How to make covalent bond in COOT

From: Saugata Hazra
Date: 6 December 2011 22:10

Hello Everyone, I'm sorry if its a silly question. I used to use "O" and recently started working with "COOT". I am wondering how to make covalent bond in coot, between a modified substrate and regular protien residue. I can not figure out how to make the bond. Thanks & Regards, Saugata

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From: Paul Emsley

You can't.  There is no user-control over the bonding. 

It sounds to me that you don't want to make a bond anyway. You can make a LINK if you like (Extensions->Modelling) but that is not the same thing.

Paul.

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From: Tim Gruene

Hello Saugata,

if you want coot to refine the bond length, you have to rename the
residue to some name coot does not yet understand and create a cif-file
which includes the restraints of the residue, the ligand, and the bond
between the two.

Tim

- --
- --
Dr Tim Gruene

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From: Paul Emsley


JLigand is the way to do this.

(the interface to JLigand will be in Coot 0.7).

Paul

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From: Andrey Lebedev

It will be also possible to launch JLigand from CCP4 GUI starting from ccp4.6.3.0.

Currently JLigand and tutorials can be downloaded from here:
http://www.ysbl.york.ac.uk/mxstat/JLigand/index.html
or from here:
ftp://ftp.ccp4.ac.uk/JLigand/index.html

Andrey
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From: matthew vetting


I think you are probably asking the wrong question, and what you are eventually going to want to know is how do I get a modified amino acid recognized in PHENIX or REFMAC so that it makes proper peptide bonds.  The making and breaking of bonds in COOT  (or O for ligands) is  not something that gets utilized downstream in PHENIX or REFMAC, that is better done in ligand construction programs. 

As far as making the modified amino acid I would use Chemdraw/Chemdraw3d then export and use PRODRG to make a cif file, though there are many nice ligand construction tools out there today (including one in PHENIX I believe).

Matt Vetting

--
Matthew W Vetting


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From: Joel Tyndall

Oops,

 

Meant to hit reply all...

 

 

Hi there,

 

You can generate a link via jligand which gives you a covalent linkage with your enzyme / ligand.as well as a cif file

 

Try the tutorial ftp://ftp.ccp4.ac.uk/JLigand/tutorial_link.html

 

J

 

_________________________________

Joel Tyndall, PhD

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From: Paul Emsley

OK, so we are still playing "guess what the question should have been"?  What fun!  OK then...

Yes, quite so.  And in Coot [1].

Anyway, you'll need to make the group of the resulting monomer "L-peptide" for Coot to draw the bond.  And the resulting atoms should be HETATMs of course (if you use the Coot interface that gets fixed on the fly).

Paul.

[1] I suspect the days of chemdraw->prodrg->graphics are numbered... (well, I can hope).