GNOM 5 doesn't recognize .cfg file

Interactive and automated data processing tools (PRIMUS, GNOM, AUTORG).
Scattering from simple bodies (BODIES), peak analysis (PEAK), data plotting (SASPLOT) etc.
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jbhopkins
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GNOM 5 doesn't recognize .cfg file

#1 Post by jbhopkins » 2017.02.01 18:28

Hi,

I recently upgraded to ATSAS 2.8.0 on Windows 7. I'm trying to run GNOM using the standard .cfg file approach (as described in the manual), but it doesn't seem to recognize it. I've put the cfg in the same folder as my data, but when I run gnom from the command line, it fails to recognize it and I have to input all parameters by hand.

See the attached screenshot for an example of this, and see the attached cfg file and sample data set. In the screenshot you'll see that it asks me for the input filename (and later would ask for the Dmax and other parameters), something which is specified in the gnom.cfg file.

I've tested, and this same config file works fine for gnom4 (ATSAS 2.7.2). Any help is appreciated.

The output of gnom -v is: "gnom, ATSAS 2.8.0 (r8972)"

Thanks!

- Jesse

P.S. Note that in order to upload the .cfg file, I had to change the extension to .txt.
Attachments
t_dat.dat
Sample data set.
(25.44 KiB) Downloaded 173 times
gnom.txt
gnom.cfg file, renamed with an allowed extension (just change .txt to .cfg).
(2.45 KiB) Downloaded 154 times
Capture.PNG
Screenshot of GNOM failing to read .cfg file in the same folder
Capture.PNG (20.35 KiB) Viewed 4580 times

franke
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Re: GNOM 5 doesn't recognize .cfg file

#2 Post by franke » 2017.02.01 22:19

gnom5 is a new development from scratch which has many advantages over gnom4; the two do not share much code. One of the things that fell under the cutting table was .cfg files. I never believed that this would be a widely used "feature"?!

Your .cfg does not seem to use any special things like slit parameters. You may simply use the command line interface (gnom -h)? Alternatively you may use input redirection for similar effect as .cfg.

HTH

Daniel

jbhopkins
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Re: GNOM 5 doesn't recognize .cfg file

#3 Post by jbhopkins » 2017.02.01 22:37

Daniel,

Thanks for the response. You're right in that this particular config file doesn't contain anything fancy (it's just lysozyme data), but I've often used the config file as an easy way to automate generation of P(r) functions, either for lots of files with the same settings (varying just Dmax, for example) or to specify some advanced settings. I can certainly do it another way, but was just surprised when this way stopped working, particularly since the gnom manual has yet to be updated removing the cfg section.

Thanks for the help.

- Jesse

franke
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Re: GNOM 5 doesn't recognize .cfg file

#4 Post by franke » 2017.02.01 22:43

Agreed, the manual has to be updated, still. And not only in that section. Sigh.

That said, gnom5 was included in 2.6 and 2.7 and announced as an eventual replacement for good-old-gnom from day one, i.e. for at least two years before it actually happened. Plenty of time to submit reports and feature requests?!

jbhopkins
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Joined: 2014.10.22 21:21
Location: BioCAT, Advanced Photon Source

Re: GNOM 5 doesn't recognize .cfg file

#5 Post by jbhopkins » 2017.02.01 23:15

Daniel,

I'm sure it was announced, but I can't say that I pay close attention to all of the package announcements. I also have to admit that I didn't test it previously, as I tend to try to stick to release versions (I have enough trouble with bugs in my own software!).

Anyways, I'm sure I can make something work. I'm currently reviving a little python program I have that grabs the stdout, processes it, and sends the correct stdin to GNOM. I never quite finished it, but this seems like a good time to do so, as it should allow powerful automation of changing advanced parameters.

- Jesse

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