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CCP4BB  April 2012

CCP4BB April 2012

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Subject:

Re: Arp/WARP for multi-chain complex

From:

Victor Lamzin <[log in to unmask]>

Reply-To:

Victor Lamzin <[log in to unmask]>

Date:

Thu, 19 Apr 2012 17:52:20 +0200

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (103 lines)

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 different chains will have  
consequtive numbers, 10 and 11:
11111111112222222222

Also imagine ARP/wARP built all residues in both fragments and is  
about to sequence-dock them. Fortunately (or not) it removes termini,  
so that you have:
-11111111--22222222-

Now, if the distance between residue 9 (the last in the first chain)  
and 12 (the first in the second chain) is longer than about  
3.8*(12-9)=11.4 A (the actual formula is a bit more complex), one of  
the fragments will not be sequence docked and its side chains will be  
chopped to glycines. Placing a few alaninines (5 to 10) in between the  
chains will certainly help.

On the other hand, one should not add too many alanines overall.  
ARP/wARP pretends to be clever and tries to figure out the NCS-order  
automatically. If you added far too many alanines, you may confuse  
ARP/wARP in thinking that your structure is, say, a trimer rather than  
a tetramer.

There could be of course better ways of sequence-docking for  
heteromers, but the above is the current status in 'ARP/wARP Classic'  
protein model building.

With best regards,
Victor



Quoting "Tim Gruene" <[log in to unmask]>:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> 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
>
> GPG Key ID = A46BEE1A
>
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> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
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>

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