unanswered Visualisation of the secondary structure in BENDIX

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1 week 2 days ago #7393 by James Starlight
James Starlight created the topic: Visualisation of the secondary structure in BENDIX
Dear Martini Users!

I have faced with a problem of the helix assignment for the CG representation of the proteins in my MARTINI system (16 GPCRs oligomers embedded within the membrane) using BENDIX vmd plugin.

Firstly, I chose the helixes using the following selection which is correctly recognized by VMD:

resid 9 to 41 and (name "CA" "B.*") or resid 46 to 70 and (name "CA" "B.*") or resid 82 to 115 and (name "CA" "B.*") or resid 122 to 150 and (name "CA" "B.*") or resid 174 to 206 and (name "CA" "B.*") or resid 220 to 252 and (name "CA" "B.*") or resid 258 to 289 and (name "CA" "B.*") or resid 291 to 289 and (name "CA" "B.*")

Than if I provide this selection string to the BENDIX Helices as an input, I obtain the following error:

list element in quotes followed by ")" instead of space
list element in quotes followed by ")" instead of space
while executing
"llength $::bendix::helix_assignment"
(procedure "::bendix::mainDrawingLoop" line 119)
invoked from within
"::bendix::mainDrawingLoop"
invoked from within
".bex.field2.boutonaffiche0 invoke"
("uplevel" body line 1)

How is possible to fix the issue?

Thanks!

James

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