Search found 685 matches

by AL
2020.08.05 11:23
Forum: ATSAS package in general
Topic: ATSAS 3.0.2 Installation Privileges
Replies: 2
Views: 104

Installing ATSAS for Windows

Thank you for posting this link.
This is also described in the Installing ATSAS for Windows manual.
by AL
2020.07.26 15:54
Forum: Mixtures and flexible systems
Topic: CORAL output pdb model
Replies: 2
Views: 105

Re: outputs from CORAL that do not make physical sense

Hi Gabriela, thank you for reporting this. Could you please briefly describe your input (how many rigid domains? any symmetry used? any contact conditions?), how did you run CORAL (ATSAS online or on your PC; what is your ATSAS version) and, if possible, could you please send your input and the outp...
by AL
2020.07.13 11:14
Forum: Rigid body modelling
Topic: SIGABRT problem with pre_bunch
Replies: 3
Views: 145

Re: SIGABRT problem with pre_bunch

Thank you for reporting this. Could you please send us 'colhbind.fasta' and the *.pdb files so that we can reproduce and fix this problem.
by AL
2020.07.10 16:55
Forum: Mixtures and flexible systems
Topic: ATSAS 3.0.2 eom cannot read .seq file
Replies: 3
Views: 353

Re: "bad filename" error using eom

Dear Cody, we cannot reproduce the "bad filename" error with ATSAS 3.0.2. E.g. this runs fine: $ranch sequence.seq -q 10 -i -w=. A test run with some stub experimental data and your sequence runs fine as well. Perhaps you could provide more details about your EOM input? Please check the full path to...
by AL
2020.06.18 11:37
Forum: ATSAS package in general
Topic: ATSAS release 3.0 is available
Replies: 5
Views: 2487

ATSAS release 3.0.2 is available

Download ATSAS 3.0.2 (academic users only) Changes in programs: crysol : do not attempt to automatically re-calculate scattering in dialogue mode if the number of harmonics is considered insufficient, fixed atomic form factors of Rhenium and Osmium; crysol 3 : ask for contrast multipliers in dialog...
by AL
2020.06.02 19:11
Forum: ATSAS package in general
Topic: I can not install the Primus
Replies: 1
Views: 233

Try installing to a folder where you have write rights

It looks like you don't have administrative rights to install programs to C:/atsas/ . If you are installing the latest version 3.0.1 it should suggest to install ATSAS to C:\Program Files (x86) . If that doesn't work, please try installing to your 'My Documents' folder, something like C:\Users\youru...
by AL
2020.05.26 14:03
Forum: ATSAS package in general
Topic: Windows 7 installation
Replies: 5
Views: 3817

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: 510

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: 2
Views: 594

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: 313

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: s max (Å -1 ), Volume (Å 3 ), MW (Da), file name --method=Qp MW from Porod...
by AL
2020.04.28 14:21
Forum: Announcements
Topic: EMBL Online Lecture Course, May 2020
Replies: 1
Views: 838

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: 532

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: 1046

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: 1046

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...