Search found 640 matches

by AL
2019.04.30 11:34
Forum: Mixtures and Flexible Systems
Topic: Problem with EOM output pdbs
Replies: 2
Views: 39

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: 5
Views: 96

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: 4
Views: 60

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: 64

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.)
by AL
2019.04.25 14:42
Forum: Mixtures and Flexible Systems
Topic: How to use EOM on glycosylated proteins
Replies: 5
Views: 96

GLYCOSYLATION

Loki03 wrote:
2019.04.20 12:08
I havent found a way to add the glycosylation into the .seg file.
If you mean the sequence file - this wouldn't work.
You may add glycan groups to your structured domains with the ATSAS command-line program GLYCOSYLATION.
by AL
2019.02.27 12:01
Forum: Mixtures and Flexible Systems
Topic: GAJOE or OLIGOMER?
Replies: 4
Views: 321

Re: GAJOE or OLIGOMER?

prithaghosh wrote:
2019.02.27 11:38
my models are that of RNA and not protein.
That doesn't matter - FFMAKER uses CRYSOL to calculate the intensities.
by AL
2019.02.26 14:35
Forum: Rigid Body Modelling
Topic: CORAL crash when selecting .con file
Replies: 4
Views: 2895

Re: the program just quits without warning or error message

aga wrote:
2018.12.31 07:06
the program just quits without warning or error message, or crashes.
We could not reproduce this. You should get an error message like "Domain 2: fixation is not compatible with initial configuration"; CORAL will exit with a non-zero exit code. Please make sure you use the latest ATSAS package.
by AL
2019.02.26 11:22
Forum: Mixtures and Flexible Systems
Topic: GAJOE or OLIGOMER?
Replies: 4
Views: 321

Re: GAJOE or OLIGOMER?

Yes, sure, why not? You could have run FFMAKER/OLIGOMER on all ten of them to begin with.
by AL
2019.02.05 11:31
Forum: Working with Models
Topic: CRYSOL: Maximum in I(q) at q=0?
Replies: 1
Views: 163

Guinier law

... However, the experimental curve has a local minimum in I(q) at q=0, whereas my I(q) curve generated from CRYSOL has a maximum at q=0. (1) My first question is, why is this the case? Hard to tell. Collecting scattering data close to q=0 is challenging - that's where the primary beam hits the bea...
by AL
2019.01.28 19:54
Forum: Mixtures and Flexible Systems
Topic: Discrepance between EOM and Crysol model dimentions
Replies: 1
Views: 218

EOM uses CRYSOL to calculate the intensities

So, I used Crysol to simulate the scattering of the models generated by the EOM software and noticed a discrepancy between the values of Rg and Dmax obtained using the two softwares. What was the difference? 1%? 10%? What values from the CRYSOL log did you use as R g and D max ? (Should be "Rg from...
by AL
2019.01.25 16:59
Forum: Working with Models
Topic: resolution effects in Cryson via the fourth column
Replies: 2
Views: 367

fourth column in SANS data

anlarsen wrote:
2019.01.24 10:06
most SANS beamlines nowadays provide the resolution effect via an uncertainty of q, in the fourth column of data.
Could you please point us to some documentation on how the fourth column should be interpreted? So far we've seen SANS data in four-column format only from KWS1 (FRM2, Munich).
by AL
2019.01.25 14:28
Forum: Rigid Body Modelling
Topic: CORAL-Domain fixation incompatible
Replies: 1
Views: 210

CORAL online doesn't support contact conditions

I am always getting the error that 'Domain 6 fixation is incompatible with the initial configuration' after grouping the domains. I am grouping (1,2), (4,5) and (3,6) domains. This means the domains 3 and 4 cannot be reasonably connected by a linker (given the distance between 5 and 6). There is no...
by AL
2019.01.04 12:29
Forum: Rigid Body Modelling
Topic: CORAL crash when selecting .con file
Replies: 4
Views: 2895

Try CORAL online

aga wrote:
2018.12.31 07:06
I'm using it for the first time, so not sure where is the error in the con file...
Does CORAL online work for you?
*ATSAS online account required
by AL
2018.12.24 13:18
Forum: Announcements
Topic: ASEAN workshop AWSAXS2019
Replies: 2
Views: 466

Re: ASEAN workshop AWSAXS2019

akgupta wrote:
2018.12.21 17:34
I just wanted to know what are the topics will be covered in this workshop? WIll you cover theory part as well?
Sure, a bit of theory, a bit of practice, a quite broad range of topics will be covered. Please check the AWSAXS2019 Program for details.
by AL
2018.12.21 16:52
Forum: Announcements
Topic: ASEAN workshop AWSAXS2019
Replies: 2
Views: 466

ASEAN workshop AWSAXS2019

https://www.embl-hamburg.de/biosaxs/img/awsaxs2019.png ASEAN Workshop on Small Angle X-ray Scattering 19 - 26 February 2019 SLRI, Thailand The ASEAN Workshop on SAXS targets scientists, researchers, lecturers, postdocs and PhD students who are interested in determination of protein structure in sol...