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
> 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
>
>
>
>
>
>
>
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.
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
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.
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
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
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
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