Great help Lachele, appreciated with many thanks.
George
> On 11 Dec 2015, at 20:28, Lachele Foley <lf.list.gmail.com> wrote:
>
> 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
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
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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 - 12:00:03 PST
