Re: [COOT] wincoot latest?

[Frank von Delft]

Thanks Bernhard!  That's very helpful.

You may (or may not!) have asked whether it's currently confusing - I 
can confirm it is, very.


The download page claims there /is/ an installer for 1.0 - so the 
Christmas Fairy helped you out a bit...? :)




Frank



On 10/01/2023 08:24, Bernhard Lohkamp wrote:

Hi Frank,

The page is correct but the latest in the 0.9 is 0.9.8.1 and there is a 1.0 as 
well (without installer though). Not sure why it says latest 0.9.4.1, this is 
ancient. Maybe some java script issue!? Anyway, you can go directly to the 
release page (where all latest releases are found):

http://bernhardcl.github.io/coot/wincoot-releases.html

Or check manually on github:

https://github.com/bernhardcl/coot/releases

Note to self: I should automate the "last update" since this is manually not 
update since then... (but releases should update automatically).

HTH,

B

***

Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent

Teaching Unit/Biomedicum D9
Dept. of Medical Biochemistry and Biophysics (MBB) |
Karolinska Institutet
SE-171 77 Stockholm
Sweden
+46 8 52487055
bernhard.lohk...@ki.se  | ki.se


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Subject: wincoot latest?

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Hello

I'm looking for wincoot, and my Google takes me to this page:

https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbernhard
cl.github.io%2Fcoot%2Fwincoot-
download.html=05%7C01%7CBernhard.Lohkamp%40KI.SE%7C107ddad9
0a7741d1e09808daf2985f6b%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%
7C0%7C638089033954601642%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4
wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C
%7C%7C=AQ5clnvJClvgtmLlfqbC7pn98Mrybf4GUvln7r0ZV0g%3D
ved=0

with the latest version being 0.9.4.1

Is that indeed (a) the official wincoot page and (b) the latest version of coot
available for windows?

(The page says "last modified 2017".)


If none of this is accurate - how can I find the Real Coot?

Thanks!
Frank

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[COOT] wincoot latest?

[Frank von Delft]

Hello

I'm looking for wincoot, and my Google takes me to this page:

http://bernhardcl.github.io/coot/wincoot-download.html

with the latest version being 0.9.4.1

Is that indeed (a) the official wincoot page and (b) the latest version 
of coot available for windows?


(The page says "last modified 2017".)


If none of this is accurate - how can I find the Real Coot?

Thanks!
Frank

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Re: [COOT] absolute map levels

[Frank von Delft]

Attaching the map contour level to the mouse scroll wheel was one of the 
most transformative things that Paul did in coot - giving access to the 
most crucial parameter of map building with an unthinking twitch of the 
finger.




On 03/05/2022 14:32, Paul Emsley wrote:

On 02/05/2022 20:19, Dale Tronrud wrote:


 When I watch people model building I see many scrolling the 
contour level up and down without regard for the numeric value of the 
level, apparently just choosing a value that makes the peaks appear 
the way they prefer the peaks to appear.



I recall a few years ago that Alex McPherson asked me how I chose the 
contour level and I said more or less this. He didn't like my answer :-).



This way of choosing a contour level seems dangerous to me as it 
seems to bias the appearance of the map towards the modeler's 
expectation.





I don't choose one level and don't recommend that others do so - the 
continuous re-contouring allow one to get a feel for where the signal 
descends into noise - so I am scrolling very frequently when deciding 
where a side-chain should go. I hum the Rawhide theme tune as I do so.



Paul.



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Re: [COOT] How to turn off prompt for nomenclature errors?

[Frank von Delft]

Eddie Snell quickly helped:

   cootrc file found in X:\YourWinCootDirectory\share\coot

   where X is the drive. Buried in the wincoot-faq.


I also found (from the BB) that I could simply create a file

   X:\YourWinCootDirectory\.coot-preferences\coot.py

and stick that line in there.

Bernard, maybe say this explicitly in the FAQ?

HNY all!
Frank



On 04/01/2022 07:14, Frank von Delft wrote:

Thanks Paul.

I assume it's RTM to figure out where that startup script is?  I 
confess I failed...  I'm on Windows, and working out where startup 
lives tends to be torrid.


Can I suggest an "edit-my-startup-script" feature from the GUI.

