Search found 404 matches

by franke
2019.05.01 20:54
Forum: Primary Data Processing
Topic: Molecular weight estimation
Replies: 4
Views: 3303

Re: Molecular weight estimation

The data looks good for both and surprisingly the Bayesian molecular weight is not only similar but exactly the same, more precisely 318450 Da (althought Rg, Dmax are similar but not the same). You didn't quote the MW range and probability for it, but I guess they are at least overlapping. The sour...
by franke
2018.08.15 13:06
Forum: Working with Models
Topic: Criteria for selecting models from Crysol output
Replies: 2
Views: 3491

Re: Criteria for selecting models from Crysol output

I want to know what should be my criteria to select these models (conformations). If I understood correctly, Chi^2 could be one... The prerequisite for this are correct error estimates and error propagation on the experimental saxs data. Unfortunately, those are still hard to come by as it depends ...
by franke
2017.08.14 20:05
Forum: Ab Initio Shape Determination
Topic: DAMMIF defaults to prolate aniso, even when entering unk
Replies: 4
Views: 4272

Re: DAMMIF defaults to prolate aniso, even when entering unk

Please update to atsas-2.8.2, there have been some teething problems with this new feature in 2.8.0.
Please let me know if the problem persists after installing 2.8.2. Thanks.
by franke
2017.08.14 12:48
Forum: Ab Initio Shape Determination
Topic: DAMMIF defaults to prolate aniso, even when entering unk
Replies: 4
Views: 4272

Re: DAMMIF defaults to prolate aniso, even when entering unk

Please double check your log. From here I'd say, your data corresponds to "Shape class: extended". In this case dammif helpfully sets the corresponding anisometry penalty - in particular if it unknown (and there is no difference between the default unknown and a user defined unknown, if classified a...
by franke
2017.03.21 23:29
Forum: Primary Data Processing
Topic: datclass: parse error (only on Ubuntu 14.04)
Replies: 2
Views: 4230

Re: datclass: parse error (only on Ubuntu 14.04)

Can't reproduce here: $ lsb_release -rd Description: Ubuntu 14.04.5 LTS Release: 14.04 $ which datclass /usr/bin/datclass $ datclass -v datclass, ATSAS 2.8.1 (r9338) $ datclass /usr/share/doc/atsas-2.8.1/dammif/example/lyz.out compact /usr/share/doc/atsas-2.8.1/dammif/example/lyz.out To be fair, thi...
by franke
2017.03.03 15:31
Forum: Primary Data Processing
Topic: why can not use the interactive mode in gnom(2.8)?
Replies: 1
Views: 3686

Re: why can not use the interactive mode in gnom(2.8)?

The gnom5 in atsas 2.8 has no interactive mode, how can I determine the Dmax value accurately? A cynical person might say: you can't. Never. Ever. However, more to the point: there is an interactive mode. Simply run the binary without arguments and get asked the ususal questions. If that is too ted...
by franke
2017.02.01 22:53
Forum: ATSAS Package in General
Topic: ATSAS 2.8 ATSASinstall.command
Replies: 2
Views: 4217

Re: ATSAS 2.8 ATSASinstall.command

In short: because Apple decided to stop support for PackageBuilder (or whatever the tool was named) and cmake didn't catch up as of yet with support for a new packager tool on Mac. We don't like it either. But Mac support is already time-consuming as is, spending yet more time on packaging distracts...
by franke
2017.02.01 22:43
Forum: Primary Data Processing
Topic: GNOM 5 doesn't recognize .cfg file
Replies: 4
Views: 5242

Re: GNOM 5 doesn't recognize .cfg file

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...
by franke
2017.02.01 22:29
Forum: SAXS & SANS Software
Topic: Fitting two conformations (pdb files) to the SAXS data
Replies: 4
Views: 4754

Re: Fitting two conformations (pdb files) to the SAXS data

I forgot to mention that both pdb files separately yield a good fit to the SAXS data - chi square 1.8 ish. Let me be the spoilsport to tell you that a chi-square of 1.8 is NOT indicative of a good fit. To the contrary. If your errors are correct, this says: no fit. If your errors are wrong, this sa...
by franke
2017.02.01 22:23
Forum: ATSAS Package in General
Topic: Illegal characters in file names - primus
Replies: 2
Views: 4126

Re: Illegal characters in file names - primus

Characters like 'č,ž,š' in file names are [....] [...] not widely supported and not a good idea in general. In all generality, it's probably a bug in primus somewhere, but so it is in many other applications out there. It's much easier to stay in the standard ascii character set and not use whitesp...
by franke
2017.02.01 22:19
Forum: Primary Data Processing
Topic: GNOM 5 doesn't recognize .cfg file
Replies: 4
Views: 5242

Re: GNOM 5 doesn't recognize .cfg file

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 ...
by franke
2016.11.22 22:15
Forum: Working with Models
Topic: Chi^2 missing in CRYSOL output
Replies: 8
Views: 6794

Re: Chi^2 missing in CRYSOL output

Thank you for the answer. Do you know what is the range of Chi^2 "too high to be displayed"?. When I use datcmp the calculated Chi^2 is -1, what is a ridiculous value. Not ridiculous. Lemme guess, no error estimates? Then that's what you get. Get accurate errors, and datcmp gives you an accurate ch...
by franke
2016.09.20 20:49
Forum: Rigid Body Modelling
Topic: Transform Ca chain (from eom or coral) to a full atoms chain
Replies: 6
Views: 6164

Re: Transform Ca chain (from eom or coral) to a full atoms c

jmarie wrote:The goal is to obtain a full atom model.
This is not the purpose of EOM. Doing this would be worse than tea leaf reading.
That's tea leaf reading without tea leafs. Or tea. Or a cup.
by franke
2016.09.20 20:44
Forum: Ab Initio Shape Determination
Topic: How DAMMIF consider water shell?
Replies: 2
Views: 4302

Re: How DAMMIF consider water shell?

dzabelskii wrote:[...] it would be great if you explain how DAMMIF consider water shell [...]
Short answer: not. At least not explicitly.