Search found 345 matches

by SaxsMax
2014.01.02 22:26
Forum: Working with Models
Topic: Excluded volume fit in CRYSOL
Replies: 5
Views: 4144

Re: Excluded volume fit in CRYSOL

1. The original Crysol paper has been published in 1995.
There were a number of changes since then.
Particularly, the total excluded volume has been decoupled
from the variation of the average atomic group radius
since Crysol v. 2.3 (in year 2001).
2. Yes, Ra is the same as r0 in the paper
by SaxsMax
2013.12.11 04:51
Forum: Working with Models
Topic: Tables of IATYPE, ATYPE/RTYPE in CRYSOL
Replies: 3
Views: 4714

Re: Tables of IATYPE, ATYPE/RTYPE in CRYSOL

1. The table in Crysol containing the number of hydrogens in an atomic group has been compiled according to the PDB hetero-atom dictionary: http://rcsb-deposit.rutgers.edu/het_dictionary.txt http://deposit.pdb.org/het_dictionary.txt 2. It is incorrect to compute the scattering from a bead model by C...
by SaxsMax
2013.12.05 14:27
Forum: Rigid Body Modelling
Topic: Selection of multiple residue ranges in Coral
Replies: 5
Views: 6054

Re: Selection of multiple residue ranges in Coral

Unfortunately, the present version of Coral only allows continuous selection of residues to be attributed to a curve. Maybe one can run Coral with a subset of data fulfilling this limitation and then use the domains and the loops of the resulting model as rigid bodies for online-sasref (which allow ...
by SaxsMax
2013.11.15 21:00
Forum: Rigid Body Modelling
Topic: bug in CORAL (on win 7, 64 bit)
Replies: 10
Views: 5860

Re: bug in CORAL (on win 7, 64 bit)

OK, got it.
It happens on Win7 when redirection is used
coral < ans0.txt
Could you please check/confirm, that coral runs properly if the same answers are given in the manual mode?
Thanks
by SaxsMax
2013.11.15 20:15
Forum: Rigid Body Modelling
Topic: bug in CORAL (on win 7, 64 bit)
Replies: 10
Views: 5860

Re: bug in CORAL (on win 7, 64 bit)

Please attach your answer file (just in case).

Do you experience similar problem if you run coral with other data (on Win 7) ?
by SaxsMax
2013.11.15 19:53
Forum: Rigid Body Modelling
Topic: bug in CORAL (on win 7, 64 bit)
Replies: 10
Views: 5860

Re: bug in CORAL (on win 7, 64 bit)

Tried on Windows 7 with atsas-2.5.1.
And could not reproduce the reported behavior
by SaxsMax
2013.11.15 15:56
Forum: Rigid Body Modelling
Topic: bug in CORAL (on win 7, 64 bit)
Replies: 10
Views: 5860

Re: bug in CORAL (on win 7, 64 bit)

Alex wrote:hi, I use coral from 2.5.1 ATSAS distribution.
On which platform?

Also, is the behavior reproducible?
by SaxsMax
2013.11.15 13:58
Forum: Mixtures and Flexible Systems
Topic: on line EOM random/native
Replies: 20
Views: 6362

Re: on line EOM random/native

Checked on Win7 machine: c:\New folder>dir /b *.seq NOTAG.seq c:\New folder>pre_bunch *** The program generates the initial approximation *** *** for the further use in BUNCH. Given the one letter *** *** sequence of the entire molecule and available *** *** atomic models of domains in PDB format th...
by SaxsMax
2013.11.15 13:44
Forum: Rigid Body Modelling
Topic: bug in CORAL (on win 7, 64 bit)
Replies: 10
Views: 5860

Re: bug in CORAL (on win 7, 64 bit)

Which version of Coral do you use? I've tried to repeat your run with the same random seed (and it gives the same initial Chi value) but then SA procedure went different path: === CORAL05 started at 15-Nov-2013 12:31:18 Computation mode ....................................... : User Project identifi...
by SaxsMax
2013.10.30 11:53
Forum: Rigid Body Modelling
Topic: Coral modelling
Replies: 9
Views: 5509

Re: Coral modelling

1. Please make sure that you have unzip.exe and dbloop.zip in your atsas installation folder If not, please download them from http://www.embl-hamburg.de/biosaxs/atsas-online/download.php Subfolder 2.5.1/addon 2. Try to execute the command in your atsas installation folder unzip -q dbloop 011/* What...
by SaxsMax
2013.09.24 09:23
Forum: Working with Models
Topic: Problems with DAMAVER versions
Replies: 7
Views: 5007

Re: Problems with DAMAVER versions

I think what is meant is that starting from one *.out file
the resulting averaged models should be similar (not identical).
But the results are vastly different
by SaxsMax
2013.09.23 15:56
Forum: ATSAS Package in General
Topic: Problem with e-mail notification?
Replies: 3
Views: 2536

Re: Problem with e-mail notification?

There is seemingly no problem with the e-mail notification.
Could your spam filtering settings have changed?
by SaxsMax
2013.09.18 10:40
Forum: Mixtures and Flexible Systems
Topic: bugs in gajoe from eom 2.0
Replies: 8
Views: 5048

Re: bugs in gajoe from eom 2.0

Thanks, the eom maintainer is informed ;)
by SaxsMax
2013.09.18 10:33
Forum: Working with Models
Topic: Problems with DAMAVER versions
Replies: 7
Views: 5007

Re: Problems with DAMAVER versions

This runs damaver on the same set of *-1.pdb? Or did you run dammif 100 times, 50 times each and came up with different results? Judging from the headers of the two damaver files, the sets of the models used for averaging were different P100D240xx-1.pdb and P100D240_xxrun-1.pdb This might explain t...
by SaxsMax
2013.09.18 10:13
Forum: Mixtures and Flexible Systems
Topic: bugs in gajoe from eom 2.0
Replies: 8
Views: 5048

Re: bugs in gajoe from eom 2.0

If I'm not mistaken, eom is not supposed to provide
the exact model(s) or the exact number of components
(24 vs 3 is somewhat unexpected though).
What it must find is the correct distributions of Rg and Dmax values.
Was this the case?