Re: [ccp4bb] Superpose program in CCP4

Dear Wenhe, Have you looked at the Additional Log File from Superpose? Cheers, Clement -Original Message- From: WENHE ZHONG Sent: Sunday, October 30, 2016 12:47 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Superpose program in CCP4 Dear all, I always use the SUPERPOSE tool in

Re: [ccp4bb] Superpose program in CCP4

I've done this sort of analysis in the past and it can be very useful depending on your story is. I'm not sure if any software offers this. My solution was to write a script to do the comparison after the superposition was done. Unfortunately I can't find the script. Best wishes, Reza Reza

Re: [ccp4bb] Superpose program in CCP4

WenHe, I'm not sure if you want to superimpose a number of structures (as rmsd would imply) or just compare two structures. If you want a complete list of the distances between corresponding atoms in two pdb files of identical sequence, you can use the fortran program

Re: [ccp4bb] Superpose program in CCP4

I think superpose does not output CAs outwith a certain cut-off based on the quality of the superimposition. It does try to match as many as give reasonable RMSDs - but it is mainly focussed on the residues in matching secondary elements as this is where it starts the superimposition. A simpler

Re: [ccp4bb] Superpose program in CCP4

Dear Wenhe, Besides this advice, have a look at the http://webapps.embl-hamburg.de/rapido/ server. Sometimes its goodo to re-think of what you want to do, and wonder why its not easily doable in software (perhaps because its not the right thing to do …)

Re: [ccp4bb] Superpose program in CCP4

Dear Wenhe, No 3D superpose tool will always align/map all Calphas. If in the one protein the loop turns left, and in the other it turns right, then mapping those loops is meaningless and thus not done by good software. The other problem is that often two proteins that get compared do not