Are you opening gnuplot or are you calling it from the command line?
Interactively, gnuplot sometimes waits to plot the file when you've
moved to something else. If it's interactive try 'set term x11', and
you might see "closing myfile.png", at which point the file will be
ready. If you're doing it on the command line, make sure that there
are no other terminal declarations in the file that might confuse
matters, and be sure that the terminal declaration occurs before any
plot statements.
Also make sure that your gnuplot install supports the output you want.
To see the available terminals, open gnuplot interactively (enter
"gnuplot" on the command line), and enter "set term" and hit return.
That will give you a list of terminals. To find out more about a
certain one, use help, for example with png: "help set term png".
BTW, if you need nice resolution, say for a journal, then it's best to
output using postscript or svg and then use an image manipulation
program (gimp or something in photoshop) to convert it to a raster
file at the proper resolution.
On Fri, Dec 11, 2015 at 10:58 AM, George Tzotzos <gtzotzos.me.com> wrote:
> 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
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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/>
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Fri Dec 11 2015 - 11:30:02 PST
