To apply distance constraint to MULTIPLE residue pairs, what’s the format?

[Anonymous]

Dear All,

I have a question about distance constraint.

For single pair of two residues, the following format:

7.0
370 A
371 B

works. But I need to apply distance constraint to MULTIPLE residue pairs. What is the format? I tried different ways as follows:

7.0
1 A
2 B
(with or without blank line)
7.0
3 A
4 B

or:

7.0
1 A
2 B
3 A
4 B

but none of them works.

Please help. Thank you in advance.

Shirley

[Anonymous]

> Dear All,
>
> I have a question about distance constraint.
>
> For single pair of two residues, the following format:
>
> 7.0
> 370 A
> 371 B
>
> works. But I need to apply distance constraint to MULTIPLE residue pairs. What is the format? I tried different ways as follows:
>
> 7.0
> 1 A
> 2 B
> (with or without blank line)
> 7.0
> 3 A
> 4 B
>
>
> or:
>
> 7.0
> 1 A
> 2 B
> 3 A
> 4 B
>
> but none of them works.
>
> Please help. Thank you in advance.
>
> Shirley
>
>
>
>
>
>
>

[bpierce]

Hi Shirley,

For rosetta++ the format for constraints (in a .cst file) is like this:

CB-CB csts from ksync alignment
measured in 1XZY.pdb
551
4 CB 19 CB 18.02 14.02 0.00
4 CB 20 CB 12.95 8.95 0.00
4 CB 22 CB 7.62 3.62 0.00
4 CB 23 CB 9.48 5.48 0.00
4 CB 24 CB 7.48 3.48 0.00
…

The number 551 refers to the total number of constraints in teh file.

I guess you are using docking. I think docking will also read the above style constraint file (but I’m not 100% sure). Try it and see.

Vanita.

[Anonymous]

Hi all,

I have the exact same question as Shirley. Much thanks to Vanita for the reply. However her example gives NOE distance constraints, if I’m not mistaken… Rather than atom-atom distances, I’d like to specify residue-residue distances as requested by Shirley.
However, Rosetta only reads in the 1st constraint specified… Is there any way to overcome this? Thanks much in advance.

Regards,
Shamima

[Anonymous]

Thank Vanita and Shamima’s response very much. Yes, I would like to specify residue-residue distance, and I intended to use a .dst file and so hope rosetta could accept more than one distance constraints in the .dst file.

I did try Vanita’s idea while using a .cst file in slightly different format as follows:

2
-1000
1 A
2 A
3 A
4 A
1 B
2 B
3 B
0 B
-100
8 A
0 A
filter -10

It seems to be running, while I’m not sure yet if it’s doing the right thing.

Any input will be appreciated,

Shirley

> Hi Shirley,
>
> For rosetta++ the format for constraints (in a .cst file) is like this:
>
> CB-CB csts from ksync alignment
> measured in 1XZY.pdb
> 551
> 4 CB 19 CB 18.02 14.02 0.00
> 4 CB 20 CB 12.95 8.95 0.00
> 4 CB 22 CB 7.62 3.62 0.00
> 4 CB 23 CB 9.48 5.48 0.00
> 4 CB 24 CB 7.48 3.48 0.00
> …
>
> The number 551 refers to the total number of constraints in teh file.
>
> I guess you are using docking. I think docking will also read the above style constraint file (but I’m not 100% sure). Try it and see.
>
> Vanita.

[Anonymous]

Hi Shirley,

If I’m not wrong, the constraints specified in a .cst file “force” Rosetta to only output decoys that contain those specified residues (1-4, 8 of Chain A and 1-3 of Chain B in your case) at the binding interface. Any decoys that do not include these residues as part of the binding interface are automatically rejected.

However, if I’m not mistaken it’s just a “loose definition” of ensuring the residues are present at the binding interface. Which is why I’m trying to achieve a closer (or accurate?) binding by specifying distance constraints in the .dst file, but to no avail thus far as far as multiple residues are concerned.

Regards,
Shamima

[Anonymous]

Hi Shamima,

Thank you for your comments. You are right, the .cst file only poses a loose definition for binding interface residues. I would also like to apply distance constraints in .dst file instead if it were available.

Best regards,

Shirley

> Hi Shirley,
>
> If I’m not wrong, the constraints specified in a .cst file “force” Rosetta to only output decoys that contain those specified residues (1-4, 8 of Chain A and 1-3 of Chain B in your case) at the binding interface. Any decoys that do not include these residues as part of the binding interface are automatically rejected.
>
> However, if I’m not mistaken it’s just a “loose definition” of ensuring the residues are present at the binding interface. Which is why I’m trying to achieve a closer (or accurate?) binding by specifying distance constraints in the .dst file, but to no avail thus far as far as multiple residues are concerned.
>
> Regards,
> Shamima

[fabio]

Unfortunately the .dst format only allows a single restraint between residues pairs in Rosetta++.

the docking_read_dist_constraint function in docking_constraint.cc defines how the dst file is read.

To add more constraints you would need change the size of the dist_constraint_residue array in interface.cc and also change the evaluation of the constraints in docking_dist_constr_bonus in docking_constraints.cc such that it iterated over all of the multiple constraints that you supply.

There are probably a couple of other things that you would need to do as well.

Alternatively you may want to ask whether the Rosetta-3.0 docking program can handle multiple residue pairs constraints. It has several advantages built in. Reisdue pair constraints may be one of them.

Kristian

[nobuyasu]

hi,
But the following contraint is just a docking site constraints.
2
-1000
1 A
2 A
3 A
4 A
1 B
2 B
3 B
0 B
-100
8 A
0 A

filter -10

not distance contraint

/// distance constraint file format: (filter only)
///
/// 10.0 distance (Angstroms)
/// 23 H residue 1
/// 24 H residue 2

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