Frank


On 22/12/2021 17:08, Paul Emsley wrote:

On 22/12/2021 15:37, Frank von Delft wrote:
Hello - when I drag a bunch of files onto my wincoot, I end up with 
a long slew of dialogues, asking me if I wan to fix nomenclature 
errors.


I've just realised I find it irritating, because I just want to 
look, not build.


How do I turn it off by default?


add this to your startup-script

set_nomenclature_errors_on_read("ignore")

Paul



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Re: [COOT] How to turn off prompt for nomenclature errors?

[Frank von Delft]

Thanks Paul.

I assume it's RTM to figure out where that startup script is?  I confess 
I failed...  I'm on Windows, and working out where startup lives tends 
to be torrid.


Can I suggest an "edit-my-startup-script" feature from the GUI.

Frank


On 22/12/2021 17:08, Paul Emsley wrote:

On 22/12/2021 15:37, Frank von Delft wrote:
Hello - when I drag a bunch of files onto my wincoot, I end up with a 
long slew of dialogues, asking me if I wan to fix nomenclature errors.


I've just realised I find it irritating, because I just want to look, 
not build.


How do I turn it off by default?


add this to your startup-script

set_nomenclature_errors_on_read("ignore")

Paul



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[COOT] How to turn off prompt for nomenclature errors?

[Frank von Delft]

Hello - when I drag a bunch of files onto my wincoot, I end up with a 
long slew of dialogues, asking me if I wan to fix nomenclature errors.


I've just realised I find it irritating, because I just want to look, 
not build.


How do I turn it off by default?

(I realise it's a difficult one - it's massively nice of coot to offer 
to do automatic things like this - and it has no way of knowing when I 
ought to need it, and when not.  :shrug:)


Frank



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Re: [COOT] accept with space bar and dynamic validation

[Frank von Delft]

Am I really the one that gets to post this?  Yay!

https://xkcd.com/1172/ 

Paul:  can I suggest hot-keys?  To save people tabbing around dialogs...


On 21/06/2021 23:33, Georg Mlynek wrote:

Dear Paul, dear all,
I am running coot on Windows10 (I guess on linux and mac it works).
However,
in past versions pressing the space bar after the Accept refinement? window 
appeared, accepted the refinement, which was very handy because space is also 
used to jump from one residue to the next one. Now pressing space in the Accept 
Refinement? windows ticks the Auto-clear option. How can I change the behaviour.

In one of your video tutorial I became aware of dynamic validation. However it 
is not pssoible to install it. The error is:

debug:: curlew_install_extension() uninstall_button 0x25e3d930
DEBUG:: in coot_get_url_and_activate_curl_hook 
https://bernhardcl.github.io/coot/extensions/curlew_find_atom_overlap_baddies.py
 coot-download/curlew_find_atom_overlap_baddies.py
checksum compare 38143 5715
WARNING:: Failure in checksum match 
coot-download/curlew_find_atom_overlap_baddies.py 38143 vs 5715

I am running wincoot 0.9.4.1 EL.

Many thanks for all the effort you put in.

Br, Georg.



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Re: [COOT] German- McClure Alpha

[Frank von Delft]

That video is rather dramatic...  did it do that on its own, or was 
there dragging-by-mouse going on?


The "youtube tutorial" - is that linked on the coot page?  I looked but 
couldn't obviously find it.  (That's the mrc page, 
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ 
)



On 12/10/2020 14:28, Robert Nicholls wrote:

Hi Sorbhi,

The Geman-McClure weight (alpha) controls robustness to outliers. As 
this value is raised, more restraints are treated as outliers and 
down-weighted. This will allow local conformational differences where 
there are dissimilarities between target and reference structures.


So if you really really want the restraints to be used (e.g. if you're 
trying to force something to be more helical) then you can use a lower 
alpha. Though if there may be some real differences between the 
restraints and the true structure - e.g. if you're using restraints 
based on a homologue - then you might want to use as slightly higher 
alpha so that regions displaying larger discrepancies from the 
restraint targets will not be influenced by the restraints. If you're 
using self-restraints then it's a balancing act - you want the 
structure to be stabilised, but you also want to allow it to deform 
enough to allow local structure to find the correct place in the map.


