Re: [ccp4bb] refining phosphorylated residues

[Boaz Shaanan]

HI, You could use the LINK command after going through Jligand for your modified residues. There is a very nice tutorial here: http://www.ysbl.york.ac.uk/mxstat/JLigand/ in case you haven't done this before.           Boaz     Boaz Shaanan, Ph.D.                                         Dept. of Life Sciences                                      Ben-Gurion University of the Negev                          Beer-Sheva 84105                                            Israel                                                                                                                  E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220  Skype: boaz.shaanan                  Fax:   972-8-647-2992 or 972-8-646-1710                          From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Rajesh kumar [ccp4...@hotmail.com] Sent: Thursday, March 22, 2012 3:54 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] refining phosphorylated residues Hi Joel, thanks for the reply. It's not phospho group but the whole residue get disconnected. In coot if I do refinement they get disconnected.  Thanks Rajesh Sent from my iPhone On Mar 21, 2012, at 7:38 PM, "Joel Tyndall" <joel.tynd...@otago.ac.nz> wrote: Hi Rajesh,   If I understand correctly, the phospho groups become disconnected from either the serine or threonine. If this is the case, you can use the SEP monomer for phosphoserine and TPO monomer for phosphothreonine. (replace the amino acid residues with these)   These are built into ccp4 and coot   Hope this helps   Joel   _________________________________ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand   Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea               +64 3 4797293 Fax / Waeawhakaahua     +64 3 4797034   From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh kumar Sent: Thursday, 22 March 2012 12:00 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] refining phosphorylated residues   Dear All,   I have a structure of a protein and peptide complex, in which peptide has modified residues ( phosphoserine and phosphothreonine).  During refinement these both gets disconnected  with adjacent residues and its hard to connect them. Could you please suggest me some options.   Thanks Rajesh