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Missing residue coordinates in PDB files

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Missing residue coordinates in PDB files
#1

Dear Sir or Madam,
I got a PDB file, in which some of the residue coordinates are not resolved (shown below, missing from 136-139). But I can still know the amino acid sequence. Can I ask what is the best way to estimate those missing coordinates?

I am thinking manually copy the coordinates of same type of residue to the PDB file, followed by minimization to some extent. Is this okay? What particular minimization protocol/restrain should I use?

Thank you very much.

Yours sincerely
Cheng

ATOM 2660 N SER H 134 -0.549 9.050 11.404 1.00 33.53 N
ATOM 2661 CA SER H 134 -1.919 8.529 11.438 1.00 38.02 C
ATOM 2662 C SER H 134 -2.105 7.408 12.463 1.00 41.85 C
ATOM 2663 O SER H 134 -3.228 6.959 12.700 1.00 39.05 O
ATOM 2664 CB SER H 134 -2.350 8.045 10.050 1.00 37.89 C
ATOM 2665 OG SER H 134 -1.498 7.022 9.570 1.00 42.01 O
ATOM 2666 N LYS H 135 -1.001 6.961 13.059 1.00 47.51 N
ATOM 2667 CA LYS H 135 -1.029 5.903 14.069 1.00 51.39 C
ATOM 2668 C LYS H 135 -0.591 6.439 15.428 1.00 53.23 C
ATOM 2669 O LYS H 135 -1.014 7.516 15.847 1.00 53.96 O
ATOM 2670 CB LYS H 135 -0.138 4.732 13.648 1.00 50.54 C
ATOM 2671 N GLY H 140 0.891 13.298 23.955 1.00 39.35 N
ATOM 2672 CA GLY H 140 1.807 13.280 22.820 1.00 38.75 C
ATOM 2673 C GLY H 140 1.763 14.558 22.001 1.00 36.71 C
ATOM 2674 O GLY H 140 0.687 15.107 21.745 1.00 37.83 O
ATOM 2675 N THR H 141 2.940 15.032 21.598 1.00 35.29 N
ATOM 2676 CA THR H 141 3.067 16.212 20.743 1.00 32.87 C
ATOM 2677 C THR H 141 3.401 15.802 19.312 1.00 31.34 C
ATOM 2678 O THR H 141 4.389 15.103 19.063 1.00 29.34 O
ATOM 2679 CB THR H 141 4.135 17.198 21.270 1.00 32.86 C
ATOM 2680 OG1 THR H 141 3.788 17.616 22.595 1.00 36.70 O
ATOM 2681 CG2 THR H 141 4.229 18.431 20.372 1.00 30.68 C

Post Situation: 
Thu, 2014-09-04 07:34
lanselibai

What you're trying to do is basically the same as loop remodeling. (In Rosetta it's called loop remodeling even if the secondary structure isn't a loop).

For regular Rosetta, I'd suggest looking at the Comparative Modeling/Homology Modeling tutorials at http://www.meilerlab.org/index.php/jobs/resources (Click on "Rosetta Tutorials") You're basically doing single template homology modeling, but the "homolog" you're using is the (partial) structure of the protein itself. The protocol is basically to "thread" the sequence you want onto the structure you have, leaving placeholder residues in the spots where you don't have structural information. You would then do loop remodeling of the insertions and gaps to try to find a backbone conformation that closes the gaps, or allows the residues to fit in.

For PyRosetta, you can insert the placeholder residues yourself with pose.append_polymer_residue_after_seqpos() or pose.prepend_polymer_residue_before_seqpos(). Remember that the position is in sequential pose numbering, so the numbers may change as you insert your residues. Then you can use one of the standard PyRosetta loop remodeling scripts to rebuild the residues you just inserted, and find good coordinates for them. I'd suggest working through Workshop #8 (http://www.pyrosetta.org/tutorials), and then applying a similar protocol to your system.

Thu, 2014-09-04 11:36
rmoretti