[ccp4bb] coot extensions for residue mutation to Cbeta

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CCP4bb <-- 2008 <-- March 2008 <-- 13 March 2008

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Subject: 2-D crystallization of membrane proteins
From: gxzhao gxzhao {- at -} FJIRSM {- dot -} AC {- dot -} CN
Date: 2008-03-13

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Subject: Re: coot extensions for residue mutation to Cbeta
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-03-13

Subject: coot extensions for residue mutation to Cbeta
From: byron delabarre byron {- dot -} ccp4 {- at -} GMAIL {- dot -} COM
Date: 2008-03-13

Hi -

I'm looking for an easy way in coot to trim residues back to Cbeta. This is
for regions of the structure where there is no or minimal electron density
for side chain location.

1) Is there an easy way to do this, other than: click mutate, click
residue, click trim to Cb, click mutate to xxxx?

2) I wrote a script but couldn't get it to work. I'm not familiar with
scheme/gui enough to pick out the problems.

The gui appears and asks for values - when I enter them and click the action
button nothing happens.
I can code in specific values for the delete-sidechain-range function and
have it work, but this defeats the purpose of having a gui.

The problem appears to be in how to transfer the values from the gui input
to the delete-sidechain-range function (you can see in the code that I tried
the scheme function of converting string to number - using the script
function indicated that coot was looking for a number instead of a string -
this still didn't work).

Thanks in advance for any help.

Byron

Here is my code:

-----
(let ((menu (coot-menubar-menu "Extensions")))

(add-simple-coot-menu-menuitem
menu "Trim back sidechains"
(lambda ()

(molecule-chooser-gui
"Save a selection from molecule: "
(lambda (imol)
(let ((cv (coot-version)))
(if (string (generic-double-entry "Residue Start: " "Residue End"
"750" "755" " Trim Side Chain(s) "
(lambda (start end)
(delete-sidechain-range imol "A" 750 755)))
(generic-double-entry "Residue Start: " "Residue End"
"750" "755" #f #f " Trim Side Chain(s) "
(lambda (start end button-state)
(delete-sidechain-range imol "A" (string->number
(start)) (string->number (end))))))))))))
----

--
Byron DeLaBarre, Ph.D.
Structural Biology Group
Millennium Pharmaceuticals
Cambridge, MA

"In Reciprocal Space, I'm a Somebody"

CCP4bb navigation

CCP4bb <-- 2008 <-- March 2008 <-- 13 March 2008

Previous message:
Subject: 2-D crystallization of membrane proteins
From: gxzhao gxzhao {- at -} FJIRSM {- dot -} AC {- dot -} CN
Date: 2008-03-13

Next message:
Subject: Re: coot extensions for residue mutation to Cbeta
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-03-13