Re: [ccp4bb] Ligand Protein Connection

2011-09-30 Thread Eleanor Dodson
On 09/29/2011 10:12 PM, Sam Arnosti wrote: Hi every one I have a problem with docking my ligand into the electron density map and make the connections ( bonds ) with the protein. It is a Lysine residue that makes a Schiff Base with a long chain aldehyde. I do not know how to make the bonds an

Re: [ccp4bb] Ligand Protein Connection

2011-09-30 Thread Andrey Lebedev
Hi Sam Except for torsion angles, here is a good tutorial for you (the second one) http://www.ysbl.york.ac.uk/mxstat/JLigand/ Andrey On 29 Sep 2011, at 22:12, Sam Arnosti wrote: > Hi every one > > I have a problem with docking my ligand into the electron density map and > make the connection

Re: [ccp4bb] Ligand Protein Connection

2011-09-29 Thread Wei-Chun Kao
Hello Sam, if the ligand dictionary file is not available from the CCP4 monomer library (refmac would stop when it recognized an unknown ligand), you have to generate it from either the PRODRG server ( http://davapc1.bioch.dundee.ac.uk/prodrg/) or PHENIX eLBOW ( http://www.phenix-online.org/docume

[ccp4bb] Ligand Protein Connection

2011-09-29 Thread Sam Arnosti
Hi every one I have a problem with docking my ligand into the electron density map and make the connections ( bonds ) with the protein. It is a Lysine residue that makes a Schiff Base with a long chain aldehyde. I do not know how to make the bonds and control the torsion angles of the ligand.