Dear Ishan, A structural alignment should be independent of the software used. However, the residues being selected for the alignment can make a big difference and different programs have different selection criteria. There are two cases:
1. Different proteins. Here one needs to decide what the equivalent residues are. Usually this is based on a sequence alignment, but once a crude superposition has been obtained, the equivalent residue pairs can be optimized. 2. The same protein undergoing a conformation change (e.g. loop or domain movement). Here one has to decide what the rigid regions are and where the moving loop or linker is. By looking at the coarse superposition with coot or any other graphics program, one quickly sees what would be the best borders. If it is really critical for your hypothesis, you will have to define manually the equivalent pairs. Best, Herman Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Eleanor Dodson Gesendet: Montag, 16. Dezember 2019 11:53 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] Problem with structural alignment EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk<mailto:owner-ccp...@jiscmail.ac.uk> Well CCP4mg does this very nicely and it is easy to check the results - all displayed on the screen so you can pinpoint outliers.. Eleanor On Mon, 16 Dec 2019 at 06:38, Ishan Rathore <ishanrathor...@gmail.com<mailto:ishanrathor...@gmail.com>> wrote: Hi, I am trying to compare multiple homologous structures of a protein, where I am analysing the active site residues and the bound substrate/peptide. I have used multiple methods for alignment in coot and pymol. Every method gives a slightly different orientation in the active site. Based on the analysis I am trying to propose a hypothesis for the catalytic mechanism of the protein. But, I am a bit wary of getting biased with the alignment if that supports my hypothesis. What are the parameters that have to be considered for a reliable alignment? What are the other Softwares available for alignment? Thanks and regards Ishan ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=u-_ryp3hi-bxLRE1TbigiQlXbeadXA4_BRTuQWI5MVk&s=rPIPTKAErk8neMYkdFvu4iFId9ycU3Pr0FU52CQRtfw&e=> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=u-_ryp3hi-bxLRE1TbigiQlXbeadXA4_BRTuQWI5MVk&s=rPIPTKAErk8neMYkdFvu4iFId9ycU3Pr0FU52CQRtfw&e=> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
