How To Find Absent Atoms In Residue Of Pdb File

I have pdb file like

ATOM   3617  N   LYS C  86      -1.628  49.011  29.273  1.00 56.40          
ATOM   3618  CA  LYS C  86      -0.754  49.219  28.124  1.00 58.75          
ATOM   3619  C   LYS C  86       0.450  50.088  28.474  1.00 60.18          
ATOM   3620  O   LYS C  86       1.588  49.594  28.327  1.00 61.37          
ATOM   3621  CB  LYS C  86      -1.531  49.872  26.975  1.00 59.36          
ATOM   3622  CG  LYS C  86      -2.813  49.151  26.583  1.00 59.82          
ATOM   3623  CD  LYS C  86      -3.910  49.367  27.614  1.00 59.53          
ATOM   3624  CE  LYS C  86      -5.185  48.643  27.225  1.00 59.49          
ATOM   3625  NZ  LYS C  86      -6.285  48.924  28.187  1.00 59.42          
ATOM   3626  N   GLU C  87       0.239  51.248  28.889  1.00 61.13          
TER

In it residue no 87 have only N atom & other backbone atoms absent, if i want to find which backbone atoms absent in which residues in pdb files at any position encountered. Kindly give me logic in R language/java language

pdb structure parsing

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updated 14.4 years ago by dimkal

• written 14.4 years ago by Sagar Nikam

Word of advice: questions that sound like "please do my work for me" are not well-received. What have you tried so far?

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written 14.4 years ago by Neilfws

2 answers

first you need to know how to parse the file. then you need to know, as Joao mentioned, what kind and how many atoms each residue type contains. If you want to fill the missing residues in I'd then you'll also need to know the geometry of each residue. My advise is to use already available modeling tools like Modeller or Prime to do these thing for you, and then use those structure in your R/java workflow.

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written 14.4 years ago by dimkal

You will need a forcefield to know which atoms belong to which residue. Or something like this.

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written 14.4 years ago by João Rodrigues