Search found 693 matches

by AL
2021.01.04 17:09
Forum: Mixtures and flexible systems
Topic: Cannot skip the "contact file name" in EOM
Replies: 5
Views: 528

Re: (CR for none)

Guðmundsdóttir wrote:
2020.12.17 18:28
What does CR mean?
I guess, carriage return, i.e. Enter.
by AL
2020.11.23 20:37
Forum: Primary data processing
Topic: Parameter to inform quality of the fitting for a Pair distance distribution to raw data
Replies: 3
Views: 1081

Re: CorMap test p-value and the reduced Chi-sq value

This fit looks pretty good.
A Chi-squared value much less than 1.0 means that your experimental error bars are a bit too high.
The CorMap test does not rely on the experimental errors and the p-value > 0.05 means that your p(r) fits your data.
by AL
2020.11.23 20:28
Forum: Ab initio shape determination
Topic: AMBIMETER Missing Database... DATCLASS Shape Classifier Initialization Failure
Replies: 1
Views: 300

Check ATSAS system variable

Most probably the ATSAS system variable is not set. Please check the ATSAS installation instructions for your OS and re-install ATSAS if necessary.
You may also use AMBIMETER online (Authentication required)
by AL
2020.11.12 17:01
Forum: ATSAS package in general
Topic: Source code?
Replies: 2
Views: 291

Re: Source code?

Currently, ATSAS is not open source.
ATSAS uses the open source libsaxsdocument library.
Some of the ATSAS tools are implemented in the open source FreeSAS suite (but not DAM2IS).
by AL
2020.10.28 11:31
Forum: ATSAS package in general
Topic: ATSAS release 3.0 is available
Replies: 6
Views: 3728

ATSAS release 3.0.3 is available

Download ATSAS 3.0.3 (academic users only) New platforms: CentOS 8 and Ubuntu 20. This is the last Ubuntu 16 release. This is the last Windows 32-bit release . Future Windows releases will be 64-bit only. Changes in programs: bodies : added option to predict scattering on "absolute scale", i.e. ass...
by AL
2020.10.13 09:32
Forum: Mixtures and flexible systems
Topic: Bug in EOM Rsigma calculation?
Replies: 6
Views: 1322

Re: Bug in EOM Rsigma calculation?

Thank you for reporting this, we are looking into it.
by AL
2020.08.11 14:35
Forum: Rigid body modelling
Topic: Repeating BUNCH X Number of Times?
Replies: 1
Views: 969

Re: Repeating BUNCH X Number of Times?

You should prepare an answer file and feed it to BUNCH in a script.
On Linux, the answer file is usually made with tee.
On Windows, you may create this file manually in a text editor.
by AL
2020.08.11 14:27
Forum: Rigid body modelling
Topic: SIGABRT problem with pre_bunch
Replies: 3
Views: 913

Check your ATSAS version; use SASREF

1) I cannot reproduce your SIGABRT error with ATSAS 3.0.2. This is what I get: pre_bunch colhbind.fasta *.pdb 1_4u6t_modeller.pdb: alignment found: 1 93 2_4jgu_modeller.pdb: error: alignment failed [followed by the sequence] Please make sure you are using the latest ATSAS version . 2) Your sequence ...
by AL
2020.08.11 12:54
Forum: Primary data processing
Topic: Parameter to inform quality of the fitting for a Pair distance distribution to raw data
Replies: 3
Views: 1081

CorMap p-value and Chi-squared value

Open your .out file in PRIMUS, uncheck the third curve. Click Processing > Data Comparison. You will get the CorMap Test p-value (Franke et al. 2015) and the reduced Chi-squared value.
by AL
2020.08.05 11:23
Forum: ATSAS package in general
Topic: ATSAS 3.0.2 Installation Privileges
Replies: 2
Views: 1153

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: 4
Views: 1033

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: 913

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: 1115

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: 6
Views: 3728

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...