VMD-L Mailing List

From: Grace Brannigan (grace.brannigan_at_rutgers.edu)
Date: Sat Jan 12 2013 - 01:01:27 CST

Hi Chola,

The program wants just the text string that goes inside the atomselect
command. You are passing it the whole atom selection when you use $seltext1
and $seltext2 - i.e., you've already set them to an atom selection using
atomselect. Then the procedure is trying to run atom select again.

I am not sure if there are any conventions on whether the script-writer
should directly pass selections, or should only pass the text and allow the
procedure to make the selection from that text. You'll find both, I think,
but maybe there is an official vmd standard that I'm not aware of. In any
case, when you're using a new procedure you'll need to figure out whether
you should pass it just the text for the selection or the selection itself.
There are usually hints, for instance when the variable is named "seltext"
rather than "sel" it means just the text.

Hope this helps,
Grace

On Fri, Jan 11, 2013 at 11:19 PM, Chola Regmi <cholaregmi_at_gmail.com> wrote:

> I am able to solve the problem by doing
> sel_sel_angle_frames 0 "myfirstselection" "mysecondselection" but still
> have no idea why it doesn't work with $seltext1 and $seltext2
>
>
> On Thu, Jan 10, 2013 at 11:45 AM, Chola Regmi <cholaregmi_at_gmail.com>wrote:
>
>> Hi
>> I need to find the angle between two domains of my selection from
>> trajectory. I used the script posted by Justin Gullingsrud.*
>> **http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/att-2279/fit_angle.tcl
>>
>>
>> When I used sel_sel_angle it works fine but when I tried to use
>> sel_sel_angle_frames I got error message as
>> atomselect: cannot parse selection text: atomselect0
>> I am using VMD 1.9.1 and the way I used the script is;
>> First I loaded my psf and dcd files in vmd
>>
>> In vmd TkConsole I wrote
>>
>> source fit_angle.tcl
>> set seltext1 [atomselect top "myfirstselection"]
>> **set seltext2 [atomselect top "mysecondselection"]*
>> sel_sel_angle_frames 0 $seltext1 $seltext2 // here 0 is my mol-id of
>> top molecule
>>
>> then I got error:* atomselect: cannot parse selection text: atomselect0
>>
>> If I do sel_sel_angle $seltext1 $seltext2 I got numerical values means it
>> works for single frame.
>> Can any one help me?
>> Thank you
>>
>> Chola Regmi
>> Florida International University
>> Miami, FL
>> *
>
>
> 

-- 
Grace Brannigan, Ph.D.
Assistant Professor
Center for Computational and Integrative Biology (CCIB) &
Department of Physics
Rutgers University, Camden, NJ
(856)225-6780
www.branniganlab.org