Thank you Daniel,
I managed to produce a gif output. I’ll try your suggestion too.
Regards
George
> On 11 Dec 2015, at 16:55, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> On Fri, Dec 11, 2015 at 7:01 AM, George Tzotzos <gtzotzos.me.com <mailto:gtzotzos.me.com>> wrote:
>> I managed to get the output I need on X-terminall. My last question is how do I produce a printable file (e.g png).
>>
>> I added to the gnuplot script
>> set term png
>> set output “myfile.png”
>>
>> The output was an empty png file.
>
> Tough to say what could be going wrong - this is a question that is
> probably better-suited for the gnuplot mailing list.
>
> However, you could try using the 'jpeg' keyword in cpptraj (should be
> enough to add 'jpeg' after 'out <file>' for the secstruct command),
> which will produce a header that will generate jpeg output when the
> file is run with gnuplot. That may give you a good place to start.
>
> Hope this helps,
>
> -Dan
>
>
>>
>>
>>> On 11 Dec 2015, at 14:43, Jason Swails <jason.swails.gmail.com> wrote:
>>>
>>> On Fri, Dec 11, 2015 at 7:22 AM, George Tzotzos <gtzotzos.me.com> wrote:
>>>
>>>> Thank you very much for the help.
>>>>
>>>> The Amber list seems to have stripped my attachment. I include it in this
>>>> email too.
>>>>
>>>> Secstruct produces a gnuplot script a sample of which is at the end of
>>>> this message. The script is then run by cpptraj on the fly.
>>>>
>>>> I guess the problem(???) is with set ytics(“ASP:1 1.000,”THR:2”, etc).
>>>>
>>>> Do I have to run gnuplot outside cpptraj by removing the ytics manually
>>>> and also changing the set yrange to [1:125] (125 is the last residue).
>>>>
>>>
>>> Unless you want to change the cpptraj source code to print the gnuplot
>>> script you want, yes. But this should not be a problem. cpptraj creates
>>> the gnuplot script for you, so all you have to do is modify that, then run:
>>>
>>> gnuplot <script>
>>>
>>> HTH,
>>> Jason
>>>
>>> --
>>> Jason M. Swails
>>> BioMaPS,
>>> Rutgers University
>>> Postdoctoral Researcher
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
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>>
>>
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>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/ <http://home.chpc.utah.edu/~cheatham/>
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>
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Received on Fri Dec 11 2015 - 08:00:09 PST
