Member Site › Forums › Rosetta++ › Rosetta++ – General › To apply distance constraint to MULTIPLE residue pairs, what’s the format?
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nobuyasu.
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AuthorPosts
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April 6, 2009 at 5:24 pm #526
Anonymous
Dear All,
I have a question about distance constraint.
For single pair of two residues, the following format:
7.0
370 A
371 Bworks. 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 Bor:
7.0
1 A
2 B
3 A
4 Bbut none of them works.
Please help. Thank you in advance.
Shirley
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April 6, 2009 at 5:25 pm #4061
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
>
>
>
>
>
>
> -
April 8, 2009 at 4:23 pm #4062
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.
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April 9, 2009 at 4:42 am #4064
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 -
April 9, 2009 at 5:22 pm #4066
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 -10It 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. -
April 10, 2009 at 9:51 am #4067
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 -
April 16, 2009 at 7:36 pm #4069
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-
April 21, 2009 at 3:05 pm #4070
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
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June 18, 2009 at 8:13 am #4102
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 Afilter -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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