Search found 651 matches

by AL
2019.08.20 13:33
Forum: Primary Data Processing
Topic: SAXS from P(r)
Replies: 3
Views: 486

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: 486

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: 814

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: 762

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.
by AL
2019.08.05 10:26
Forum: Mixtures and Flexible Systems
Topic: EOM online error
Replies: 4
Views: 762

Re: EOM online error

In order to reproduce the problem we'd need all the files you have submitted. Could you please send us these files via email or post them here?
by AL
2019.08.02 09:47
Forum: Mixtures and Flexible Systems
Topic: EOM online error
Replies: 4
Views: 762

change sequence file extension

Thank you for reporting this.
Could you please change the extension of your sequence .fasta file to ".seq"?
by AL
2019.07.31 10:19
Forum: Ab Initio Shape Determination
Topic: DAMMIN Web inferface
Replies: 1
Views: 821

DAMMIN online runs only once

DAMMIN online runs only once, DAMAVER does not run here. If you wish to re-run DAMMIN online please go to My Projects and click re-run with new id.
by AL
2019.07.31 09:58
Forum: Announcements
Topic: CEITEC practical course in Brno, September 2019
Replies: 0
Views: 1078

CEITEC practical course in Brno, September 2019

BioSAXS practical course 2019 CEITEC practical course, 10 - 11 September 2019, Brno, Czech Republic https://www.embl-hamburg.de/biosaxs/img/ceitec-course-brno.png A short practical course on basics of biological SAXS in Brno, Central European Institute of Technology (CEITEC) introducing the practic...
by AL
2019.07.30 14:00
Forum: Ab Initio Shape Determination
Topic: Problem running DAMMIN on GNOM output files
Replies: 1
Views: 380

use DAMMIN online

It looks like you are using an outdated Windows-only "QuickWin" version of DAMMIN. Please use the command-line version or use DAMMIN online.
by AL
2019.06.03 17:34
Forum: Primary Data Processing
Topic: Question about chi^2
Replies: 2
Views: 584

reduced chi-squared

I'm fitting some data and I was wondering how do you calculate the scaling factor present in the formula for chi^2 The scaling factor minimizes chi-squared (least squares method). and also, I would like to understand the k-1 factor...IN your paper there is not any explanation about that factor... N...
by AL
2019.05.31 11:40
Forum: Working with Models
Topic: Generate theoretical I vs q curves
Replies: 5
Views: 1553

CRYSOL in fitting mode

The theoretically generated scattering curves have a four to five fold difference in intensity than the experimental curves. Just treat the intensity of the theoretical curves as some arbitrary units and scale (multiply) them to match your experimental data. Please note that you may fit the compute...
by AL
2019.04.30 11:34
Forum: Mixtures and Flexible Systems
Topic: Problem with EOM output pdbs
Replies: 2
Views: 658

Re: Problem with EOM output pdbs

Am I missing a setting to preserve residue order in the output PDBs? Hi Jesse, unfortunately that's how RANCH works - it calls everything chain A and the order of the residues is a complete chaos. We've opened a bug report for this issue. Perhaps there is a script that can properly rename the chain...
by AL
2019.04.30 10:30
Forum: Mixtures and Flexible Systems
Topic: How to use EOM on glycosylated proteins
Replies: 6
Views: 1083

Re: How to use EOM on glycosylated proteins

Loki03 wrote:
2019.04.25 20:04
... it still asks for a sequence and then doesnt match it to the pdb that I glycosylated with the GLYCOSYLATION program.
So EOM runs fine with your domain(s) an the sequence before you run GLYCOSYLATION but after you run GLYCOSYLATION it says the sequence doesn't match?
by AL
2019.04.30 10:27
Forum: Working with Models
Topic: Generate theoretical I vs q curves
Replies: 5
Views: 1553

Re: Generate theoretical I vs q curves

prithaghosh wrote:
2019.04.25 17:20
How can I output the theoretical I vs q curve for a model that is calculated by CRYSOL?
$ crysol model.pdb

The output file model00.int will contain the calculated scattering intensity.
by AL
2019.04.25 14:46
Forum: Rigid Body Modelling
Topic: How to use Massha in ubuntu?
Replies: 1
Views: 980

SASpy

MASSHA is available only on Windows. Please use the PyMOL plugin SASpy instead.
(The SASpy plugin from ATSAS 2.8.4 is for PyMOL version 2.2 or earlier.)