In Refmac values around 0.01-0.02 are typical. In Coot it varies - 
potential use cases during model building can be more varied than in 
refinement. The overall strength of the restraint weights also plays a 
big part, so it's a case of trial and error. Maybe Paul can advise 
about his preferred strategy? Fortunately in Coot it's easy to try 
different values, and the real time visual feedback of refinement 
performance should make it intuitive to see whether the alpha should 
be increased or decreased, especially when looking at more difficult 
regions.


Paul's got some videos of this in action, e.g.: 
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/files/movies/refine-example-nov.ogv


Regards,
Rob


On 12 Oct 2020, at 13:44, Sorbhi Rathore > wrote:


Dear all,

Could anyone please suggest the best way to decide which German- 
McClure Alpha value to use during refinement (both at a higher 
resolution and lower resolution areas for a cryo-EM map)?

I am using coot 0.9.1 pre EL(ccpem).

Best wishes,
Sorbhi



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Re: [COOT] Automatic rotation during "Next/Previous Residue"-Action

[Frank von Delft]

That's officially awesome...

On 19/11/2018 11:29, Paul Emsley wrote:

On 18/11/2018 16:08, Paul Emsley wrote:
And for those who don't want animation but do want reorientation, we 
have "snap" mode:


https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/files/movies/residue-reorientation-snap-mode.mov 





And here, because Jan mentioned it, is residue reorientation along a 
helix:


https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/files/movies/rolling-along-a-helix.mov 



Paul



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Re: [COOT] wincoot 8.1 - empty menus?

[Frank von Delft]

Yes, bug is resolved for me:  I'm Windows 7 Enterprise, Service Pack 1, 
64bit.


On 14/01/2015 19:36, Anshul Bhardwaj wrote:

Hello all,
I am having similar empty extension sub-menus issue with recently released 
WinCoot-0.8.1. (snapshot is in attachment)
Bernhard: I followed your suggestion of replacing coot_utils.py with revised 
version, nevertheless for me issue still seems to exist. It seems to be OS 
specific (or python path environment variable related) as new coot is running 
fine on my Linux boxes. I am running Windows Professional 64 bit with Service 
Pack 1.
Frank: Is this bug resolved for you? Could you please share your Windows OS 
version?
Let me know if it helps to provide a list of programs installed on my machine 
that uses python to resolve this issue.
Thanks so much!
Anshul



Anshul Bhardwaj, PhD
Faculty, Department of Biochemistry and Molecular Biology
Manager, X-ray Crystallography and Molecular Interactions
Sidney Kimmel Cancer Center
Thomas Jefferson University
233 South 10th Street
BLSB, Suite 822
Philadelphia, PA 19107
Tel: (215) 503-4587
anshul.bhard...@jefferson.edu
http://www.jefferson.edu/jmc/departments/biochemistry/faculty-staff/faculty/bhardwaj.html
http://www.kimmelcancercenter.org/kcc/kccnew/research/resources/xray/index.htm


From: Mailing list for users of COOT Crystallographic Software COOT@JISCMAIL.AC.UK 
on behalf of Bernhard Lohkamp bernhard.lohk...@ki.se
Sent: Monday, January 12, 2015 7:40 AM
To: COOT@JISCMAIL.AC.UK
Subject: Re: wincoot 8.1 - empty menus?

A (crude, temporary) fix is available for this now.

Please replace coot_utils.py in
YOUR_WINCOOT_DIRECTORY\python27\lib\site-packages\coot\
with this one:

https://coot.googlecode.com/svn/trunk/python/coot_utils.py

This should do the trick.

B

On 09/01/2015 12:00, Frank von Delft wrote:

Hi, I installed wincoot 8.1 but most of the Extensions sub-menus are
empty...  is it something I said?

Screenshot below.
Frank





--
***

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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[COOT] pdb info - where?

[Frank von Delft]

Hi all - does coot have a way to let me see the pdb header?

(Yes, I know I can open a text browser - but that's typically about 20 
clicks, especially if I pulled the coordinates directly from the PDB.)


Specifically, where can I see cell and symmetry info?  Apart from 
scrolling through the console window?


phx

Re: [COOT] script to delete waters below 0.8 e/A^3

[Frank von Delft]

Surely using an absolute sigma cut-off is not a very sensible thing to 
do - given that sigma is a function of so many different things that 
have nothing to do with noise?


