atsas-2.8.0: datgnoms and partistr/parcoor?

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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Alex
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atsas-2.8.0: datgnoms and partistr/parcoor?

#1 Post by Alex » 2017.03.06 23:04

Dear ATSAS developers,
In whatsnew.txt there is a line:
Changes ATSAS-2.8.0
===================
Renamed programs
=================
* gnom5 - renamed to gnom
* datgnom5 - renamed to datgnom

Removed programs
=================
* datgnom (version 4)

--
However, there is still datgnom4 present in the package. I assume that this is an old version (datgnom v4)? is version 4 going to be obsolete? I liked to use it because it did not require Rg as an input. So i wonder why in datgnom5 Rg became a required parameter?

Also in my ATSAS installation on Mac OS i don't see:
* partistr - Divide protein coordinates (PDB) into subdomains according to
dynamics (NMA)

however, there is '/Applications/ATSAS/bin/parcoor'. Are they identical?

Thank you in advance, Alex

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AL
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Re: atsas-2.8.0: datgnoms and partistr/parcoor?

#2 Post by AL » 2017.03.07 11:33

Alex wrote:However, there is still datgnom4 present in the package. I assume that this is an old version (datgnom v4)?
That's correct, datgnom v.4 was renamed to datgnom4, not removed. Thank you for reporting this!
The announcement seems to be more correct than whatsnew.txt.
Alex wrote:is version 4 going to be obsolete?
Eventually - yes.
Alex wrote:I liked to use it because it did not require Rg as an input. So i wonder why in datgnom5 Rg became a required parameter?
If Rg is not provided datgnom4 determines it internally; the way how Rg is determined is not consistent with autorg and not easily reproducible. In certain cases datgnom4 finds a wrong Rg which leads to a wrong Dmax. It is strongly recommended to provide the --rg option to datgnom4.
Alex wrote:Also in my ATSAS installation on Mac OS i don't see:
* partistr - Divide protein coordinates (PDB) into subdomains according to
dynamics (NMA)

however, there is '/Applications/ATSAS/bin/parcoor'. Are they identical?
Yes, partistr was a working title for parcoor.
Thanks!

Alex
Active member
Posts: 692
Joined: 2007.08.09 21:10
Location: Planet Earth

Re: atsas-2.8.0: datgnoms and partistr/parcoor?

#3 Post by Alex » 2017.03.07 13:49

Thanks for the reply!
If Rg is not provided datgnom4 determines it internally; the way how Rg is determined is not consistent with autorg and not easily reproducible. In certain cases datgnom4 finds a wrong Rg which leads to a wrong Dmax. It is strongly recommended to provide the --rg option to datgnom4.
I have seen example for highly flexible constructs at low concentration recorded using sec-saxs when datgnom4 provided some estimate of Rg/I0 whereas AutoRg could
not do that. That was enough to pick up frame range that could be potentially good for averaging. That of course being not the most optimal case, as SNR is still
quite poor. However, though I have to admit i don't know how Rg is determined "internally" in datgnom4, it may still be useful to have it in case when Rg should be determined from
full or almost full scattering curve rather than from Guinier region.

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