Re: [ccp4bb] Comparing two proteins

2011-04-14 Thread Bosch, Juergen
Katie Carr University of Nottingham -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eleanor Dodson Sent: 14 April 2011 11:51 To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Comparing two proteins On 04/13/2011 09

Re: [ccp4bb] Comparing two proteins

2011-04-14 Thread Katie Carr
Sent: 14 April 2011 11:51 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Comparing two proteins On 04/13/2011 09:18 PM, REX PALMER wrote: > Dear All > What is the best program to use for comparing two protein structures which > are very similar both structurally and wrt aa sequence?

Re: [ccp4bb] Comparing two proteins

2011-04-14 Thread Eleanor Dodson
On 04/13/2011 09:18 PM, REX PALMER wrote: Dear All What is the best program to use for comparing two protein structures which are very similar both structurally and wrt aa sequence? ie to get the rms deviations both generally and in selected regions. Rex Palmer Birkbeck College Using CCP4 g

Re: [ccp4bb] Comparing two proteins

2011-04-14 Thread Francois Berenger
This tool looks cool also (especially to all the maximum likelihood fans of this list I guess): http://www.theseus3d.org/ --- Theseus is a program that simultaneously superimposes multiple macromolecular structures. Instead of using the conventional least-squares criteria, Theseus finds the opt

Re: [ccp4bb] Comparing two proteins

2011-04-14 Thread Tim Gruene
Yes, I forgot about escet. The more up to date wab address is http://webapps.embl-hamburg.de/escet/ even though that page still lists Thomas' address in Italy Tim On Thu, Apr 14, 2011 at 10:05:47AM +0200, Gergely Katona wrote: > ESCET is also very useful to reveal small, but significant > differe

Re: [ccp4bb] Comparing two proteins

2011-04-14 Thread Gergely Katona
ESCET is also very useful to reveal small, but significant differences. It also identifies conformationally invariant regions for superposition. http://schneider.group.ifom-ieo-campus.it/escet/index.html Gergely On Thu, Apr 14, 2011 at 9:34 AM, Tim Gruene wrote: > Hello Rex, > > most programs p

Re: [ccp4bb] Comparing two proteins

2011-04-14 Thread Tim Gruene
Hello Rex, most programs probably use similar algorithms for superpositions, so you can pick your choice: - O - lsqman - lsqkab - coot - ... are all similarily comfortable to use in my opinion. Tim On Wed, Apr 13, 2011 at 09:18:27PM +0100, REX PALMER wrote: > Dear All > What is the best program

Re: [ccp4bb] Comparing two proteins

2011-04-13 Thread Eric Pettersen
On Apr 13, 2011, at 4:00 PM, Rex Palmer wrote: What is the best program to use for comparing two protein structures which are very similar both structurally and wrt aa sequence? ie to get the rms deviations both generally and in selected regions. Best is kind of subjective, but you can use

Re: [ccp4bb] Comparing two proteins

2011-04-13 Thread Pavel Afonine
Hi Rex, (not claiming it is the best) may be you can use structure comparison tool that allows you to load a bunch of similar structures, superpose them and corresponding maps, and it will highlight various differences (Ramachandran, rotamers, secondary structure, etc..). Have a look at page #17

[ccp4bb] Comparing two proteins

2011-04-13 Thread REX PALMER
Dear All What is the best program to use for comparing two protein structures which are very similar both structurally and wrt aa sequence? ie to get the rms deviations both generally and in selected regions.   Rex Palmer Birkbeck College