(Has anybody explored using local non-protein rmsd as sigma?)

phx.


On 07/06/2011 22:58, Seth Harris wrote:

Thanks Paul,

You think of everything, if only I always knew how to find it...

I added this line to my key bindings:

(add-key-binding Goodbye weak waters z (lambda () 
(delete-checked-waters-baddies 0 300 0.8 2.0 3.8 0 0 1)))


which followed from your post with arguments of imol, b factor limit, 
sigma level limit, min dist, max dist, part_occ_contact_flag, 
zero_occ_flag, logical_and_or_flag


So as advertised this seems to remove mostly the weak waters below 0.8 
sigma of the (current?) map. And I was generous on the B factors and 
the distances since often I find that a weak water near a good one can 
taint the good one by its proximity, so best to remove the weak before 
checking the remaining for distance.


Which brings to mind is there a check-checked-waters-baddies that I 
could key bind?


Thanks a bunch,
Seth



On Fri, Jun 3, 2011 at 4:37 PM, Paul Emsley 
paul.ems...@bioch.ox.ac.uk mailto:paul.ems...@bioch.ox.ac.uk wrote:


On 03/06/11 23:11, Seth Harris wrote:

Hi all,

I often use the Check/Delete waters dialog to delete only
those waters below 0.8 level in the map. I do this often
enough that it is high time to find/create a script version,
preferably even something I could launch from the command
line, or barring that maybe could generate a single-click
button on the main menu/control panel.

Would that be as simple as falling off a log for some out
there to give me pointers or a template to work from?
Basically it is scripting whatever that Validate 
Check/Delete waters dialog is doing.

Thanks so much,
Seth


Maybe this will be of some use?


http://lmb.bioch.ox.ac.uk/coot/doc/coot/delete_002dchecked_002dwaters_002dbaddies.html#delete_002dchecked_002dwaters_002dbaddies

If you need some help working that up into a menu item we can do
that tomorrow.

Paul.

[COOT] missing keyboard rotate on windows7 laptop?

[Frank von Delft]

Hi, I have coot 0.6.1 installed on my windows7 laptop (may it fry in hell).

So I tried the Q/W/E/R/T/Y keys which are meant to rotate about the 
X/Y/Z axes respectively.  Nothing happens, except a console message saying:

Key 113 not found in bindings

Is that deliberate?  Those keys are quite useful, every so often...
Cheers
phx

Re: [COOT] missing keyboard rotate on windows7 laptop?

[Frank von Delft]

On 02/03/11 12:00, Frank von Delft wrote:

Hi, I have coot 0.6.1 installed on my windows7 laptop (may it fry in hell).

So I tried the Q/W/E/R/T/Y keys which are meant to rotate about the
X/Y/Z axes respectively.  Nothing happens, except a console message saying:
   Key 113 not found in bindings

Is that deliberate?

Yes.  It was mentioned some time ago.

Ah - mentioned maybe, but not changed in the documentation:
http://www.biop.ox.ac.uk/coot/coot-keys-and-buttons.pdf
which, as instructed on the webpage, is printed out and stuck to my wall.




Those keys are quite useful, every so often...

Agreed... to add a Y screen rotation (10 steps of 0.2 in this case) on
pressing the q key:

(add-key-binding Rotate screen Y q (lambda () (rotate-y-scene 10 0.2)))
;; etc
;; note the e and w, r, t and y keys are already bound to
useful functions on using standard extra key-bindings.
I hugely support Paul and Bernhard's key-bindings (coot wiki) being the 
default in future releases.  (I certainly don't have different mappings.)

phx

Re: [COOT] Is there a way to dump the text from the command window in Windows7

[Frank von Delft]

To enable both on windows you have to do something slightly subtle:

 - Click on the title-bar icon (top-left corner) of the command window, 
and select Properties.
 - Under the Options tab, check QuickEdit mode (this will allow you 
to select things)
 - Under the Layout tab, increase Screen Buffer Size to have a 
Height of  (the maximum).
 - When you hit OK and it asks you how to change this, check for all 
future sessions (something like that).


