VMD-L Mailing List

From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Tue Jul 12 2011 - 14:22:35 CDT

Just an update. The automation of the carriage returns can be done by using
the following:

(
 echo "D"
 echo ""$name"_"$i".qpt"
 echo ""$name"_"$i".vmd_plot"
 echo "1"
 ) | qpt_conv

Maria
On Tue, Jul 12, 2011 at 8:08 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> Based on my reading of the HOLE page, you may need to write the intended
> input for qpt_conv to a file first, and then run qpt_conf with input
> redirected
> from the file. I think that you may want to do it that way so you can
> get the proper carriage return characters into the input stream for
> qpt_conv.
> Without the carriage returns, I don't know what it would do. I just read
> the man page here and haven't tried it personally:
> http://d2o.bioch.ox.ac.uk:38080/doc/hole_d04.html
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Jul 07, 2011 at 12:21:00PM +0200, maria goranovic wrote:
> > Sorry for spamming, but this is what i am trying to do to automate
> > qpt_conv:
> > echo D temp.qpt temp.vmd_plot 1 | qpt_conv
> > Although qpt_conv takes in the first argument (D), it does not take
> the
> > rest and exits. I have no idea what I am doing wrong. In its
> interactive
> > form, qpt_conv does need the user to press a return key after each
> entry,
> >
> > any suggestions?
> > On Tue, Jul 5, 2011 at 5:05 PM, maria goranovic <
> mariagoranovic_at_gmail.com>
> > wrote:
> >
> > I am trying to use Hole to find and display cavities in a protein.
> Hole
> > uses the executable qpt_conv to convert sph output to a format
> readable
> > by vmd. However, qpt_conv seems to be interactive. It requires
> entering
> > "D" and a few return strokes to produce the vmd_plot file format.
> How
> > can one get around this without recompiling the hole code?
> > Additionally, how does one display an entire trajectory alongwith a
> > series of hole-produced vmd_plot files which hold the dotted
> > representation of the cavity? I am hoping some one has done this
> before,
> > and will be kind enough to share the experience?
> > Thank you in advance,
> > -Maria-
> > --
> > Maria G.
> > Technical University of Denmark
> > Copenhagen
> >
> > --
> > Maria G.
> > Technical University of Denmark
> > Copenhagen
>
> --
> NIH Resource 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/ Fax: 217-244-6078
> 

-- 
Maria G.
Technical University of Denmark
Copenhagen