Search found 345 matches

by SaxsMax
2015.04.08 12:32
Forum: Rigid Body Modelling
Topic: MASSHA error reading alm file
Replies: 3
Views: 4782

Re: MASSHA error reading alm file

Are the alm and pdb files located in the same folder?
Also for xxx.pdb Crysol creates xxx00.alm. Did you add "00" to the alm name in Massha?
by SaxsMax
2015.03.25 20:31
Forum: Ab Initio Shape Determination
Topic: GASBOR -> DAMAVER -> ?
Replies: 2
Views: 3058

Re: GASBOR -> DAMAVER -> ?

1. I calculated 20 structures by GASBOR, and I run DAMAVER to get the averaged model. However, the outputted damaver.pdb is not the dummy "residue" model but the dummy "atom" model. The damfilt model does not basically fit the data. How should I get the average model after the GASBOR calculation an...
by SaxsMax
2015.03.16 19:56
Forum: Ab Initio Shape Determination
Topic: GASBOR issue with sequence and symmetry
Replies: 1
Views: 2327

Re: GASBOR issue with sequence and symmetry

Thanks for the report, the issue should be fixed in the next Atsas release.
For the moment the workaround as you correctly mention is to duplicate
the sequence n times (where n is the number of symmetry mates)
by SaxsMax
2015.01.13 12:58
Forum: Working with Models
Topic: Question on CRYSOL
Replies: 3
Views: 2675

Re: Question on CRYSOL

We do not have the atomic density distribution in the explicit form,
just the corresponding atomic formfactor which is given by
the International Tables, Vol. IV, page 71.
Sorry for not being very helpful.
by SaxsMax
2015.01.09 15:39
Forum: Working with Models
Topic: Question on CRYSOL
Replies: 3
Views: 2675

Re: Question on CRYSOL

There might be some confusion between the five-Gaussian approximation and the Gaussian sphere. The five-Gaussian approximation is related to the atomic scattering in vacuum. Corresponding theory and parameters can be found in the International Tables for X-ray Crystallography, Volume IV, page 71 (2....
by SaxsMax
2014.11.28 21:08
Forum: Working with Models
Topic: Command line changes from crysol 2.8.2 to 2.8.3 ?
Replies: 2
Views: 1965

Re: Command line changes from crysol 2.8.2 to 2.8.3 ?

In the new crysol versions both slash and dash are supported
Apparently, this is only true for Win version. For linux only dash is available in fact
by SaxsMax
2014.11.28 20:17
Forum: Working with Models
Topic: Command line changes from crysol 2.8.2 to 2.8.3 ?
Replies: 2
Views: 1965

Re: Command line changes from crysol 2.8.2 to 2.8.3 ?

I found: arguments can be passed with a slash in 2.8.2 (e.g. /err) while they require a dash in 2.8.3 (e.g. -err) crysol_summary.txt reports chi in version 2.8.2, but chi^2 in version 2.8.3 In the new crysol versions both slash and dash are supported, it should be actually more convenient This was ...
by SaxsMax
2014.11.12 12:20
Forum: Ab Initio Shape Determination
Topic: Monsa input files
Replies: 5
Views: 3543

Re: Monsa input files

The provided radius of the search volume is obviously too small.
One should run Gnom on all of the input data files to define the required
dimensions of the search volume
by SaxsMax
2014.08.26 11:15
Forum: Mixtures and Flexible Systems
Topic: Polydisperse sample
Replies: 1
Views: 1901

Re: Polydisperse sample

For the described purpose the tandem of
ffmaker and oligomer programs should be used
by SaxsMax
2014.08.26 11:03
Forum: Mixtures and Flexible Systems
Topic: ab initio modelling of oligomeric complex
Replies: 1
Views: 1813

Re: ab initio modelling of oligomeric complex

Yes, it is possible if the heterodimer is considered as a monomer and
the tetramer then would be a dimer with P2 symmetry
by SaxsMax
2014.07.16 11:23
Forum: Ab Initio Shape Determination
Topic: Problems with DAMMIF in batch mode, DAMSEL, SUPCOMB
Replies: 1
Views: 2227

Re: Problems with DAMMIF in batch mode, DAMSEL, SUPCOMB

Probably, one needs to add Atsas bin directory to the system PATH

Just to mention: Dammif-online performs also post-processing of the resulting ab initio models
by damaver suite (including damsel) and damclust
by SaxsMax
2014.07.16 11:18
Forum: FAQ
Topic: convert ab initio model back into pair distribution function
Replies: 1
Views: 10615

Re: convert ab initio model back into pair distribution func

One can use gasborp version which directly fits p(r).
The resulting *.hst file contains the comparison of the target
and computed distance distribution functions.
by SaxsMax
2014.07.16 11:16
Forum: Rigid Body Modelling
Topic: Bug: CORAL treats phosphoSer as two residues
Replies: 2
Views: 4633

Re: Bug: CORAL treats phosphoSer as two residues

" Ca " and " P " are treated as backbone atoms.
This should be taken into consideration when composing the contacts conditions file.
by SaxsMax
2014.07.16 11:13
Forum: Primary Data Processing
Topic: Compare scattering profiles
Replies: 1
Views: 1896

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: 3715

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)