Hi all,
Just to conclude on this - ARCIMBOLDO via CCP4 in coiled coil mode worked quite
nicely in the end now that I finally had time to work through it - took a few
days with 8 x 20 aa peptides as the search set
on my old iMac but the end result was fine :). So didn't have to try other
options
d Strelkov paper cited above.
Sergei
From: CCP4 bulletin board on behalf of Sergei Strelkov
Sent: Tuesday, October 8, 2019 14:14
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] coiled coil molecular replacement
Dear Tommi,
With coiled coils you certain
P4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] coiled coil molecular replacement
Hello,
We have a bit tricky case of coiled coil protein with good data (2.05Å) for
dimeric coiled coil (dimer in AU) - looks like AMPLE might be a way
to solve such cases, if you know other good programs please suggest (Better yet
Hi Tommi, as sent by Kay ARCIMBOLDO has a specific mode to solve coiled
coils (http://scripts.iucr.org/cgi-bin/paper?cb5097).
Here you can find the tutorial: http://chango.ibmb.csic.es/tutorial_coiled,
it explains how to launch it through the command line and a summary
explaining the improvements
Hi Tommi
Yes, AMPLE does well with coiled-coils. The QUARK route is the easiest
to try. In your position I would simply trim a bit of sequence off
either end. Maybe you can see homologs that are a bit shorter at one
terminus? In any case, that's unlikely to affect the modelling and we've
seen
Hi Tommi,
Arcimboldo is a good program for that - see
http://scripts.iucr.org/cgi-bin/paper?cb5097
HTH
Kay
On Mon, 7 Oct 2019 21:33:44 +, Kajander, Tommi A
wrote:
>Hello,
>
>We have a bit tricky case of coiled coil protein with good data (2.05Å) for
>dimeric coiled coil (dimer in AU)
Hello,
We have a bit tricky case of coiled coil protein with good data (2.05Å) for
dimeric coiled coil (dimer in AU) - looks like AMPLE might be a way
to solve such cases, if you know other good programs please suggest (Better yet
if there is a clear how-to manual)
Some technical tips on usag
