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pdb_fixinsert does not perform renumbering properly when a residue with insertion code is missing.
For example,
1-1) Input : full PDB of 7JMO heavy chain
ATOM 2306 N ALA H 99 -52.017 1.887 12.504 1.00 37.00 N
ATOM 2307 CA ALA H 99 -51.622 0.503 12.717 1.00 46.76 C
ATOM 2308 C ALA H 99 -50.170 0.230 12.336 1.00 43.32 C
ATOM 2309 O ALA H 99 -49.696 -0.891 12.551 1.00 42.90 O
ATOM 2310 CB ALA H 99 -52.554 -0.435 11.942 1.00 29.26 C
ATOM 2311 N GLY H 100 -49.452 1.207 11.780 1.00 38.57 N
ATOM 2312 CA GLY H 100 -48.031 1.013 11.563 1.00 45.52 C
ATOM 2313 C GLY H 100 -47.348 1.851 10.499 1.00 38.13 C
ATOM 2314 O GLY H 100 -46.260 1.485 10.051 1.00 46.04 O
ATOM 2315 N GLY H 100A -47.951 2.963 10.083 1.00 41.11 N
ATOM 2316 CA GLY H 100A -47.279 3.829 9.122 1.00 41.50 C
ATOM 2317 C GLY H 100A -46.986 3.152 7.785 1.00 45.26 C
ATOM 2318 O GLY H 100A -47.531 2.098 7.446 1.00 43.32 O
ATOM 2319 N MET H 100B -46.097 3.786 7.016 1.00 38.57 N
ATOM 2320 CA MET H 100B -45.665 3.253 5.722 1.00 40.39 C
ATOM 2321 C MET H 100B -44.512 2.288 5.965 1.00 44.36 C
ATOM 2322 O MET H 100B -43.340 2.670 5.985 1.00 40.96 O
ATOM 2323 CB MET H 100B -45.262 4.377 4.774 1.00 33.52 C
ATOM 2324 CG MET H 100B -46.433 5.114 4.139 1.00 41.30 C
ATOM 2325 SD MET H 100B -45.911 6.355 2.934 1.00 46.75 S
ATOM 2326 CE MET H 100B -47.492 6.828 2.238 1.00 50.79 C
ATOM 2327 N ASP H 101 -44.847 1.010 6.143 1.00 46.96 N
ATOM 2328 CA ASP H 101 -43.864 0.026 6.576 1.00 38.63 C
ATOM 2329 C ASP H 101 -43.156 -0.683 5.429 1.00 46.59 C
ATOM 2330 O ASP H 101 -42.049 -1.195 5.632 1.00 48.32 O
ATOM 2331 CB ASP H 101 -44.528 -1.019 7.480 1.00 46.37 C
ATOM 2332 CG ASP H 101 -45.602 -1.817 6.762 1.00 54.42 C
ATOM 2333 OD1 ASP H 101 -46.242 -1.270 5.839 1.00 43.57 O
ATOM 2334 OD2 ASP H 101 -45.803 -2.996 7.119 1.00 51.72 O
ATOM 2335 N VAL H 102 -43.751 -0.734 4.239 1.00 39.00 N
ATOM 2336 CA VAL H 102 -43.159 -1.425 3.100 1.00 41.76 C
ATOM 2337 C VAL H 102 -42.959 -0.433 1.967 1.00 44.62 C
ATOM 2338 O VAL H 102 -43.911 0.234 1.539 1.00 42.63 O
ATOM 2339 CB VAL H 102 -44.017 -2.614 2.634 1.00 46.36 C
ATOM 2340 CG1 VAL H 102 -43.351 -3.304 1.450 1.00 43.45 C
ATOM 2341 CG2 VAL H 102 -44.224 -3.591 3.778 1.00 40.81 C
1-2) Ouput of pdb_fixinsert , for this case work successful
ATOM 2306 N ALA H 102 -52.017 1.887 12.504 1.00 37.00 N
ATOM 2307 CA ALA H 102 -51.622 0.503 12.717 1.00 46.76 C
ATOM 2308 C ALA H 102 -50.170 0.230 12.336 1.00 43.32 C
ATOM 2309 O ALA H 102 -49.696 -0.891 12.551 1.00 42.90 O
ATOM 2310 CB ALA H 102 -52.554 -0.435 11.942 1.00 29.26 C
ATOM 2311 N GLY H 103 -49.452 1.207 11.780 1.00 38.57 N
ATOM 2312 CA GLY H 103 -48.031 1.013 11.563 1.00 45.52 C
ATOM 2313 C GLY H 103 -47.348 1.851 10.499 1.00 38.13 C
ATOM 2314 O GLY H 103 -46.260 1.485 10.051 1.00 46.04 O
ATOM 2315 N GLY H 104 -47.951 2.963 10.083 1.00 41.11 N
ATOM 2316 CA GLY H 104 -47.279 3.829 9.122 1.00 41.50 C
ATOM 2317 C GLY H 104 -46.986 3.152 7.785 1.00 45.26 C
ATOM 2318 O GLY H 104 -47.531 2.098 7.446 1.00 43.32 O
ATOM 2319 N MET H 105 -46.097 3.786 7.016 1.00 38.57 N
