Hi all,
Just writing an update, as I have had two people contact me asking if I had
found a solution and if I could share. I would like to apologize first for not
phrasing my question to describe the situation simply. I had several
suggestions that Coot, and PISA could do it but actually can no
eudi 26 février 2015 15h00
Objet : Re: [ccp4bb] RMSD of dimers
Dear CCP4bbers,
If I remember correctly you can do this in LSQMAN (EXPLICIT superimposition
command if I remember well): the superimposition is made between residues of
chain A2 onto those of chain A1, then you apply the rotatio
s5.fr/ ,
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18
De : Eugene Krissinel
À : CCP4BB@JISCMAIL.AC.UK
Envoyé le : Jeudi 26 février 2015 14h17
Objet : Re: [ccp4bb] RMSD of dimers
No, the question seems to be slightly different. While one can use either
CCP4's SSM or
No, the question seems to be slightly different. While one can use
either CCP4's SSM or GESAMT to superpose 2 dimers, these algorithms
would balance RMSD between both chains and produce something optimal for
both chains. What is required, however, is optimal superposition on one
pair of chains
Doesnt pisa give you some of this information? It lists all likely
homodimers and I think gives RMSD too
Eleanor
On 24 February 2015 at 22:00, Thomas Holder
wrote:
> Hi Dan,
>
> gaps/insertions should be no problem for PyMOL's rms_cur command, as long
> as chain identifiers match (and all other
Hi Dan,
gaps/insertions should be no problem for PyMOL's rms_cur command, as long as
chain identifiers match (and all other atomic identifiers!).
See http://pymolwiki.org/index.php/Fit for a description of the matchmaker
argument.
Cheers,
Thomas
On 24 Feb 2015, at 16:30, D Bonsor wrote:
>
I have a family of homodimers (denoted A1B1, A2B2, A3B3...) which I have
superimposed using Chain A. Several programs will produce the RMSD of Chain A2,
A3, A4... to Chain A1. However, I would like to know the RMSDs of Chain B2, B3,
B4... to Chain B1 when I have superimposed the structures relat
