deviation or use expectation value for the mean in his case is another 
question.  

In contrast, if we sample a population, we do not know what all members of the 
population look  like. We have only per CLT an expectation value of the sample 
distribution mean, with an associated variance/sigma. Here, the term 
expectation value and standard error/sigma do convey exactly that meaning.

So I think the distinction between an entire population and its measures and 
the measures of its/a sampling distribution is important. Some well-known and 
not remotely pathological looking distributions do not even have a defined 
variance/sigma, cf. Cauchy but that is another theme.
 
Best, BR



-Original Message-
From: Mailing list for users of COOT Crystallographic Software 
 On Behalf Of Edward A. Berry
Sent: Thursday, April 19, 2018 09:44
To: COOT@JISCMAIL.AC.UK
Subject: Re: Calculating sigma value

On 04/19/2018 08:57 AM, Ian Tickle wrote:
>
> Hi, first maps are produced by Refmac, not Coot, and second it shouldn't be 
> called sigma because it's not an uncertainty, it's a root-mean-square 
> deviation from the mean.  The equation for the RMSD can be found in any basic 
> text on statistics, e.g. just type 'RMSD' in Wikipedia.
>
> Cheers
>
> -- Ian


With all due respect, and I may be misunderstanding something here, but I think 
that that is an unnecessarily restrictive definition of sigma! I'm assuming 
sigma stands for the standard deviation. Although standard deviation is often 
associated with a probability distribution, it is defined for (any?) kind of 
distribution. From the Wikipedia page on standard deviation, "the standard 
deviation (SD, also represented by the Greek letter sigma σ or the Latin letter 
s, is a measure that is used to quantify the amount of variation or dispersion 
of a set of data values", and "There are also other measures of deviation from 
the norm . . .".  That together with the formula for population standard 
deviation suggests standard deviation is exactly the RMS Deviation from the 
mean.

For an analogy, suppose a dietician weighs a dozen mice that have undergone the 
same regimen, and calculates a certain mean value with a standard deviation 
deviation of 1.2 g. Now he weighed the mice on a scale reading to the tenth of 
a gram, so the standard deviation of the measurement is around 0.1 g or less. 
Nonetheless he is going to report the deviation of his population, which is 1.2 
g.  Likewise even if we knew precisely the electron density at every point in 
the unit cell of a crystal, that density would still have a distribution, and 
that distribution would have a standard deviation. The important thing, and I 
think this was the main point of Ian's remark, is that that standard deviation 
would have nothing to do with the uncertainty of our estimate of the density.

You could make a probability distribution out of the weight distribution of the 
mice. Say if I pick a random mouse and weigh it, or if I repeat the experiment 
with only a single mouse, that standard deviation tells me something about how 
likely my result is to be close to the population mean. In the latter case, 
this could also be viewed as a measure of the error in the experiment. But in 
the same way, you could say if I pick a random point in the asymmetric unit and 
sample the density there, the RMSD tells me something about the probability 
that my result will be close to the mean value for the map.

However, in keeping with the main point mentioned above, it may be a good 
convention to use sigma only for standard deviation of a probability function 
such as normally (or otherwise) distributed error of a measurement, and RMSD 
for standard deviation in all other cases.

I think the way most people use coot nowadays, refmac (or other) is producing 
map coefficients, and coot is calculating the map (presumably using the FFT 
alogorithm as mentioned) and contouring it for us to see.

eab


>
>
> On 19 April 2018 at 13:20, Mohamed Ibrahim  > wrote:
>
> Dear COOT users,
>
> Do you know how to extract the equations that COOT uses for generating 
> the maps and calculating the sigma values?
>
> Best regards,
> Mohamed
>
> --
> ​
> --
> /*
> ​
> --*/
> /*Mohamed Ibrahim
> *//**//*
> */
> /*Humboldt University
> */
> /*Berlin, Germany
> */
> /*Tel: +49 30 209347931
>
> */
>
>

[COOT] SSM output

[Bernhard Rupp]

Hi Fellows,

 

is there a way to redirect the SSM Superpose output from the console to a
file? Or is there a log file already?

I'd like to simply read the per-residue list from the console window for
plotting purposes.