Now you have some approximately unix shell-like behaviour in that 
window.  To select text to the clip-board, you have to first 
left-click--drag it, and then right-click:  the highlight goes away, 
but the text has been copied.  To paste it in another command window, 
right-click again.  (Or do paste any other way in WYSIWYG, e.g. nedit, 
word, etc.)


HTH
phx





On 13/02/2011 07:32, Jason Yano wrote:

Hi All,

Is there an easy way to dump the text from the command window to a 
text file in Windows 7? I want to dump all of the information from SSM 
superpose into a text file. Currently there are 2 problems, 1) I can't 
select any of the text from the command window to copy it and 2) the 
window only scrolls so far.


Any help would be great.

Jason

Re: [COOT] americanisms in 0.6.1....

[Frank von Delft]

Translating coot?  With google, that's a doddle!

/French/:  foulque f
/Spanish: /focha
/Portuguese: /galeirão


:)


On 28/01/2010 10:50, Paul Emsley wrote:

Kevin Cowtan wrote:

Ezra Peisach wrote:
I move that the names in the scheme scripts be changed to the 
american names and that a new script British.scm be put in place.


Well, that's just crazy talk. The scripting interface should clearly 
use the established language of science, which transcends national 
boundaries and has been the lingua franca for the bulk of the history 
of science.


I therefore propose that Coot scripting interface be translated to 
Latin.


There may be some technical neologisms which do not yet have 
appropriate Latin equivalents. I'm sure these people will be glad to 
help...
http://www.vatican.va/roman_curia/institutions_connected/latinitas/documents/index_en.htm 



At some stage I (at least) would like to have the GUI translated into 
various languages.  We have a start for Spanish and French and I'd 
like others, for example Chinese, Japanese and Portuguese, So we'll be 
putting out a call for translators later (Latin_Vatican is a 
possibility). No time to look at this before next year though.


Paul.

Re: [COOT] Loading monomers (Bug!!)

[Frank von Delft]

H... 

What I read when I select from the menu is the menu label, not the 
manual.  Yes, *now* I know it should take 30 seconds :)


I suggest a little radio-button to select between re-generate fresh 
from library and use existing in working dir or something like that. 


I don't mind what the feature does, only not knowing about it :)

phx.



Frank von Delft wrote:
Hi, maybe it's fixed in pre-release, but in our version of coot 
(v0.5.2):


When you load a monomer (e.g. NAP), and coot finds that 
monomer-NAP.pdb already exists in the working directory, it will 
simply load that file, rather than generating a new one.
This is a profoundly evil bug:  


It is a feature...

to me, load monomer does not mean load the next convenient file in 
the working directory, it means load the monomer from the dictionary.
(Just wasted a day or so trying to find out why my NAP won't 
real-space refine :)


:-(   It does say that that is what it will do in the Importing 
Monomers section of the manual.


Wasn't your 'suspicious' radar tweaked by the fact the solution 
appears instantly, rather than taking 30 seconds (for libcheck to run)?


Hmmm...

Perhaps the status bar should say that it is loading pre-generated 
files... (or something).


P.

Re: [COOT] Loading monomers (Bug!!)

[Frank von Delft]

Well, before I figured it out, I was surprised - pleasantly!  It turned 
unpleasant only later :)


Yes, it was the Get Monomer dialog, but would apply to the Search 
Monomer Lib as well.





Frank von Delft wrote:

H...
What I read when I select from the menu is the menu label, not the 
manual.  Yes, *now* I know it should take 30 seconds :)


I suggest a little radio-button to select between re-generate fresh 
from library and use existing in working dir or something like that.

I don't mind what the feature does, only not knowing about it :)




Hi Frank,

[After sleeping on it]

Like good software, Coot has pretensions of  being able to be used 
without reading the manual.  The naive user will not expect to wait 
for libcheck to run (there is no progress bar, for example) and will 
not be surprised when things appear instantaneously (that's the way 
things should happen, right? - its a GUI program) and will not read 
or check the console where the libcheck/refmac is run (or not).


I take you points on board completely.  I will add the interface you 
suggest (for the record, it will not be straightforward to do so).
Oh, I presume that we are talking about Get Monomer?  (Search 
Monomer Library only partially uses the same underlying code and will 
have to be modified differently.)


