Search found 345 matches

by SaxsMax
2014.07.10 11:02
Forum: Rigid Body Modelling
Topic: Coral P2 Symmetry contacts
Replies: 15
Views: 15031

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: 15031

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: 15031

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: 15031

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: 15031

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: 2465

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: 2721

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: 2234

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: 2393

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: 3654

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: 3485

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: 4364

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: 2311

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.
by SaxsMax
2014.01.06 18:54
Forum: Working with Models
Topic: Excluded volume fit in CRYSOL
Replies: 5
Views: 4144

Re: Excluded volume fit in CRYSOL

Does eqn 1 from the paper then become, I(s) = <|Aa(s)+ (V/V0)*p0*Ac(s)+dp*Ab(s)|^2>omega ? Yes Also, is V0 part of the output log file? It is written in the log file in the prediction mode (i.e. w/o fitting) as "Excluded Volume" In the fitting mode it is present indirectly as the limits "ExVol(Min/...
by SaxsMax
2014.01.06 17:48
Forum: Working with Models
Topic: Excluded volume fit in CRYSOL
Replies: 5
Views: 4144

Re: Excluded volume fit in CRYSOL

Now a coefficient (V/V0) is used for the excluded volume amplitude. V is adjusted within 0.925*V0 to 1.075*V0 where V0 is the volume computed by default. In a way it is equivalent to the adjustment of the bulk solvent density. You could have a look at the SASdoc manual delivered with Atsas package o...