Previous Thread
Next Thread
Print Thread
Page 2 of 2 1 2
Re: error Computi RMSD and Rg using CORREL
rmv #22962 12/03/09 07:58 PM
Joined: Nov 2007
Posts: 20
L
Forum Member
OP Offline
Forum Member
L
Joined: Nov 2007
Posts: 20
Thanks Rick,
the insignificance to measure the Rg for two residues is to apreciate the movements present of them and another intro the DM, and the reason is to obtain data that allows me to obtein the best pair of residues on a mutations list which has capacity to generate structural resistance about a mesofilic protein to generate a new thermofilic protein;
and the aim I follow is to moor structural dominions by means of these mutations (forming to salt bridge).
Would you have some suggestion (or scripts) to obtain a better analysis of my work?
Thanks.


MenB Leonardo David Herrera Zúñiga
POSGRADO EN QUÍMICA UAMI Biofisicoquímica
Universidad Autonoma Metropolitana Iztapalapa
Tel. +52 (55) 5804 4674
Re: error Computi RMSD and Rg using CORREL
LHerrera #22965 12/03/09 08:27 PM
Joined: Sep 2003
Posts: 4,794
Likes: 2
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,794
Likes: 2
I do not quite understand everything in your post, but perhaps a simple distance measeurement would be sufficient?


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: error Computi RMSD and Rg using CORREL
lennart #22967 12/03/09 08:38 PM
Joined: Nov 2007
Posts: 20
L
Forum Member
OP Offline
Forum Member
L
Joined: Nov 2007
Posts: 20
yes, and more !!!!
thanks


MenB Leonardo David Herrera Zúñiga
POSGRADO EN QUÍMICA UAMI Biofisicoquímica
Universidad Autonoma Metropolitana Iztapalapa
Tel. +52 (55) 5804 4674
Re: error Computi RMSD and Rg using CORREL
LHerrera #22968 12/03/09 08:43 PM
Joined: Sep 2003
Posts: 8,499
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,499
Rg is a polymer statistic, related to the compactness of a folded polymer, and most meaningful for a polymer chain that folds into a roughly spherical shape.

CHARMM has several tools for looking at relative motions of residues, such as COOR COVAriance and COOR PAXA (corman.doc). I believe some of the fluctuation based time series in CORREL (correl.doc) can also be useful for evaluating relative motion vectors.

Also, normal mode calculations and quasiharmonic analysis (vibran.doc) might provide some insight into "hot" residues.

For distances, the DISTance time series works fairly well for a single pair of atoms, one from each residue.

Last edited by rmv; 12/03/09 08:49 PM.

Rick Venable
computational chemist

Page 2 of 2 1 2

Moderated by  lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.009s Queries: 22 (0.006s) Memory: 0.9275 MB (Peak: 1.0102 MB) Data Comp: Off Server Time: 2020-09-30 21:52:42 UTC
Valid HTML 5 and Valid CSS