Thanks,

Paul.

[COOT] Loading monomers (Bug!!)

[Frank von Delft]

Hi, maybe it's fixed in pre-release, but in our version of coot (v0.5.2):

When you load a monomer (e.g. NAP), and coot finds that 
monomer-NAP.pdb already exists in the working directory, it will 
simply load that file, rather than generating a new one.



This is a profoundly evil bug:  to me, load monomer does not mean 
load the next convenient file in the working directory, it means load 
the monomer from the dictionary. 

(Just wasted a day or so trying to find out why my NAP won't real-space 
refine :)


Cheers
phx

[COOT] Symops: coot vs ccp4

[Frank von Delft]

Hi, any particularly cogent reason why the order of symops is different 
in coot and ccp4?  (E.g. below: P6522.)


It's fantastically annoying, e.g. when trying to reconstruct symmetry 
mates via ccp4, if the symop number is not what is shown in the coot 
status bar.  Or e.g. when trying to sort out inter-unit cell 
disulphides.  Etc.


phx.


.
CCP4 (SYMOP.LIB)
X,Y,Z
-Y,X-Y,2/3+Z
Y-X,-X,1/3+Z
-X,-Y,1/2+Z
Y,Y-X,1/6+Z
X-Y,X,5/6+Z
Y,X,2/3-Z
X-Y,-Y,-Z
-X,Y-X,1/3-Z
-Y,-X,1/6-Z
Y-X,Y,1/2-Z
X,X-Y,5/6-Z

COOT (syminfo.lib)
symop x,y,z
symop x-y,x,z+5/6
symop -y,x-y,z+2/3
symop -x,-y,z+1/2
symop -x+y,-x,z+1/3
symop y,-x+y,z+1/6
symop -y,-x,-z+1/6
symop x-y,-y,-z
symop x,x-y,-z+5/6
symop y,x,-z+2/3
symop -x+y,y,-z+1/2
symop -x,-x+y,-z+1/3

[COOT] Keybindings extension bug

[Frank von Delft]

Hi, for those better at scheme than I:

In coot (stable or pre-release), when I run the extension Keybindings, 
the error below pops up.  This is for the fedora-8+python+gtk2 version.  
Any idea?


phx.


--
In /usr/local/coot/prel/share/guile/gtk-2.0/gtk.scm:
147: 0* [apply #procedure #f () ()]
In unknown file:
  ?: 1  [#procedure #f ()]
In /usr/local/coot/prel/share/coot/scheme/coot-gui.scm:
  ...
2073: 2  (let* (# # # ...) (gtk-signal-connect close-button clicked 
...) ...)
2121: 3* (let* ((scm+py-keybindings #)) ((letrec # loop) 
scm+py-keybindings) ...)

2128: 4* [loop (# # # # ...)]
2129: 5  (cond (# #) (else # #))
  ...
2129: 6  (cond (# #) (else # #))
2132: 7* [box-for-binding ...
2132: 8*  [car #unspecified]
/usr/local/coot/prel/share/coot/scheme/coot-gui.scm:2132:28: In 
procedure car in expression (car items):
/usr/local/coot/prel/share/coot/scheme/coot-gui.scm:2132:28: Wrong type 
(expecting pair): #unspecified

---

[COOT] misleading wincoot on google

[Frank von Delft]

Hi Bernard (I guess?)

If you google for wincoot, you get to the old glasgow page, which still 
advertises 0.3.3.1 or something.  You may want to make it redirect to 
the new york page? 


Cheers
phx

[COOT] scheme-to-python?

[Frank von Delft]

Hi, since Paul's offline or busy (good luck to him!), can anyone provide 
me with a scheme-to-python translation for this code snippet?  Paul sent 
it to me, it's for re-loading a file into the same molecule.


In particular, I don't know how to translate the last two lines, because 
I apparently misunderstood what they do in scheme (being no schemer).


 (define mol2-pdbFile somePDBfile.pdb )
 (define mol2-model (read-pdb mol2-pdbFile))
 (define (read-mol-again)
 (clear-and-update-model-molecule-from-file mol2-model mol2-pdbFile))
 (read-mol-again)


Am I correct in observing that wincoot does not do scheme?

Cheers
phx