From: Ban Arn (ban.arn_at_gmail.com)
Date: Mon Jun 25 2012 - 04:16:28 CDT

Dear John

Running the command "porcupineplot Help" shows option as

-Diff
first 2 are mandatory arguments
1st atom selection as starting point in space
2nd atom selection as final point in space
and optional arguments
-min: range min
-max: range max
-arrowres: arrow resolution
-ressel: residue selection

-Traj
Mandatory arguments:
1st argument: atom selection
and optional arguments
-min: range min
-max: range max
-arrowres: arrow resolution
-ressel: residue selection.

I'm using Trajectory files that contain only CA atoms separated for
different PCA's.

I'm phrasing the command as porcupineplot Traj name CA and it shows error
as invalid command.

I also tried specifically mentioning the atom number porcupineplot Traj
resid 50, it shows same error.

Kindly advice.

Many Thanks
Balaji

On Fri, Jun 22, 2012 at 6:30 PM, Ban Arn <ban.arn_at_gmail.com> wrote:

> Dear John
>
> Running the command " Run ::porcupineplot::Help" shows error as invalid
> command.
>
> Balaji
>
>
> On Fri, Jun 22, 2012 at 6:13 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>>
>> Balaji,
>> Run ::porcupineplot::Help and it should print out a description of
>> the parameters you have to provide to Traj and the other routines.
>>
>> Cheers,
>> John Stone
>>
>>
>> On Fri, Jun 22, 2012 at 06:04:04PM +0100, Ban Arn wrote:
>> > Dear John
>> > Calling the commands "procupineplot::Traj" shows error as invalid
>> command
>> > Could you please help me what i'm missing in the command .
>> > Many Thanks
>> > Balaji
>> >
>> > On Fri, Jun 22, 2012 at 5:59 PM, John Stone <johns_at_ks.uiuc.edu>
>> wrote:
>> >
>> > Sourcing or playing the script won't do anything initially.
>> > You have to call the routines that the script contains, as pointed
>> > out in Axel's previous reply on this:
>> > http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/17155.html
>> >
>> > Cheers,
>> > John
>> > On Fri, Jun 22, 2012 at 05:54:15PM +0100, Ban Arn wrote:
>> > > Dear John
>> > > I find the script in the link
>> > >
>> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/17154.html
>> > > Balaji
>> > >
>> > > On Fri, Jun 22, 2012 at 5:53 PM, Ban Arn <ban.arn_at_gmail.com>
>> wrote:
>> > >
>> > > Dear John
>> > > Kindly find the attachment for the script i'm using.
>> > > Its slightly different from the one you send.
>> > > However, running the script by commands
>> > > source script.tcl or play script.tcl doesn't give me any
>> outputs.
>> > > Kindly advice
>> > > Many Thanks
>> > > Balaji
>> > > On Fri, Jun 22, 2012 at 5:44 PM, John Stone <
>> johns_at_ks.uiuc.edu>
>> > wrote:
>> > >
>> > > Hi,
>> > > I assume you're using this script? Where did you get
>> the copy
>> > you're
>> > > using, is it exactly this one?:
>> > >
>> >
>> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/att-15365/PorcupinePlot.tcl
>> > >
>> > > Cheers,
>> > > John Stone
>> > > vmd_at_ks.uiuc.edu
>> > > On Fri, Jun 22, 2012 at 04:01:38PM +0100, Ban Arn wrote:
>> > > > Dear VMD users
>> > > > I'm using procupine_plot.tcl script to visualise the
>> > individual
>> > > motions of
>> > > > PCA.
>> > > > I run the script using command "play
>> procupine_plot.tcl.
>> > > > Running the above command shows that
>> > > > "cant create procedure "ProcupinePlot ::set
>> ColorScale":
>> > unkown
>> > > namespace
>> > > > cant create procedure "ProcupinePlot ::Porc
>> > ColorScaleBar":
>> > > unkown
>> > > > namespace
>> > > > cant create procedure "ProcupinePlot
>> > ::PorcDrawColoredArrow":
>> > > unkown
>> > > > namespace"
>> > > > Kindly advice how to use the script.
>> > > > Many Thanks
>> > > > Balaji
>> > >
>> > > --
>> > > 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
>> >
>> > --
>> > 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
>>
>> --
>> 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
>>
>
>