[gmx-users] Visualizing the system

[Shima Arasteh]

Selection of Ribbons draw style for the protein, shows an incomplete ribbon, broken fragments of ribbon. I guess something is mixed! Protein is not recognized somehow!
However, I don't know the reason?!

 
Sincerely,
Shima


----- Original Message -----
From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Saturday, September 22, 2012 10:14 AM
Subject: Re: [gmx-users] Visualizing the system

What you suggested, worked. I mean not resname POPC solved the problem. But I'd like to know why that  problem happens?! I followed the steps of KALP15 exactly.

Anyway, thanks Peter.


 
Sincerely,
Shima


----- Original Message -----
From: Peter C. Lai <pcl at uab.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Saturday, September 22, 2012 9:57 AM
Subject: Re: [gmx-users] Visualizing the system

This is a VMD question, but try using manual selections, like:

"not resname POPC and not resname SOL and not resname NA and not resname CL" 
as a selection that doesn't show popc, water, and ions, for example.

I haven't had issues with VMD confusing what a protein is or not, so maybe
there is a residue ordering issue or something going on with the gro file?

On 2012-09-21 11:19:51PM -0700, Shima Arasteh wrote:
> 
> 
> Hi,
> In order to see a system of protein and lipids, I use VMD. I called system.gro something similar to what is produced in KALP15 in DPPC. When I load system.gro and select protein, one of lipids is loaded with it. 
> I am wondering if it is a problem with my system.gro? Or something with the applied visualization tool? 
> 
> Thanks in advance.
> 
> Sincerely,
> Shima
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-- 
==================================================================
Peter C. Lai            | University of Alabama-Birmingham
Programmer/Analyst        | KAUL 752A
Genetics, Div. of Research    | 705 South 20th Street
pcl at uab.edu            | Birmingham AL 35294-4461
(205) 690-0808            |
==================================================================

-- 
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

--
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists