[Chimera-users] Problem during Residue interaction network generation

[Aditya Padhi]

Dear Eric,

Thank you very much for your quick response.
I have used the 1mtx.pdb file sent by you and did exactly as you suggested
to generate the RIN.
Yes, this file worked without any delay or issues, and I could generate the
RIN successfully.
Can you please suggest whether something is wrong in my input MD
trajectory?
FYI, I have tried almost 10 different mutant systems, each represents 100ns
trajectory generated from Gromacs.

I look forward to hear from you.
With best regards
Aditya

On Thu, Feb 20, 2020 at 7:18 AM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Aditya,
> I don’t know why your system is so slow.  All the tests I tried just now
> worked reasonably quickly, even with large trajectories.  I’d like you to
> try something.  Do exactly what you were doing before, but instead of using
> your trajectory, use the attached multi-MODEL PDB file for the trajectory
> (when you start the MD Movie tool, choose “PDB” as the trajectory format
> and “single file” within that format).  Does computing a residue
> interaction network using that trajectory also get hung up?
>
> —Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
> On Feb 19, 2020, at 1:01 AM, Aditya Padhi <adi.uoh at gmail.com> wrote:
>
> Dear Chimera users,
>
> I am using the StructueViz plugin of Cytoscape to launch Chimera and then
> loading the MD trajectory from Gromacs, where I need to generate the
> residue interaction network. After this step, when I click "apply" for
> displaying the interaction network in Cytoscape, it often shows "Importing
> Residue Network from Chimera", sometimes "getting data for attribute
> secondarystructure" and sometimes "getting data for attribute ishelix".
> Even after I wait for half a day, the message continues to show and I am
> not able to work on Cytoscape.
> I have even tried to reduce the number of frames of the MD trajectory to
> see if that helps, but that doesn't work even.
>
> Can anyone help me to how to resolve this problem?
> With best regards
> Aditya
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription:
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>

-- 
******************************************
Aditya Kumar Padhi, Ph.D. (IIT Delhi)
JSPS Postdoctoral Researcher
RIKEN - Yokohama, Japan
Contact no: +81-70-3999-2091
******************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20200220/b3162924/attachment.html>