 

Best, BR

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 767 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

[COOT] List of solvents

[Bernhard Rupp]

Hi Fellows,

 

where can I modify/preserve (in my preferences probably) the list of solvent
molecules appearing 

as pre-selected in the  "Solvent models added to molecule" panel that
appears

from Extensions/Modelling/Add other Solvent?

 

I want to keep the ones I need and not always add them again upon a coot
restart.

 

Thx!

BR

 

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 767 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

Re: [COOT] ccp4 QTMG

[Bernhard Rupp (Hofkristallrat a.D.)]

..and clipped around the fragment I wanted and it is fine.

...and realizing the risk and temptations that come with it. ;-)

Cheers, BR

-Original Message-
From: Mailing list for users of COOT Crystallographic Software
[mailto:COOT@JISCMAIL.AC.UK] On Behalf Of PC
Sent: Tuesday, August 19, 2014 9:41 AM
To: COOT@JISCMAIL.AC.UK
Subject: Re: ccp4 QTMG

Hi Jon and Bernhard,

Thank you-yes, I now opened with QTMG and clipped around the fragment I
wanted and it is fine. 

Patrick

 -Original Message-
 From: bernhard.lohk...@ki.se
 Sent: Tue, 19 Aug 2014 18:37:35 +0200
 To: coot@jiscmail.ac.uk
 Subject: Re: ccp4 QTMG
 
 Hi,
 
 this looks odd. I am not entirely sure I follow how you produced and 
 imported the map and what you figure shows. Anyway, the maps exported 
 from Coot are written for one asymmetric unit which will (should) be 
 expanded by symmetry in Coot and MG. In case you have a map not 
 restricted to an asu this will not work (and you only see one map). I 
 assume you are not centred on the ligand, so MG (and Coot as well) 
 shows you the map parts in the different asus (clipped around the centre).
 Centred on the ligand everything should be in one place.
 
 Not necessarily a direct solution to this problem, but why dont you 
 open you map from the mtz in MG and show (clip) only the map around 
 the ligand.
 
 B
 
 On 19/08/2014 18:13, PC wrote:
 Hi,
 
 I used COOT mask map by atom selection and cut out a fragment of the 
 map, then exported it and now I tried to open it in QTMG.
 
 It displays it as a unit cell,  I want one for a presentation, how 
 can I combine it to display one image ?
 
 Thank you,
 Patrick
 -
 --- 3D Earth Screensaver Preview http://www.inbox.com/earth *Free 
 3D Earth Screensaver* Watch the Earth right on your desktop! Check it 
 out at www.inbox.com/earth http://www.inbox.com/earth
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 --- 3D Earth Screensaver Preview http://www.inbox.com/earth *Free 
 3D Earth Screensaver* Watch the Earth right on your desktop! Check it 
 out at www.inbox.com/earth http://www.inbox.com/earth
 
 --
 ***
 
 Dr. Bernhard Lohkamp
 Associate Professor/Docent
 Div. Molecular Structural Biology
 Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska 
 Institutet
 S-17177 Stockholm
 Sweden
 
 phone: (+46) 08-52487651
 fax:   (+46) 08-327626
 email: bernhard.lohk...@ki.se
 
 ---
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FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop!
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Re: [COOT] [ot]: will we move structures with our hands?

[Bernhard Rupp (Hofkristallrat a.D.)]

I have already talked to a few people about that, because I have gotten the
Kinect part going. The depth image and getting smooth coordinates from
decent gesture recognition is not the problem. A bit more tricky is the
inter-process-communication. I did it via a throttled http stream that gets
sent from one application (Kinect reading) to the second one (display). A
crude version (sans gesture recognition but with process communication) is
available on my dropbox. 

 

http://dl.dropbox.com/u/30662912/interprocess_comm.m4v

 

 

You see the hand position (x,y) and z depth (color) transferred into a
client window. So the mouse interrupt handler or whatever would need to read
those from a stream.

 

It seems to me useful not for bona fide building for public exhibit displays
of molecules, and that is what I intend to use the Kinect for. Resolution is
not an issue and smoothing and gesture recognition are also done. The most
difficult part was to get the openNI drivers to work with the X-box Kinect,
with the usual 32/64 bit hassles etc. ( I am not using the windows Kinect
which came out later and not the MS Kinect SDK). I use Processing for the
Kinect control.

