Search found 662 matches

by AL
2020.01.27 16:36
Forum: Ab Initio Shape Determination
Topic: DAMMIN using Symmetry D2
Replies: 1
Views: 22

Anisometry direction: Along 2-fold axis

D2 is symmetric under reflection through a line, correct? I don't think DAMMIN can do D2 but you can specify:
  • Symmetry: P2
  • Anisometry: Prolate
  • Anisometry direction: Along 2-fold axis
That would be a command line like:
$ dammin --sy=P2 --an=P --dr=L gnomfile.out
by AL
2019.12.16 15:21
Forum: Ab Initio Shape Determination
Topic: error trying to run dammif
Replies: 1
Views: 245

Re: error trying to run dammif

Thank you for reporting this. Which ATSAS version do you have? (you may check it in Primus: Help > About primus)
by AL
2019.12.03 12:57
Forum: Rigid Body Modelling
Topic: Pre-bunch Issue
Replies: 3
Views: 333

Re: Pre-bunch Issue

jaala wrote:
2019.11.15 00:53
...Then it continues to ask me to input pdb file name and will not continue to the next step...
This means pre_bunch cannot find the pdb file. Are you are running pre_bunch from the command line in the folder with your pdb files?
by AL
2019.12.03 12:53
Forum: Primary Data Processing
Topic: R2 value for Guinier plot
Replies: 1
Views: 1761

Re: R2 value for Guinier plot

In ATSAS there is no R2 value calculation for the Guinier fit yet.
Please update your ATSAS version.
by AL
2019.12.03 12:48
Forum: Primary Data Processing
Topic: How to normalize/process I(0)
Replies: 1
Views: 2422

Re: intensities need to be normalized by some parameter

I am working with several SEC-SAXS curves obtained at Petra III during different trips... If you want to use I(0) from the Guinier approximation for MW calculations you need data collected on an absolute scale and you need to know the concentration in each frame. In theory, you can use the UV trace...
by AL
2019.11.20 07:10
Forum: Working with Models
Topic: ATSAS 3.0 damaver error
Replies: 2
Views: 262

Re: ATSAS 3.0 damaver error

Indeed. Thank you for reporting this.
by AL
2019.11.20 07:00
Forum: Rigid Body Modelling
Topic: Pre-bunch Issue
Replies: 3
Views: 333

Check your file name

Does your file name contain special characters, spaces etc.?
by AL
2019.11.11 20:11
Forum: Rigid Body Modelling
Topic: CORAL crash when selecting .con file
Replies: 6
Views: 7603

Try CORAL online

asherat wrote:
2019.10.31 16:30
When starting my CORAL run the windows closes in the independent actions:
Does CORAL online work for you?
*ATSAS online account required
by AL
2019.11.11 00:14
Forum: ATSAS Package in General
Topic: Request for Python3 version of saspy.py
Replies: 1
Views: 7168

Try ATSAS 3.0

SASpy from ATSAS 3.0 works with Python 2.7 as well as with Python 3.7, please upgrade.
by AL
2019.11.01 14:40
Forum: ATSAS Package in General
Topic: ATSAS release 3.0 is available
Replies: 3
Views: 923

ATSAS release 3.0 is available

Download ATSAS 3.0 (academic users only) Supported platforms: Windows 7, 8 and 10; macOS 10.12 Sierra, 10.13 High Sierra, 10.14 Mojave; Ubuntu 16 and 18; Debian 9; Red Hat/CentOS 7. New programs: cif2pdb - converts mmcif files to pdb format; temporary module to use for ATSAS programs that are not y...
by AL
2019.10.31 15:08
Forum: ATSAS Package in General
Topic: ATSAS 2.8.4-1 installation and SASpy PATH errors
Replies: 1
Views: 2160

Try ATSAS 3.0

Please remove ATSAS 2.8.4, download ATSAS 3.0 and follow these installation instructions.
by AL
2019.08.20 13:33
Forum: Primary Data Processing
Topic: SAXS from P(r)
Replies: 3
Views: 7355

Re: pddffit

You may take any "template" curve, run pddffit, then remove the second and third column from the output file.
by AL
2019.08.19 08:42
Forum: Primary Data Processing
Topic: SAXS from P(r)
Replies: 3
Views: 7355

pddffit

Sure, it is called pddffit. $ pddffit --help Usage: pddffit <PDDFFILE> <DATFILE> [OPTION] Fits a pair distance distribution function to experimental data. Known Options: -o, --output=FILE write the output to this file instead of stdout -v, --version print version information and exit -h, --help prin...
by AL
2019.08.19 08:37
Forum: Announcements
Topic: EMBO Global Exchange Lecture Course, October 2019, Chile
Replies: 1
Views: 5450

Registration deadline extended

Due to multiple gentle requests, we have decided to reopen the Course registration. The new deadline is August 31 2019.
by AL
2019.08.07 18:32
Forum: Mixtures and Flexible Systems
Topic: EOM online error
Replies: 4
Views: 5708

spaces in file names are not allowed

Thank you for sending the files. The sequence file name contains spaces, apparently, this is not allowed. Please replace spaces with e.g. underscores and EOM will start.