representatives.
**
-Original Message-
From: Antony Oliver [mailto:antony.oli...@sussex.ac.uk]
Sent: Thursday, April 19, 2012 11:57 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Arp/WARP for multi-chain complex
Thanks Victor - for giving a rational and detailed
Thanks Victor - for giving a rational and detailed explanation. I obviously got
carried away with the number of alanines to intersperse!
With regards,
Tony.
On 19 Apr 2012, at 16:52, "Victor Lamzin" wrote:
> Dear Tony, Tongqing, Tim,
>
> Adding some alanine spacer is good for a simple rea
Dear Tony, Tongqing, Tim,
Adding some alanine spacer is good for a simple reason - during
sequence docking ARP/wARP checks the distance between the ends of the
fragments.
Imagine you have two chains, 10 residues each. If you concatenate them
together, terminal residues belonging to differ
Dear Tongqing,
On Apr 19, 2012, at 5:26 AM, Zhou, Tongqing (NIH/VRC) [E] wrote:
> I am trying to use Arp/wArp to build an antibody-antigen complex with 1.65 A
> data, there are three chains (heavy, light chains of antibody and the
> antigen) in the complex, my question is how to put the sequenc
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Dear Tony, dear Tongqing,
the way I understand the working mechanism of arp/warp works I do not
see the point introducing the polyALA spacer into the sequence. Just
concatenate all sequences into one file as though it was one molecule.
Cheers,
Tim
O
In the absence of a likely, more sensible, answer - I think the trick is/was to
simply put everything in one pir file, but "link" each sequence with a run of
20 or so alanines i.e. sequence A followed by ... sequence B
sequence C.
There may well be a more el
Dear All,
I am trying to use Arp/wArp to build an antibody-antigen complex with 1.65 A
data, there are three chains (heavy, light chains of antibody and the antigen)
in the complex, my question is how to put the sequences in the *.pir file so
that it still identifies different chains. It looks
