Re: [ccp4bb] Arp/WARP for multi-chain complex
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) ** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its 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 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 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: > 1122 > > 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: > ---- > > 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" : > >> -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 ... sequence B >>> 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]" >>> 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 >> >> -BEGIN PGP SIGNATURE- >> Version: GnuPG v1.4.12 (GNU/Linux) >> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ >> >> iD8DBQFPj8ZVUxlJ7aRr7hoRAqu6AKDff8lY6Ehj2A8u76UfTgiIcNoqMACfd7Wr >> 3cDlEfHVVWxASrw9qxMTwMY= >> =sFT8 >> -END PGP SIGNATURE- >>
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" 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: > 1122 > > 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: > ---- > > 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" : > >> -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 ... sequence B >>> 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]" >>> 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 >> >> -BEGIN PGP SIGNATURE- >> Version: GnuPG v1.4.12 (GNU/Linux) >> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ >> >> iD8DBQFPj8ZVUxlJ7aRr7hoRAqu6AKDff8lY6Ehj2A8u76UfTgiIcNoqMACfd7Wr >> 3cDlEfHVVWxASrw9qxMTwMY= >> =sFT8 >> -END PGP SIGNATURE- >>
Re: [ccp4bb] Arp/WARP for multi-chain complex
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: 1122 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: ---- 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" : -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 ... sequence B 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]" 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 -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPj8ZVUxlJ7aRr7hoRAqu6AKDff8lY6Ehj2A8u76UfTgiIcNoqMACfd7Wr 3cDlEfHVVWxASrw9qxMTwMY= =sFT8 -END PGP SIGNATURE-
Re: [ccp4bb] Arp/WARP for multi-chain complex
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 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. You can put the chains into a single *.pir file and separate each chain with 10 Alanines. For instance (assuming the antigen is protein): Heavy_chain_sequence_AA_Light_chain_sequence_AA_Antigen_sequence To do this you need to edit the *.pir file in a text editor. Details on the file format are in the link below: http://www.bioinformatics.nl/tools/crab_pir.html Please contact me if you hit any problems or this suggestion isn't clear. Saul Hazledine
Re: [ccp4bb] Arp/WARP for multi-chain complex
-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 ... sequence B > 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]" > 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 -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPj8ZVUxlJ7aRr7hoRAqu6AKDff8lY6Ehj2A8u76UfTgiIcNoqMACfd7Wr 3cDlEfHVVWxASrw9qxMTwMY= =sFT8 -END PGP SIGNATURE-
Re: [ccp4bb] Arp/WARP for multi-chain complex
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 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]"
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
[ccp4bb] Arp/WARP for multi-chain complex
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
