Search found 712 matches

by AL
2021.09.05 15:38
Forum: ATSAS package in general
Topic: ATSAS release 3.0 is available
Replies: 7
Views: 5532

ATSAS release 3.0.4 is available

Download ATSAS 3.0.4 (academic users only) New PyMOL plugin: mpbuilder: membrane-protein support application. Changes in programs: bodies : fixed calculation of volume of rotation ellipsoid, fixed calculation of hard-sphere structure-factor, fixed crash on calculation of hard-sphere structure-facto...
by AL
2021.08.04 21:34
Forum: Ab initio shape determination
Topic: Modeling Non-Interacting Species with MONSA?
Replies: 1
Views: 246

Re: Modeling Non-Interacting Species with MONSA?

Based on the P(r) fitting, I am confident that we have two separate populations (two distinct peaks). Please note, if the PDDF has two peaks it does not necessarily mean that it is a mixture of two non-interacting molecules, see e.g. SASDAG6 or SASDC56 . MONSA assumes that the input data are from m...
by AL
2021.08.04 13:25
Forum: Mixtures and flexible systems
Topic: EOM seq file error
Replies: 1
Views: 244

Re: EOM seq file error

What exactly are you trying to do?
EOM works with one chain only.
by AL
2021.07.21 16:33
Forum: Model evaluation and manipulation
Topic: Change limits on fitting parameters: command line
Replies: 1
Views: 452

crysol < answers.txt

No. To see all CRYSOL command-line options please type crysol --help To run CRYSOL multiple times when specifying options in the "interactive" mode, you could prepare an answer file and feed it to CRYSOL in a script. On Linux, the answer file is usually made with tee . On Windows, you may create thi...
by AL
2021.07.21 16:23
Forum: Primary data processing
Topic: DATVC for RNA data
Replies: 1
Views: 255

Re: DATVC for RNA data

DATVC output is for protein data, right? Yes. MW is calculated as mass = (Q R / e c ) L where Q R = V c 2 /R g . According to (Rambo & Tainer, 2013) Figure 3a , for proteins e c = 0.1231 and L = 1.0. These values are used in DATVC. According to Figure 3b, for RNA e c = 0.00934 and L = 0.808. Thus y...
by AL
2021.05.31 09:51
Forum: Model evaluation and manipulation
Topic: Cryson. Individual chain perdeuteration option
Replies: 1
Views: 665

cryson < answers.txt

There is only the "Perdeuteration of all chains" option . To run CRYSON multiple times when specifying the perdeuteration for individual chains, you could prepare an answer file and feed it to CRYSON in a script. On Linux, the answer file is usually made with tee . On Windows, you may create this fi...
by AL
2021.05.28 10:37
Forum: Rigid body modelling
Topic: SASREF/Crysol CORAL DNA atoms not recognized
Replies: 3
Views: 978

Re: SASREF/Crysol CORAL DNA atoms not recognized

Apparently, the DC nucleotide does not have an atom C5* , it should be C5' . C5* seems to be an older naming convention . You may try using CRYSOL with the -old option, it will resolve some but not all of the warnings. We recommend using PDB files in the latest format. I am worried that these atoms ...
by AL
2021.05.27 16:06
Forum: Rigid body modelling
Topic: SASREF/Crysol CORAL DNA atoms not recognized
Replies: 3
Views: 978

Re: Example files

Thank you for providing an example, we will investigate this.
by AL
2021.05.21 10:57
Forum: Mixtures and flexible systems
Topic: OLIGOMER - fit issues
Replies: 1
Views: 3201

OLIGOMER vs. CRYSOL fitting

Second case: due to the previously mentioned problem, I decided to use OLIGOMER for the monomer only. I have a crystal structure (.pdb) and experimental data where I have only the monomer. Using CRYSOL, I am getting a good fit between SAXS and pdb file.However, when I run OLIGOMER using monomer.pdb...
by AL
2021.05.17 15:58
Forum: Rigid body modelling
Topic: SASREF/Crysol CORAL DNA atoms not recognized
Replies: 3
Views: 978

Example files

Thank you for reporting this.
Could you please attach some examples?
by AL
2021.05.17 15:46
Forum: Ab initio shape determination
Topic: Ab initio model for big proteins
Replies: 1
Views: 1468

Re: Ab initio model for big proteins

The problem comes when I tried to run Dammif (online or at ATSAS 3.0.2). It recognized the data as Å instead of nm. When it runs as a Å (wrong units), the shape I obtain is quite similar to what we get for this protein in cryoEM but of course the size is completely wrong. However, when I force the ...
by AL
2021.04.19 15:04
Forum: Mixtures and flexible systems
Topic: SREFLEX generates models with severe clashes
Replies: 1
Views: 428

Re: SREFLEX generates models with severe clashes

You may try adjusting these settings:
-r, --ratio=<FLOAT> set convergence ratio, default 0.7, range [0.5:0.9]
-n, --nmtop=<INT> top normal mode to consider, default 16, range [9:64]
-s, --skip=<STAGE> skip RESTRAINED or UNRESTRAINED refinement stage
by AL
2021.04.19 15:00
Forum: Mixtures and flexible systems
Topic: EOM - size distribution of selected ensemble
Replies: 1
Views: 1174

Re: EOM - size distribution of selected ensemble

By default, GAJOE performs the fitting 100 times - to collect enough statistics for the Rg distribution histogram.
I'm not sure where the "selected" models come from, perhaps it's the smallest ensemble from all 100 runs.
by AL
2021.04.19 14:53
Forum: ATSAS package in general
Topic: Problem with Primus under Linux
Replies: 3
Views: 921

Re: set the shared lib path to the ATSAS lib folder

Cool, thank you for sharing this.
by AL
2021.04.12 18:36
Forum: Mixtures and flexible systems
Topic: SREFLEX on WAXS
Replies: 2
Views: 523

angular units?

Probably the units were guessed wrong. I think SREFLEX guesses the experimental data units based on the angular range. If your data are in A-1 try to convert it to nm-1 (e.g. with
datregrid --scale 10).