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

Elaine Meng meng at cgl.ucsf.edu
Sat May 18 14:09:52 PDT 2013


Hi Albie,
I see at least a couple of issues:

(1) the atomspec you gave with the selRestrict keyword includes spaces.  As mentioned in the "findhbond" manual page, to handle this you have to enclose the atomspec in quote marks:

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findhbond.html>

(2) all of the atoms in that specification are also in the selection, so I don't see why you wouldn't just use "selRestrict both" in the findhbond command instead of that long atomspec.  Or, maybe there are other potentially H-bonding atoms in those same residues that you wish to exclude?  In that case, you could give that atomspec in the "select" command (i.e. only select those specific atoms) and then still use "selRestrict both" in the findhbond command.  See the link above for explanations of the selRestrict options.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

P.S. your question came through three times.  No need to keep sending, but perhaps maybe you thought the question wasn't going to the list?  The chimera-users archive is online...
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/index.html>

On May 18, 2013, at 12:32 AM, Albert Lyons wrote:

> 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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