Error in Gnom when it uses Gnuplot - in Ubuntu and on Mac

[franke-biosaxs]

On 2012-02-24 18:34:50, user spark wrote:

Dear ATSAS Team,

I just installed ATSAS on Ubuntu and on Mac.
I intended to use gnom in the command line of both OX.
But I get the same error:

G N O M --- Version 4.6
Please reference: D.Svergun (1992) J.Appl.Cryst. 25, 495-503
Copyright (c) ATSAS Team
EMBL, Hamburg Outstation, 1991 - 2009

---

Configuration file not found, dialogue mode assumed
Printer type [ postscr ] :
Input data, first file : dat_files.dat
Output file [ gnom.out ] :
No of start points to skip [ 0 ] :
Run title: Merge of: dat_file.dat
Number of points in the run is 412
Input data, second file [ none ] :
No of end points to omit [ 0 ] : 240
Total number of input data points read is 172
Angular range as read: from 0.11715 to 2.22577
Angular scale (1/2/3/4) [ 1 ] :
Plot input data (Y/N) [ Yes ] :

set xlabel "s"15,0.5
^
"dsgnucmd.tmp", line 17: ';' expected

Inappropriate ioctl for device
ERROR running Gnuplot

Gnom stops.

In both systems gnuplot works but not with with Gnom. Above output is from the Mac console, in the Ubuntu I receive the same error.

How can I fix this?

Used versions:

atsas-2.4.2-3.dmg
atsas-2.4.1-2_i386.deb from the Ubuntu folder.

Thanks for help.
Spark.

[franke-biosaxs]

On 2012-02-24 20:50:20, user franke wrote:

spark wrote

set xlabel "s"15,0.5
              ^
"dsgnucmd.tmp", line 17: ';' expected

How can I fix this?

By finding the gnuplot version that (still) understands the syntax used by gnom. Alternatively, use the primus/qt "Distance Distribution" GUI to get a somewhat interactive plot.

As of ATSAS-2.5.0 (due end of this year), the gnuplot facility of gnom will most likely be removed - in case you want it preserved, speak out now ;)

HTH

Daniel

[franke-biosaxs]

On 2012-02-24 22:25:57, user spark wrote:

franke wrote

By finding the gnuplot version that (still) understands the syntax used by gnom. Alternatively, use the primus/qt "Distance Distribution" GUI to get a somewhat interactive plot.

As of ATSAS-2.5.0 (due end of this year), the gnuplot facility of gnom will most likely be removed - in case you want it preserved, speak out now ;)

HTH

Daniel

Hi Daniel.
Thanks for the reply. Which gnuplot version would this be, please? Furthermore, I don't understand what the problem is. The gnuplot syntax is

set xlabel {" < label > "} {offset < offset > } {font " < font > {, < size > }"}

Does it mean the command "offset" is missing?

The reason I wanted to use the command line is because I found a perl script running several times GNOM to go through a range of Dmax and plotting it later. By comparing various curves, a Dmax could maybe justified as it is a soft parameter?

Gnuplot is probably not a bad idea, however I have written already a Matlab code to plot my P(r) functions. But that does not work, of course, with this perl script.
Why would you like to remove Gnuplot?

Thank you again and best regards
Spark

[franke-biosaxs]

On 2012-02-24 22:33:04, user franke wrote:

spark wrote

set xlabel {"<label>"} {offset<offset>} {font "<font>{,<size>}"}
Does it mean the command "offset" is missing?

Sorry, I can't tell, neither I'm I proficient with gnuplot, nor with that part of the gnom sources.

spark wrote

The reason I wanted to use the command line is because I found a perl script running several times GNOM to go through a range of Dmax and plotting it later. By comparing various curves, a Dmax could maybe justified as it is a soft parameter?

In case you haven't tried it, give the primus/qt a try. You might find the GUI useful for this :)

spark wrote

Why would you like to remove Gnuplot?

Because the syntax apparently keeps changing with versions and users have various versions installed, or none at all. And, in my personal opinion, having an inherently command-line oriented tool attempting to open windows and plot stuff is ... suboptimal ... in any case.

Cheers

Daniel

[franke-biosaxs]

On 2014-09-29 05:32:43, user Cougar wrote:

I just wanted to confirm whether or not GNUPLOT (version 4.6) should run with GNOM and CRYSOL (Mac OSX ATSAS version 2.5.2). I am getting an error message and then noticed in previous posts that there were plans to remove GNUPLOT.

Thank you!