Re: [COOT] torsion general

[Paul Emsley]

Cathy Lawson wrote:

Thanks Paul.

I thought it would be something like that.   Now I've tested again,
I see that torsion general works fine for side chain bonds, 
but it doesn't seem to work for main-chain, does this sound right?



It works for only a single residue/monomer.


In some earlier vintage crystallography graphics programs 
it was possible to "tor" main chain bonds and make a large

chunk of structure twirl around on the screen along with the rotating
bond 



Frank von Delft asked for this too.  I would guess that he uses the same 
"vintage crystallography graphics programs" as you do/did. :-).  I'll 
make a note.


Thanks,

Paul.

Re: [COOT] torsion general

[Cathy Lawson]

Thanks Paul.

I thought it would be something like that.   Now I've tested again,
I see that torsion general works fine for side chain bonds,
but it doesn't seem to work for main-chain, does this sound right?

In some earlier vintage crystallography graphics programs
it was possible to "tor" main chain bonds and make a large
chunk of structure twirl around on the screen along with the rotating
bond (a very amusing sight!).

 I was hoping to be able to do exactly this for the purpose of
repositioning of a relatively large chunk of atoms in a
 a theoretical model, guess I will look for another way.

Cathy


On Mar 2, 2009, at 8:15 PM, Paul Emsley wrote:



Cathy Lawson wrote:

I'd be grateful for a short click-by-click description of how to use
"torsion general."  I haven't been able to find documentation for  
this.

Thanks in advance.


Hi Cathy,

Thanks for pointing out the lack of documentation on this. I'll  
make a note to

add some.

You need to click on the torsion-general icon, then click 4 atoms  
that describe
the torsion - the first atom will be the base (non moving) part of  
the atom
tree, on clicking the 4th atom a dialog will pop up with a  
"Reverse" button [1].
 Move this dialog out of the way and then left mouse click and drag  
in the main
window will rotate the moving/"top" part of the residue round the  
clicked atoms

2 and 3.  When you are happy, click "Accept".

Window focus may be an issue - depending on your setting, the  
window manager may
eat one of your clicks as you change focus between the dialog and  
the main
graphics window (this I find annoying and there are instructions in  
the FAQ on

how to turn that off for various systems).

Paul.

[1] which may not work in 0.6-pre (grumble/sigh/sorry).  If it  
doesn't not work,
the "Reverse" button should invert the moving and "base" part of  
the residue.


--oo-o-o-|--o-o-o-|---
http://rutchem.rutgers.edu/~lawson

Re: [COOT] torsion general

[Paul Emsley]

Cathy Lawson wrote:
> I'd be grateful for a short click-by-click description of how to use
> "torsion general."  I haven't been able to find documentation for this.  
> Thanks in advance.

Hi Cathy, 

Thanks for pointing out the lack of documentation on this. I'll make a note to
add some.

You need to click on the torsion-general icon, then click 4 atoms that describe
the torsion - the first atom will be the base (non moving) part of the atom
tree, on clicking the 4th atom a dialog will pop up with a "Reverse" button [1].
 Move this dialog out of the way and then left mouse click and drag in the main
window will rotate the moving/"top" part of the residue round the clicked atoms
2 and 3.  When you are happy, click "Accept".

Window focus may be an issue - depending on your setting, the window manager may
eat one of your clicks as you change focus between the dialog and the main
graphics window (this I find annoying and there are instructions in the FAQ on
how to turn that off for various systems).

Paul.

[1] which may not work in 0.6-pre (grumble/sigh/sorry).  If it doesn't not work,
the "Reverse" button should invert the moving and "base" part of the residue.

[COOT] torsion general

[Cathy Lawson]

I'd be grateful for a short click-by-click description of how to use
"torsion general."  I haven't been able to find documentation for this.  
Thanks in advance.

[COOT] coot - torsion general

[Jan Abendroth]

Hi all,
I kind of like the new look of coot 0.5-pre1 from Bill's fink site.
I miss, though, the "torsion general" and especially the "reverse selection"
key. This was a fabulous feature - where can I find it?

Cheers
Jan

--
Jan Abendroth
deCODE biostructures
Seattle / Bainbridge Island WA, USA
work: JAbendroth_at_decode.is
home: Jan.Abendroth_at_gmail.com