ATOM 2320 CA MET H 105 -45.665 3.253 5.722 1.00 40.39 C
ATOM 2321 C MET H 105 -44.512 2.288 5.965 1.00 44.36 C
ATOM 2322 O MET H 105 -43.340 2.670 5.985 1.00 40.96 O
ATOM 2323 CB MET H 105 -45.262 4.377 4.774 1.00 33.52 C
ATOM 2324 CG MET H 105 -46.433 5.114 4.139 1.00 41.30 C
ATOM 2325 SD MET H 105 -45.911 6.355 2.934 1.00 46.75 S
ATOM 2326 CE MET H 105 -47.492 6.828 2.238 1.00 50.79 C
ATOM 2327 N ASP H 106 -44.847 1.010 6.143 1.00 46.96 N
ATOM 2328 CA ASP H 106 -43.864 0.026 6.576 1.00 38.63 C
ATOM 2329 C ASP H 106 -43.156 -0.683 5.429 1.00 46.59 C
ATOM 2330 O ASP H 106 -42.049 -1.195 5.632 1.00 48.32 O
ATOM 2331 CB ASP H 106 -44.528 -1.019 7.480 1.00 46.37 C
ATOM 2332 CG ASP H 106 -45.602 -1.817 6.762 1.00 54.42 C
ATOM 2333 OD1 ASP H 106 -46.242 -1.270 5.839 1.00 43.57 O
ATOM 2334 OD2 ASP H 106 -45.803 -2.996 7.119 1.00 51.72 O
ATOM 2335 N VAL H 107 -43.751 -0.734 4.239 1.00 39.00 N
ATOM 2336 CA VAL H 107 -43.159 -1.425 3.100 1.00 41.76 C
ATOM 2337 C VAL H 107 -42.959 -0.433 1.967 1.00 44.62 C
ATOM 2338 O VAL H 107 -43.911 0.234 1.539 1.00 42.63 O
ATOM 2339 CB VAL H 107 -44.017 -2.614 2.634 1.00 46.36 C
ATOM 2340 CG1 VAL H 107 -43.351 -3.304 1.450 1.00 43.45 C
ATOM 2341 CG2 VAL H 107 -44.224 -3.591 3.778 1.00 40.81 C
However, when I delete the residue with number 100B and 101
2-1) Input, delete line for residue number 100B and 101
ATOM 2306 N ALA H 99 -52.017 1.887 12.504 1.00 37.00 N
ATOM 2307 CA ALA H 99 -51.622 0.503 12.717 1.00 46.76 C
ATOM 2308 C ALA H 99 -50.170 0.230 12.336 1.00 43.32 C
ATOM 2309 O ALA H 99 -49.696 -0.891 12.551 1.00 42.90 O
ATOM 2310 CB ALA H 99 -52.554 -0.435 11.942 1.00 29.26 C
ATOM 2311 N GLY H 100 -49.452 1.207 11.780 1.00 38.57 N
ATOM 2312 CA GLY H 100 -48.031 1.013 11.563 1.00 45.52 C
ATOM 2313 C GLY H 100 -47.348 1.851 10.499 1.00 38.13 C
ATOM 2314 O GLY H 100 -46.260 1.485 10.051 1.00 46.04 O
ATOM 2315 N GLY H 100A -47.951 2.963 10.083 1.00 41.11 N
ATOM 2316 CA GLY H 100A -47.279 3.829 9.122 1.00 41.50 C
ATOM 2317 C GLY H 100A -46.986 3.152 7.785 1.00 45.26 C
ATOM 2318 O GLY H 100A -47.531 2.098 7.446 1.00 43.32 O
ATOM 2335 N VAL H 102 -43.751 -0.734 4.239 1.00 39.00 N
ATOM 2336 CA VAL H 102 -43.159 -1.425 3.100 1.00 41.76 C
ATOM 2337 C VAL H 102 -42.959 -0.433 1.967 1.00 44.62 C
ATOM 2338 O VAL H 102 -43.911 0.234 1.539 1.00 42.63 O
ATOM 2339 CB VAL H 102 -44.017 -2.614 2.634 1.00 46.36 C
ATOM 2340 CG1 VAL H 102 -43.351 -3.304 1.450 1.00 43.45 C
ATOM 2341 CG2 VAL H 102 -44.224 -3.591 3.778 1.00 40.81 C
2-2) Output, WRONG numbering compare it with 1-2. Different residue numbering with 1-2
ATOM 2306 N ALA H 102 -52.017 1.887 12.504 1.00 37.00 N
ATOM 2307 CA ALA H 102 -51.622 0.503 12.717 1.00 46.76 C
ATOM 2308 C ALA H 102 -50.170 0.230 12.336 1.00 43.32 C
ATOM 2309 O ALA H 102 -49.696 -0.891 12.551 1.00 42.90 O
ATOM 2310 CB ALA H 102 -52.554 -0.435 11.942 1.00 29.26 C
ATOM 2311 N GLY H 103 -49.452 1.207 11.780 1.00 38.57 N
ATOM 2312 CA GLY H 103 -48.031 1.013 11.563 1.00 45.52 C
ATOM 2313 C GLY H 103 -47.348 1.851 10.499 1.00 38.13 C
ATOM 2314 O GLY H 103 -46.260 1.485 10.051 1.00 46.04 O
ATOM 2315 N GLY H 104 -47.951 2.963 10.083 1.00 41.11 N
