Difference between revisions of "Task 9 - Journal (PKU)"
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(Created page with "==Renumbering Atoms in PDB file== To compare structures in normal mode analysis, the sequence and atom numbering has to be identical. We used a very simple python script to renu…") |
(→Renumbering Atoms in PDB file) |
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for line in open(filename): |
for line in open(filename): |
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if line.startswith("ATOM"): |
if line.startswith("ATOM"): |
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| − | + | head = line[:11].split() |
|
| − | + | at = int(head[1])-offset |
|
| − | l = head.split() |
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| − | at = int(l[1])-offset |
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i = 7-len(str(at)) |
i = 7-len(str(at)) |
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| − | head = |
+ | head = head[0]+" "*i+str(at) |
| − | print head+ |
+ | print head+line[11:], |
else: |
else: |
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print line, |
print line, |
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Revision as of 14:46, 9 July 2012
Renumbering Atoms in PDB file
To compare structures in normal mode analysis, the sequence and atom numbering has to be identical. We used a very simple python script to renumber a PDB file after we deleted an extra residue:
<source lang="python">
- !/usr/bin/env python
- first argument: the pdb file
- second argument: the number of deleted atoms (would be nice if no number means "start with 1", but that's an effort..)
import sys
filename = sys.argv[1] offset = int(sys.argv[2]) for line in open(filename):
if line.startswith("ATOM"):
head = line[:11].split()
at = int(head[1])-offset
i = 7-len(str(at))
head = head[0]+" "*i+str(at)
print head+line[11:],
else:
print line,