 

So if somebody is seriously interested in making the basic display program
part (coot? Pymol? Other?) work, we can try to crowdsource it or ask the
IUCr for some money for IYCr2014 purposes.

 

BR

From: Mailing list for users of COOT Crystallographic Software
[mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Sebastiano Pasqualato
Sent: Monday, May 21, 2012 5:01 AM
To: COOT@JISCMAIL.AC.UK
Subject: [ot]: will we move structures with our hands?

 

 

Hi guys,

wouldn't it be nice to see this working with COOT?

 

http://www.theverge.com/2012/5/21/3033634/leap-3d-motion-control-system-vide
o

 

ciao,

s


-- 
Sebastiano Pasqualato, PhD
Crystallography Unit

Department of Experimental Oncology

European Institute of Oncology

IFOM-IEO Campus

via Adamello, 16

20139 - Milano
Italy


tel +39 02 9437 5167
fax +39 02 9437 5990

 

 

 

 

 

 

Re: [COOT] clean install on RHEL 6.2

[Bernhard Rupp (Hofkristallrat a.D.)]

Maybe it was not a wise decision to go with RHEL in the first place. 
My gripe is not with coot itself but the OS dependency hunting.
Remember I still use for r3d illustrations XtalView, which hasn't been
updated since Middle Earth,
to give you some idea of my latest Linux install experience.

I'll try the other binary packages that were suggested, while I Yum away...

Best, BR

-Original Message-
From: Mailing list for users of COOT Crystallographic Software
[mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Paul Emsley
Sent: Thursday, February 09, 2012 9:33 PM
To: COOT@JISCMAIL.AC.UK
Subject: Re: clean install on RHEL 6.2

On 09/02/12 07:10, Bernhard Rupp (Hofkristallrat a.D.) wrote:
 Dear Cootsies,

 following Paul's advice I started to autobuild coot using 
 http://lmb.bioch.ox.ac.uk/coot/build-install-coot-from-scratch.html

 It is a little bit like whacking hamsters - it needs swig, which needs 
 pcre...



Sorry about this.   RHEL 6.x binaries should be available shortly after 
I get back [1].  I have a such a machine under my desk now.

I need to make the release for 0.7,
Find a monitor and keyboard and switch for the beastie, Then I can log in,
run the script and feel your pain.

I would have thought (without checking) that yum would provide a
sufficiently recent swig to make coot compile script happy... not so much
manual begetting?

Paul.

[1] from Melbourne.

Re: [COOT] Coot Book of the Genesis

[Bernhard Rupp (Hofkristallrat a.D.)]

Hi  Fellows,
 
following Kay's idea, I unpacked
coot-0.6.2-binary-Linux-x86_64-centos-5-python-gtk2.tar.gz:

./bin/coot-real: error while loading shared libraries: libssl.so.6: cannot open 
shared object file: No such file or directory

ok, I yum it to be safe, find it in 
/usr/lib/libssl.so.6 
and export LD_LIBRARY_PATH=/usr/lib

Now the vengeance of the ELF (soon coming to a workstation near you) is 
unleashed upon me:

./bin/coot-real: error while loading shared libraries: libssl.so.6: wrong ELF 
class: ELFCLASS32
coot-exe: ./bin/coot-real

Maybe I need the CLASS of 64 for my elf reunion?

I guess I better let the pro's deal with this and wait for a new binary.

Anyhow, thanks for all the tips. Cheers, BR

PS: current rhel build version
coot-0.6.2-binary-Linux-x86_64-rhel-4-gtk2.tar.gz
./bin/coot-real: error while loading shared libraries: libldap-2.2.so.7: cannot 
open shared object file: No such file or directory
Yum:
No package libldap-2.2.so.7 available.

PPS: latest (32 bit?) prebuild
coot-0.7-pre-1-revision-3999-binary-Linux-i386-rhel-5-python-gtk2.tar.gz
After a lot of yumming 
Coot actually starts, but I get a lengthy error log and a version of the 
previously reported problem with the icon SVGs (sidebar mostly empty) 

PPPS:
coot-0.7-pre-1-revision-3999-binary-Linux-x86_64-rhel-4-python-gtk2.tar.gz
same as above with coot-0.6.2-binary-Linux-x86_64-rhel-4-gtk2.tar.gz

S: definition of insanity: doing the same thing over and over and expecting 
a different outcome.

