Unable to add inclusion/exclusion/seed

[Former user]

Using Epock VMD plugin, have tried on MAC and linux. Both versions appear to be installed correctly but I'm having multiple issues.

1) If multiple files are loaded when I drop down molID and select one and then run it I get the error expected integer but got "0 1"Not valid molecule id 0 1 in atomselect's 'molId'

when only loading one molecule and trying to hit "add inclusion" I get this error: 2) atomselect: cannot parse selection text: atomselect: cannot parse selection text: while executing "atomselect $::epock::molid $::epock::target" (procedure "::epock::addSmth" line 137) invoked from within "::epock::addSmth 1 1 0 0 0 0 0 0 0" invoked from within ".epock.nb.tab1.inclusion invoke" ("uplevel" body line 1) invoked from within "uplevel #0 [list $w invoke]" (procedure "tk::ButtonUp" line 23) invoked from within "tk::ButtonUp .epock.nb.tab1.inclusion" (command bound to event)

in this situation my atomselect just says protein (the default) as I'm new to epock and just trying to get it to work at this point

3) what is target1 for? 4) what is the seed for?

[Benoist LAURENT]

Dear user,

You are actually reporting 2 different things.

1) Is a bug. I've just created a specific issue for it (see Issue 64). We will do our best to fix it ASAP.

2) This may just be a user error as "cannot parse selection text" usually comes from a bad user request.

3) target1 is a selection of atoms. The center of this selection will be used be Epock VMD plugin to add inclusion/exclusion/seed shapes. See Epock official documentation.

4) Seed is used along with the "Non-contiguous Points Removal" feature (see official documentation)

The picture you joint is not manageable by bitbucket. Can you provide another one ? probably in png or jpg format ?

Cheers, Ben

[cmae]

1) thanks, looking forward to the update 2) my selection was just "protein" 3)/4) I've read through all official documentation however other than showing target and seed in the picture they are never defined or explained how to use them

Can you give me an example of what you would put to do an inclusion? My protein has an empty cavity, not sure what to select/target to show the location of the spheres

[cmae]

thanks!!

[Benoist LAURENT]

Hi,

In the picture below, I want to calculate the volume of the pocket located between residues 242, 255, 259 on chain A. This is what goes in the Target 1 field. The simplest way to do so is to create a simple sphere englobing the pocket. In my case, I chose a 10 Å radius. I hit the Add Inclusion button and here I am.

The Selection field tells VMD which atoms should be taken into account for the volume calculation. Meaning that if for instance there are water atoms in your pocket, they won't be taken into account for the pocket calculation.

Hope this helps. Cheers.

[cmae]

super helpful! thank you. This program could really use a tutorial, I'm sure many more people would want to use it. Can you also provide some insight into what the profile and contrib.options are for? Martini FF?

Protein cyan, ligand yellow. I'm trying to define my catalytic pocket which should encompass the entire ligand. I have one seed sphere located on one part of the ligand and a large inclusion sphere covering the entire area. I'm using contiguous option. I've been trying multiple grid res/contig cut-off/grid sphere size, most recently (0.5/4.0/1) but can't seem to cover the entire ligand