Search found 3 matches

by kamurani
Mon May 06, 2024 4:08 am
Forum: Main Forum
Topic: Restricting TM-align to a given superposition
Replies: 4
Views: 94212

Re: Restricting TM-align to a given superposition

@zcx Thanks for replying. Can you explain why you think it's not implementable...? I am happy to look into modifying the underlying source code for TMalign with some tips / pointers. Unless I misunderstand, there must be a way to modify the dynamic programming approach to find the optimal rotation t...
by kamurani
Thu Apr 18, 2024 1:43 am
Forum: Main Forum
Topic: Restricting TM-align to a given superposition
Replies: 4
Views: 94212

Re: Restricting TM-align to a given superposition

Thanks for your reply. I used the `-se` option, but this prevents the alignment from using superposition entirely. What I want to do, is generate an optimal alignment using ROTATION, but WITHOUT TRANSLATION. For example, aligning two structures with default USalign settings, I get the following rota...
by kamurani
Wed Apr 03, 2024 1:29 am
Forum: Main Forum
Topic: Restricting TM-align to a given superposition
Replies: 4
Views: 94212

Restricting TM-align to a given superposition

Thank you for your continued development of the TM-align tool. I am interested in using TM-align for a research project where I am comparing the local structural regions of proteins to eachother. For example, I might want to calculate the TM score between the atoms within a 20Å radius of a "cen...