VMD-L Mailing List

From: Ebert Maximilian (m.ebert_at_umontreal.ca)
Date: Thu Aug 28 2014 - 13:58:58 CDT

Hi,

I will try to make it more clear. I have a trajectory with 10000 frames of a protein with a substrate. I am interested in the position of the substrate. If it is at a certain distance of the protein I want to store its position and display it later. My idea was to write a TCL script which checks in every frame the relative position of the substrate to the protein. This is working fine. I have a script which aligns the system and runs through every frame and checks the relative position. What I did if the relative position indicates that the substrate is at an interesting distance to the protein I safe the substrate by using:

set plm($i) [atomselect top "resname PLM" frame now]

At the end I have an array full of positions of my substrate from different frames. Now I want to go to frame 0 and write out all the substrate position to the main screen. This would superimpose on the protein all the different substrate orientations which meet my criteria. Basically I want the substrate position from different frames all drawn in frame 0 based on a distance criteria. This should look similar to what you get if you go to representations -> trajectory -> Draw multiple frames. I could also use the:

mol drawframes top 0 {1 4 6 7 ….}

Command but when working with multiple DCD files this approach isn’t working.

Thanks,

Max

On Aug 28, 2014, at 2:25 PM, Ebert Maximilian <m.ebert_at_umontreal.ca> wrote:

>
>
>
> ________________________________________
> From: John Stone
> Sent: Thursday, August 28, 2014 2:25:19 PM (UTC-05:00) Eastern Time (US & Canada)
> To: Ebert Maximilian
> Cc: <vmd-l_at_ks.uiuc.edu>
> Subject: Re: vmd-l: Save position of entire molecule and draw it later
>
> Hi,
> Your question doesn't really make it clear what you mean by
> "saving the position". If you're loading a simulation trajectory,
> the atomic coordinates of the structure are already "saved".
> I'm assuming that what you want is to make a list of the trajectory frames
> that meet some particular criteria, and then show those at a later time?
> If you can provide more details and be more specific that would be helpful.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Aug 28, 2014 at 03:37:34PM +0000, Ebert Maximilian wrote:
>> Hi there,
>>
>> I am looking for a console way to store the position of a molecule in a frame if it meets certain conditions. At the end I want to draw all molecules stored on top of the first frame to analyze the positions of each molecule. In there a way to store an entire molecule in a variable and draw it out later?
>>
>> Thanks for your help,
>> Max
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/