Ccp4's Gesamt (new algorithm, interfaced jointly with SSM in ccp4i) should do what you want -- Eugene ________________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Zhijie Li [zhijie...@utoronto.ca] Sent: Thursday, October 25, 2012 12:45 AM To: ccp4bb Subject: Re: [ccp4bb] CCP4superpose_only superpose interesting residues
Hi Wenhe, Superpose allows you to specify residue (as well as Ca/main chain/side chain) ranges. Also in COOT you can select the range of residues used in the LSQ superpose calculation. For superposing parts of the proteins only, a little trick is to cut the interested fragments from the original PDBs and make PDB files that contain the fragments only (simplest way is to edit the PDB files in a text editor) and superpose the fragments. If the whole proteins need to be superposed too, then superpose the proteins to their respective fragments. This is especially useful when the program does not give you options on residue ranges (for example, COOT SSM superpose). Zhijie From: WENHE ZHONG<mailto:wenhezhong.xmu....@gmail.com> Sent: Wednesday, October 24, 2012 6:59 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] CCP4superpose_only superpose interesting residues Dear members, I have one difficult task on hand and would like to ask for your advice. I want to superpose two enzyme structures just based on several residues (e.g. 5 residues) which we are interested in. But these two structures do not have similarity for overall structures. In this case, I can not really use CCP4 Superpose to do it. May I ask do you have any idea managing to do it? Thank you. King regards, Wenhe -- Scanned by iCritical.
