Missing manual for datmw?

ATSAS for Linux and Mac, general installation issues, ATSAS online etc.
Post Reply
Message
Author
jbhopkins
Active member
Posts: 15
Joined: 2014.10.22 21:21
Location: BioCAT, Advanced Photon Source

Missing manual for datmw?

#1 Post by jbhopkins » 2020.04.24 22:52

Hi folks,

There doesn't seem to be a manual for datmw. It would be nice to have one, both to help me remember it exists, and to easily see what options are available (plus, I'd like the information on how to cite it!). The datmw -h command from the command line actually prints a pretty good description, I'd be happy with that as a first step towards a manual.

All the best.

- Jesse

User avatar
AL
Administrator
Posts: 714
Joined: 2007.08.03 18:55
Location: EMBL Hamburg, Germany
Contact:

datmw manual

#2 Post by AL » 2020.04.30 14:10

Thank you for reporting this.
In the meantime here is the datmw --help output:

Usage: datmw [OPTIONS] [FILE(S)]

Molecular weight (MW) by multiple methods:
--method=Porod
MW from Porod Volume (Petoukhov et al., 2012)
Output: smax (A^-1), Volume (A^3), MW (Da), file name
--method=Qp
MW from Porod Invariant (Hajizadeh et al., 2018)
Output: smax (A^-1), MW (Da), file name
--method=Vc
MW from Volume of Correlation (Rambo & Tainer, 2013)
Output: smax (A^-1), Vc, MW (Da), file name
--method=MoW
MW from Apparent Volume (Fischer et al., 2010)
Output: smax (A^-1), Q', V', Volume (A^3), MW (Da), file name
--method=sizeshape
MW from Size and Shape (Franke et al., 2018)
Output: MW (Da), file name
--method=bayes
MW from Bayesian inference (Hajizadeh et al., 2018)
Output: MW (Da), MW Score, CI lower, CI upper, CI prob., file name
--method=absolute
MW from absolute scale (Mylonas & Svergun, 2007)
Output: MW (Da), file name
--method=relative
MW from relative scale and standard (Mylonas & Svergun, 2007)
Output: MW (Da), file name

I0 is required for all methods, rg and first are required for Porod, Qp, Vc, MoW, sizeshape, and Bayes.

Partial specific volume and contrast are optional for method=absolute but data must be on absolute scale.

I0_standard/mw_standard are required for method=relative only.

Known Arguments:
FILE Data file(s)

Known Options:
--i0=<VALUE> Experimental forward scattering
--rg=<VALUE> Experimental Radius of Gyration
--first=<N> Index of the first point to be used (default: 1)
--psv=<X> Partial Specific Volume in units of cm^3/g (default: 0.7425)
--contrast=<X> Contrast in units of 10^10 cm^-2 (default: 2.8086)
--i0_standard=<VALUE> Experimental forward scattering of standard
--mw_standard=<VALUE> Expected MW of standard
--method=<NAME> One of: Porod, Qp, Vc, MoW, sizeshape, Bayes, absolute or relative (default: Bayes)
-h, --help Print usage information and exit
-v, --version Print version information and exit

Mandatory arguments to long options are mandatory for short options too.

Post Reply