ATOM 2316 CA GLY H 104 -47.279 3.829 9.122 1.00 41.50 C
ATOM 2317 C GLY H 104 -46.986 3.152 7.785 1.00 45.26 C
ATOM 2318 O GLY H 104 -47.531 2.098 7.446 1.00 43.32 O
ATOM 2335 N VAL H 106 -43.751 -0.734 4.239 1.00 39.00 N
ATOM 2336 CA VAL H 106 -43.159 -1.425 3.100 1.00 41.76 C
ATOM 2337 C VAL H 106 -42.959 -0.433 1.967 1.00 44.62 C
ATOM 2338 O VAL H 106 -43.911 0.234 1.539 1.00 42.63 O
ATOM 2339 CB VAL H 106 -44.017 -2.614 2.634 1.00 46.36 C
ATOM 2340 CG1 VAL H 106 -43.351 -3.304 1.450 1.00 43.45 C
ATOM 2341 CG2 VAL H 106 -44.224 -3.591 3.778 1.00 40.81 C
The text was updated successfully, but these errors were encountered:
I don't know if this is a bug because the insertion is correctly addressed (to my knowledge and expectations). But, for what I understood, you were expecting VAL106 to become VAL105, is that it? The philosophy of pdbtools is "one-tool-one-job". Therefore, I think other tools should take the residue number correction. You may need to chain several tools for example: 1. split the chain in two, 2. correct the numbers, 3. merge the chain again.
I was expecting VAL106 (in 2-2) to become VAL107 (as in 1-2). Because input protein (1-1) and input protein(2-1) is essentially same. The only difference is there is missing residue( ex. not resolved) in input protein(2-1)
I would like to ask about the algorithm of this program.
1)Can "pdb_fixinsert" also be used for PDB files where there is missing residue in ATOM line?
For example, the structure of residue 100B and 101 is not determined. Therefore, there is no ATOM line for residue number 100B and 101. Can "pdb_fixinsert" renumber input PDB considering this kind of missing using SEQRES line?
I thought that this program creates a reference sequence through the SEQRES line and renumbers the ATOM line information by aligning it with the reference sequence. Is it right?
I think the second question is related with first question.
Can "pdb_fixinsert" renumber input PDB considering this kind of missing using SEQRES line?
No. pdb_fixinsert operates only by reading the ATOM/HETATM lines. Therefore, I don't expect VAL102 to become VAL107 because 100B and ASP101 are not there, contrarily to 1-1. pdb_fixinsert behaves as we expect it to behave. The 2-2 scenario is correct to our expectations and tests.
Having clarified your concerns and the fixinsert algorithm, I see this is not a bug, but instead feature request 😉 Thanks for this insightful conversation! 🚀
@JoaoRodrigues@amjjbonvin should pdb_fixinsert give priority to SEQRES lines in case they are present? Is this a feature we would be willing to add?
pdb_fixinsert does not perform renumbering properly when a residue with insertion code is missing.
For example,
1-1) Input : full PDB of 7JMO heavy chain
1-2) Ouput of pdb_fixinsert , for this case work successful
However, when I delete the residue with number 100B and 101
2-1) Input, delete line for residue number 100B and 101
2-2) Output, WRONG numbering compare it with 1-2. Different residue numbering with 1-2
The text was updated successfully, but these errors were encountered: