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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
On 04/19/12 08:51, Antony Oliver wrote:
> 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 AAAA ... AAAA sequence B AAAA .... AAAA .... AAAA
> sequence C.
>
> There may well be a more elegant solution - but I'm fairly sure
> this worked previously for us.
>
> With regards,
>
> Tony.
>
>
> On 19 Apr 2012, at 04:26, "Zhou, Tongqing (NIH/VRC) [E]"
> <[log in to unmask]> wrote:
>
>> 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 like Arp/wArp only accepts *.pir file
>> with one sequence id.
>>
>> Thanks,
>>
>>
>> Tongqing
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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