On Fri, Dec 11, 2015 at 7:01 AM, George Tzotzos <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
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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/
(801) 587-9652
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Received on Fri Dec 11 2015 - 08:00:07 PST
