Search found 347 matches

by SaxsMax
2014.07.16 11:13
Forum: Primary Data Processing
Topic: Compare scattering profiles
Replies: 1
Views: 1984

Re: Compare scattering profiles

I would say that the green curve has larger Rg than the blue one in contrast to the label on the figure
by SaxsMax
2014.07.16 11:07
Forum: Working with Models
Topic: Known problem in Crysol 2.8
Replies: 0
Views: 3851

Known problem in Crysol 2.8

Biological unit downloaded from PDB may contain
MODEL-ENDMDL sections similarly to an NMR ensemble.
In this case Crysol takes only the first entity (MODEL 1)
which is counter intuitive in case of oligomeric molecule.
This issue will be corrected in the next release of ATSAS (2.5.3)
by SaxsMax
2014.07.10 11:02
Forum: Rigid Body Modelling
Topic: Coral P2 Symmetry contacts
Replies: 15
Views: 16860

Re: Coral P2 Symmetry contacts

emded wrote: a1.pdb
LINK 22
a2.pdb
b1.pdb
LINK 22
b2.pdb
This means that there are two chains:
a1.pdb-LINK 22-a2.pdb and
b1.pdb-LINK 22-b2.pdb

Therefore, contact restraint should look like

dist 7.0
1 53 53 2 56 56
dist 7.0
1 56 56 2 53 53
by SaxsMax
2014.07.09 11:03
Forum: Rigid Body Modelling
Topic: Coral P2 Symmetry contacts
Replies: 15
Views: 16860

Re: Coral P2 Symmetry contacts

emded wrote:
Any suggestions why restrain file is not working?
Maybe you could actually post the content of the *.con and *cnd files
and also specify the number of Ca atoms in each domain (individual pdb file).
This would make the diagnostics easier
by SaxsMax
2014.07.09 10:13
Forum: Rigid Body Modelling
Topic: Coral P2 Symmetry contacts
Replies: 15
Views: 16860

Re: Coral P2 Symmetry contacts

The name restrain.cnd should work.
What exactly is the error message?
by SaxsMax
2014.07.08 17:55
Forum: Rigid Body Modelling
Topic: Coral P2 Symmetry contacts
Replies: 15
Views: 16860

Re: Coral P2 Symmetry contacts

It should be ~3.8 A between the DR and the Ca atom in the structure
by SaxsMax
2014.07.08 17:27
Forum: Rigid Body Modelling
Topic: Coral P2 Symmetry contacts
Replies: 15
Views: 16860

Re: Coral P2 Symmetry contacts

I don't know if the number of the residue needs to be the number specified in the PDB file or the number from the end of the N-terminus. As an example I have cut the protein into two parts so that Coral can build a loop in between. Therefore the chain two starts at residue 124 and not at residue 1....
by SaxsMax
2014.05.28 13:08
Forum: Rigid Body Modelling
Topic: How does SASREF handle the hydration layer for close bodies?
Replies: 1
Views: 2546

Re: How does SASREF handle the hydration layer for close bod

Possible hydration layers overlap is considered as a small effect in rigid body modelling programs and is currently neglected.
by SaxsMax
2014.05.28 13:06
Forum: Working with Models
Topic: contrast and hydration layer electron density in CRYSOL
Replies: 1
Views: 2798

Re: contrast and hydration layer electron density in CRYSOL

Semax is the maximum s in experimental data used
Average electron density is computed for the particle (total number of electrons divided by the volume)
Hydra is computed as 1.8*Volume of the shell*(0.334+Dro0) / Molecular weight
by SaxsMax
2014.05.28 12:58
Forum: Rigid Body Modelling
Topic: SASREF Partial model from crystal
Replies: 1
Views: 2299

Re: SASREF Partial model from crystal

You might wish to use Coral/Bunch instead of Sasref in case of incomplete pdb file.
by SaxsMax
2014.05.28 12:55
Forum: Ab Initio Shape Determination
Topic: Questions about GNOM, GASBOR and DAMMIN.
Replies: 1
Views: 2468

Re: Questions about GNOM, GASBOR and DAMMIN.

The Gnom file is incomplete. You need to run Gnom program
till the end so that the *.out file is properly written
by SaxsMax
2014.05.19 11:52
Forum: ATSAS Package in General
Topic: server issue
Replies: 5
Views: 3773

Re: server issue

Download links should work now. Please try again.
by SaxsMax
2014.04.25 11:07
Forum: ATSAS Package in General
Topic: atsas 2.5.2-1 bunch segmentation fault
Replies: 3
Views: 3579

Re: atsas 2.5.2-1 bunch segmentation fault

Please try to open the data file in primus/qt,
determine the Rg and Guinier interval using
Tools->Radius of Gyration and save the data as a new file.
This will remove bad data points at the beginning
and should be usable in bunch.
by SaxsMax
2014.04.23 18:51
Forum: ATSAS Package in General
Topic: sasrefmx
Replies: 6
Views: 4523

Re: sasrefmx

Yes, you are right,
if you used equimolar ratio (i.e. specified 1 and 1 in the last row of the table) for the dissociation products,
then the ratio between their volume fractions is equal to Va/VB
by SaxsMax
2014.02.05 21:56
Forum: Rigid Body Modelling
Topic: More than 10 subunits in Sasref?
Replies: 1
Views: 2388

Re: More than 10 subunits in Sasref?

Sasref supports up to ten subunits in asymmetric part.
In case you have an oligomer, symmetry can be applied
to reduce the number of independent rigid bodies.