File: contact.pml

package info (click to toggle)
pymol 1.8.4.0%2Bdfsg-1~bpo8%2B1
  • links: PTS, VCS
  • area: main
  • in suites: jessie-backports
  • size: 42,248 kB
  • sloc: cpp: 474,635; python: 75,034; ansic: 22,888; sh: 236; makefile: 78; csh: 21
file content (37 lines) | stat: -rw-r--r-- 1,019 bytes parent folder | download | duplicates (5)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
# load pdb file which has a CRYST1 record

fetch 1DN2, async=0
# load 1DN2.pdb,1dn2

# create neighbor with contact near a certain atom

symexp s,1dn2,(c; F and i;12 and n;N),4.0

# hide everything outside region of interest

hide (!(byres ((1dn2 and c; F and i;12 and n;N) x;12)))

# color-by-atom-cyan on 1dn2 to distinguish it from symmetry-related copy

util.cbac 1dn2

# restore view saved using from get_view in a previous session

set_view (\
    -0.042664494,   -0.003409438,    0.999083281,\
    -0.617746830,    0.786019623,   -0.023697896,\
    -0.785219014,   -0.618191123,   -0.035642438,\
    -1.056621075,   -1.729980350,  -39.743129730,\
    29.859001160,   38.402999878,   19.087999344,\
    27.443143845,   46.443149567,    1.000000000 )                              

# show the single hydrogen bond in the interface

dist ( s01000000 & segi '' & chain B & resn TYR & resi 296 & name O ),\
     ( 1dn2 & segi '' & chain F & resn CYS & resi 12 & name N )

# image

set antialias=1
ray
png contact.png