-Original Message-
From: Mailing list for users of COOT Crystallographic Software 
[mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Kay Diederichs
Sent: Thursday, February 09, 2012 11:39 PM
To: COOT@JISCMAIL.AC.UK
Subject: Re: Coot Book of the Genesis

Bernhard,

the CentOS5 binaries used to work well on RHEL6 /CentOS6/ SL6 ; there was a 
glitch a few weeks ago which was fixed after I reported it ( 
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=coot;31d9d7f5.1201 ). I install 
the latest nightly build every couple of months / weeks, and this works very 
well.

So for those who are not interested in learning to build coot (including me) 
the binaries are the way to go.

If the CentOS5 binary needs libraries on RHEL6 /CentOS6/ SL6 , this can be 
fixed in the way that applies to all s/w packages: from the error message, find 
the name of the library; yum install thatlibrary; repeat until success. Works 
very well, even with a mix of 32bit and 64bit libraries.

good luck,

Kay

[COOT] Kluge solving lib*so.6 problem

[Bernhard Rupp (Hofkristallrat a.D.)]

Hi Fellows,

 

Kip has suggested a kludge by making links to the 64 bit libraries. I
actually works as described, and

the resulting coot 0.6.2 (revision 3562) does not have the known problem of
the missing SVG icons 

the 0.7 had (see old PPSes below).

 

Thx for all the tips, BR

 

From: Kip Guja [mailto:k...@pharm.stonybrook.edu] 
Sent: Friday, February 10, 2012 4:40 PM
To: b...@hofkristallamt.org
Subject: Re: Coot Book of the Genesis

 

Hi Bernhard,

 

I hope this doesn't add your frustration, but I just wanted to let you know
that I have solved a similar issue by doing the following: 

1) Download coot-0.6.2-binary-Linux-x86_64-centos-5-python-gtk2.tar.gz

2) Running ./bin/coot will complain (as you noted) about libssl.so.6

3) cd to /usr/lib64

4) ls -ltr libssl.so* should list the libssl.so file you currently have
installed as well as some symbolic links to it.  For example, on my RHEL
installation I have libssl.so.1.0.0d (your file may have a different ending,
that's fine)

5) Make a symbolic link to libssl.so.1.0.0d (or whatever your version is)
called libssl.so.6 by doing this: sudo ln -s libssl.so.1.0.0d libssl.so.6

6) Run ./bin/coot again...for me it then complains about libxml.so.6

7) Make another symbolic link for libxml.so.6 in the same way...if you
repeat this for about 4 libraries it should stop complaining and work
perfectly (or at least it does for me)

 

I am not a programmer so I apologize if this is not the ideal solution,
but like I said it works for me -- I hope this helps solve your problem too!

 

Best 

Kip

 

 


PPS: latest (32 bit?) prebuild
coot-0.7-pre-1-revision-3999-binary-Linux-i386-rhel-5-python-gtk2.tar.gz
After a lot of yumming 
Coot actually starts, but I get a lengthy error log and a version of the
previously reported problem with the icon SVGs (sidebar mostly empty) 

PPPS:
coot-0.7-pre-1-revision-3999-binary-Linux-x86_64-rhel-4-python-gtk2.tar.gz
same as above with coot-0.6.2-binary-Linux-x86_64-rhel-4-gtk2.tar.gz


-Original Message-
From: Mailing list for users of COOT Crystallographic Software
[mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Kay Diederichs
Sent: Thursday, February 09, 2012 11:39 PM
To: COOT@JISCMAIL.AC.UK
Subject: Re: Coot Book of the Genesis

Bernhard,

the CentOS5 binaries used to work well on RHEL6 /CentOS6/ SL6 ; there was a
glitch a few weeks ago which was fixed after I reported it (
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=coot;31d9d7f5.1201 ). I
install the latest nightly build every couple of months / weeks, and this
works very well.

So for those who are not interested in learning to build coot (including me)
the binaries are the way to go.

