[Chimera-users] showing salt bridges in pdb trajectory movie

[Albert Lyons]

Hi all,

I am having a problem trying to show salt bridges between selected atoms in a movie of my pdb format trajectory. I am using the following commands in the Per-Frame script, to display H-bonds between the residues but with a less strong distance criterion (to bring the distance of interaction to 6 A) and angle criterion (to make the angle 0deg and so make all angles available):

select :1,6,7,10,16,18
findhbond  selRestrict :1 at HZ1,HZ2,HZ3 :6 at 2HH2,2HH1,HE,2HH1,1HH1 :7 at O3P,O2P,O1P :10 at HZ1,HZ2,HZ3 :16 at HZ1,HZ2,HZ3 :18 at 2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145

When I apply this script I get a Chimera error saying:

Error while sourcing select :1,6,7,10,16,18
findhbond  selRestrict :1 at HZ1,HZ2,HZ3 :6 at 2HH2,2HH1,HE,2HH1,1HH1 :7 at O3P,O2P,O1P :10 at HZ1,HZ2,HZ3 :16 at HZ1,HZ2,HZ3 :18 at 2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145
,line 1:
"findhbond  selRestrict :1 at HZ1,HZ2,HZ3 :6 at 2HH2,2HH1,HE,2HH1,1HH1 :7 at O3P,O2P,O1P :10 at HZ1,HZ2,HZ3 :16 at HZ1,HZ2,HZ3 :18 at 2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145"
Non-alphanumeric character in keyword
':6 at 2HH2,2HH1,HE,2HH1,1HH1'

I have tried tweaking it different ways but just get other error messages, I can't seem to write it in the correct format. Can anyone see a problem with this script and how I might fix it?

Cheers
Albie
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