Hi Tony, Tim, Victor and Saul,

Thank you very much for the help on Arp/wARP setup. I did it with one big pir file last night without inserting the poly Ala, most of the terminal residues at the "sequence junctions" were not fitted or removed as Tony mentioned. I am amazed how well ArpwArp worked overall!

Regards,

Tongqing

Tongqing Zhou, Ph.D. 
Staff Scientist
Structural Biology Section
Vaccine Research Center, NIAID/NIH
Building 40, Room 4607B
40 Convent Drive, MSC3027
Bethesda, MD 20892
(301) 594-8710 (Tel)
(301) 793-0794 (Cell)
(301) 480-2658 (Fax)
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-----Original Message-----
From: Antony Oliver [mailto:[log in to unmask]] 
Sent: Thursday, April 19, 2012 11:57 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] Arp/WARP for multi-chain complex

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" <[log in to unmask]> wrote:

> 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
>> 
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