If the CentOS5 binary needs libraries on RHEL6 /CentOS6/ SL6 , this can be
fixed in the way that applies to all s/w packages: from the error message,
find the name of the library; yum install thatlibrary; repeat until
success. Works very well, even with a mix of 32bit and 64bit libraries.

good luck,

Kay

 

__
Kip E. Guja, M.Sc.
Fellow, Medical Scientist Training Program, School of Medicine
MD/PhD Student, Garcia-Diaz Group, Dept. of Pharmacology
Basic Science Tower, Floor T-7, Room 170

Stony Brook University Medical Center

101 Nicolls Road
Stony Brook, NY 11794 
Tel: (917) 855-3628
kip.g...@hsc.stonybrook.edu
k...@pharm.stonybrook.edu

 

 

 

Re: [COOT] Coot Book of the Genesis

[Bernhard Rupp (Hofkristallrat a.D.)]

...because the precompiled binary from the Coot site looks for some
libraries it (and I) cannot find (see that January thread 'Help needed...'
on the subject)
and the suggestion there is to 'do it right and build from scratch'.

But if you have another link to a RHEL binary I am happy to try again...

Thx, BR

-Original Message-
From: Frank Thommen [mailto:structures...@embl-heidelberg.de] 
Sent: Thursday, February 09, 2012 1:17 AM
To: COOT@JISCMAIL.AC.UK
Cc: b...@hofkristallamt.org
Subject: Re: Coot Book of the Genesis

...and why not simply use the binary RHEL 5 version?  At least the CentOS 5
binary distribution works fine on CentOS 6.

Why making one's life harder than needed?

Cheers

   frank

Frank Thommen - Structures IT Management and Support - EMBL Heidelberg
structures...@embl-heidelberg.de - +49 6221 387 8353

[COOT] clean install on RHEL 6.2

[Bernhard Rupp (Hofkristallrat a.D.)]

Dear Cootsies,

following Paul's advice I started to autobuild coot using 
http://lmb.bioch.ox.ac.uk/coot/build-install-coot-from-scratch.html

It is a little bit like whacking hamsters - it needs swig, which needs
pcre...

Ok then it gets going, but an error appears

2012-02-08 10:45:46 (67.0 KB/s) -
“/root/coot/autobuild/sources/guile-gtk-2.1.tar.gz” saved [781985/781985]
awk: cmd. line:1: fatal: cannot open file
`/usr/include/gtk-2.0/gtk/gtkversion.h' for reading (No such file or
directory)

which seems to be a guile version conflict and
rears its ugly head when upon ./config make from the newly created package
I get

checking for GLIB... configure: error: Package requirements (glib-2.0) were
not met:
No package 'glib-2.0' found

I think these problems are connected and I wonder how they can be fixed?

Best regards, BR
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org/
-
No animals were hurt or killed during the 
production of this email.
-

[COOT] Coot Book of the Genesis

[Bernhard Rupp (Hofkristallrat a.D.)]

Fellow Cooties,

If it wasn't such a  waste of time this would actually be funny: 

This installation on clean RHEL 6 turns out very much like the Book of
Genesis:

where Adam begets Seth  who begets Enosh who begets Kenan who begets
Mahalalel who 
begets Jared who eventually after a lot of fucking around begets Emsley who
begets Coot:

Coot_configure then begets Swig which begets Pcre which begets Glib which
begets Zlib which begets Libffi
which begets Gettext 

and after that bloodline is established by serious effing on my side, a
little infidelity from  Coot_configure then 
establishes a degenerate sideline by begetting mmdb, upon which in 2012 per
Mayan calendar the Genesis 
apocalyptically ends in: 

checking if this is MINGW on Windows... no
checking for MMDB... no
Error locating necessary mmdb

Ok we download and install

checking for SSMLib... no!
checking for Clipper... no!
Error locating Clipper - a CNS-enabled version of Clipper (2.1-090520-ac or
later) is required now

maybe - just maybe - my own CNS which is already shutting down envisions
that a  functioning ccp4 installation should already be present?

The major difference between my installing efforts  and the Book actually is
that per Genesis creation of the World took only 7 days...

Best regards, BR

PS: No more  - zero please - bitching about Windows. Thank you. /flame
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org/
-
No animals were hurt or killed during the 
production of this email.
-