Prodrg does very good job in guessing atom types and bond orders. Once
it guessed things right it does extremely good job in generating bond
lengths, angles etc.
But it still depends on accuracy of coordinates. You need to check
carefully bonding orders before using them in refinement.
You c
Wasnt there recently a similar discussion(?):
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg16099.html
Maybe try JLigand (www.ysbl.york.ac.uk/mxstat/)
B
Hi all,
I need to create a cif file for a new ligand that does not exist in
the pdb, so far. Normally refmac created such a cif fil
Hi Paul,
the command
phenix.ready_set model_with_unknown_ligand.pdb
will create a CIF file for all novel ligands in your input PDB files.
You can do it from the command line or using the main GUI.
phenix.elbow will do this too.
Pavel.
On 6/21/10 3:40 AM, Paul Lindblom wrote:
Hi all,
I n
Received from Peter Zwart:
Original Message
Subject:Re: [ccp4bb] creating new ligand cif file
Date: Mon, 21 Jun 2010 07:08:18 -0700
From: Peter Zwart
To: Vellieux Frederic
References: <4c1f4f26.2070...@ibs.fr>
it is the same format actually.
201
Hi Paul,
you can use PRODRG server at Dundee university (
http://davapc1.bioch.dundee.ac.uk/prodrg/ )
It generates libraries in different formats... you just need to
copy/paste in your preferred text editor.
HTH
Marco
Paul Lindblom wrote:
Hi all,
I need to create a cif file for a new liga
r NAD.
Fred.
> Message du 21/06/10 12:41
> De : "Paul Lindblom"
> A : CCP4BB@JISCMAIL.AC.UK
> Copie à :
> Objet : [ccp4bb] creating new ligand cif file
>
> Hi all,
>
> I need to create a cif file for a new ligand that does not exist in
the pdb,
> so far.
Hi Paul,
Usually I just Sketch the molecule, I make sure that the bond types are
OK (single, double, aromatic etc.) and I do an idealization in Sketcher,
then use the resulting .cif file in RefMac.
Flip
Paul Lindblom wrote:
Hi all,
I need to create a cif file for a new ligand that does not
Hi all,
I need to create a cif file for a new ligand that does not exist in the pdb,
so far. Normally refmac created such a cif file when I merged the ligand to
the structure, but this time it stops with a "fatal error". I think the
alternatives are "sketcher" and the prodrg server. Can anybody te
