Search found 347 matches

by SaxsMax
2014.01.06 18:54
Forum: Working with Models
Topic: Excluded volume fit in CRYSOL
Replies: 5
Views: 4292

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: 4292

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...
by SaxsMax
2014.01.02 22:26
Forum: Working with Models
Topic: Excluded volume fit in CRYSOL
Replies: 5
Views: 4292

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: 4835

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: 6160

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: 6076

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: 6076

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: 6076

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: 6076

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: 6657

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: 6076

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: 5692

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: 5130

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: 2661

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: 5216

Re: bugs in gajoe from eom 2.0

Thanks, the eom maintainer is informed ;)