Search found 678 matches

by AL
2020.05.26 14:03
Forum: ATSAS Package in General
Topic: Windows 7 installation
Replies: 5
Views: 3408

Re: the same problem on windows 10

filport wrote:
2020.05.19 14:54
"libgcc_s_sjlj-1.dll
libgfortran-3.dll libsaxsdocument.dll" missing.
What command/program are you running before you see this message?
by AL
2020.05.11 11:20
Forum: Primary Data Processing
Topic: Points (Number of points in real space) in GNOM
Replies: 1
Views: 91

Re: Number of points in real space in GNOM

GNOM's number of points in real space cannot be higher than the number of input points in reciprocal space. And it cannot be more than 256. When you use GNOM from PRIMUSqt, the number of points might be automatically decreased when you decrease the input data range. Please note, the GNOM manual is a...
by AL
2020.05.11 11:08
Forum: SAXS & SANS Software
Topic: SCATTER IV: Guinier Approximation of Rg and Normalized Kratky Inquiry
Replies: 1
Views: 93

AUTORG

In addition, I am also looking for tips in manually calculating the Rg of samples, in excel, from raw .dat files. Any tips or best practices for this are appreciated, but not necessary. Excel might be a bit challenging. Try ATSAS AUTORG for an automatic Guinier approximation or DATRG for calculatin...
by AL
2020.04.30 14:10
Forum: ATSAS Package in General
Topic: Missing manual for datmw?
Replies: 1
Views: 88

datmw manual

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 In...
by AL
2020.04.28 14:21
Forum: Announcements
Topic: EMBL Online Lecture Course, May 2020
Replies: 0
Views: 244

EMBL Online Lecture Course, May 2020

https://www.embl-hamburg.de/biosaxs/courses/embl2020/img/poster-small.png Solution Scattering from Biological Macromolecules EMBL Online Lecture Course, May 5 - June 2, 2020 Tuesdays and Thursdays 9:20-10:30, CEST This online course aims at young biochemists/biophysicists and researchers active in ...
by AL
2020.04.28 09:50
Forum: Rigid Body Modelling
Topic: pre_bunch in new version?
Replies: 1
Views: 116

Usage: pre_bunch [OPTIONS] <SEQFILE> <FILE(S)>

Indeed the manual has to be updated. Please run pre_bunch it like this: $pre_bunch sequence.seq domain1.pdb domain2.pdb --output my_pre_bunch.pdb For details see: $pre_bunch --help Usage: pre_bunch [OPTIONS] <SEQFILE> <FILE(S)> Generates an initial approximation for further use in BUNCH Known Argume...
by AL
2020.03.18 15:50
Forum: Ab Initio Shape Determination
Topic: Overlay abi initio with crystal structure
Replies: 3
Views: 430

Assuming you are a Windows user...

han yin wrote:
2020.03.17 13:48
...i could not open the supcomb command function: the command prompt window opens then instantly closes.
How to use the Windows command line
ATSAS: how to update/modify your PATH settings
by AL
2020.03.09 10:41
Forum: Ab Initio Shape Determination
Topic: Overlay abi initio with crystal structure
Replies: 3
Views: 430

SASpy

Please install the SASpy plugin. Open your ab initio model and the crystal structure in PyMOL. Open SASpy, switch to the 'supalm' tab. Under 'Model selection' choose the two models and click 'Execute'. This will work well for globular models like lysozyme. If you have very elongated models it is bet...
by AL
2020.03.09 10:33
Forum: Ab Initio Shape Determination
Topic: Help with GNOM/Gasbor
Replies: 8
Views: 5825

Re: bump

oavina24 wrote:
2020.02.21 09:26
What i meant to say is that if its necessary to increase the whole range of data when calculating the pair distance distribution.
Could you please rephrase your question?
by AL
2020.03.02 18:04
Forum: Ab Initio Shape Determination
Topic: Chi-Squared Values
Replies: 14
Views: 7702

Re: Chi-Squared Values

Which input data file ? target.dat - it should contain the experimental SAXS data, three columns: q , I(q) , sigma(q) . ( q and s both mean the same). If your SAXS data file does not have the third sigma column then CRYSOL will invent the experimental errors and compute the chi-squared using these.
by AL
2020.02.28 16:12
Forum: Ab Initio Shape Determination
Topic: Chi-Squared Values
Replies: 14
Views: 7702

Re: how sigma(s), the experimental errors, are calculated

The experimental errors sigma(s) are taken from the input data file, third column.
by AL
2020.02.26 16:07
Forum: Working with Models
Topic: Trying to run DAMSEL with an input file detailing a bunch of PDB files
Replies: 1
Views: 641

Usage: damsel [OPTIONS] <PDBFILE(S)>

The option to provide a single file listing the input models was removed a while ago. Please run DAMSEL like this instead:

damsel model-2-1.pdb model-1-1.pdb model-3-1.pdb model-4-1.pdb model-6-1.pdb model-5-1.pdb model-7-1.pdb model-8-1.pdb model-9-1.pdb
by AL
2020.02.20 11:56
Forum: Ab Initio Shape Determination
Topic: Help with GNOM/Gasbor
Replies: 8
Views: 5825

Re: My data is pretty noisy at high q

If your experimental SAXS data at q > 8/Rg is just noise around zero (check by plotting your data on an absolute scale) there is not much point in using GASBOR. Just use DAMMIF.
by AL
2020.02.12 20:44
Forum: ATSAS Package in General
Topic: ATSAS release 3.0 is available
Replies: 4
Views: 1782

ATSAS release 3.0.1 is available

Download ATSAS 3.0.1 (academic users only) New platform: Debian 10. Framework changes: updated to Qt-5.12.6 and QtIFW-3.2.0: fixes the issue of numpad not working in primus/qt on Linux; fixes black text on black widget installer on MacOS with dark mode; fixes issues with the ATSAS environment varia...
by AL
2020.02.12 20:11
Forum: Ab Initio Shape Determination
Topic: Refinement with DAMMIN
Replies: 4
Views: 546

Re: the command prompt will not accept any value

You should start DAMMIN in the folder where your .out file is and provide the file name, e.g. 'lyz.out'.