Search found 350 matches

by SaxsMax
2020.03.05 14:57
Forum: Ab Initio Shape Determination
Topic: Chi-Squared Values
Replies: 14
Views: 8103

Re: Chi-Squared Values

I've used the crysol binary from Atsas-3.0.1 release and obtained the attached fit file.
The obtained chi^2 value is 3.355. The chi^2 computed from the fit file taking lines 3 to end is also 3.355.
Can you reproduce this result?
by SaxsMax
2020.03.05 09:57
Forum: Ab Initio Shape Determination
Topic: Chi-Squared Values
Replies: 14
Views: 8103

Re: Chi-Squared Values

Could you please attach the resulting fit file?
by SaxsMax
2020.03.03 14:28
Forum: Ab Initio Shape Determination
Topic: Chi-Squared Values
Replies: 14
Views: 8103

Re: Chi-Squared Values

It does polynomial smoothing of the non-negative data. If the smoothed array still has significant systematic
deviations, 3% relative error is assigned.
In practice, the third column in the resulting *.fit file is the used error value.
by SaxsMax
2019.11.11 10:54
Forum: ATSAS Package in General
Topic: ATSAS release 3.0 is available
Replies: 5
Views: 2165

Re: ATSAS release 3.0 is available

Hi Thiago, so far there is no publication dedicated to FlexBin
by SaxsMax
2019.09.27 16:35
Forum: Working with Models
Topic: cryson output.fit
Replies: 1
Views: 1056

Re: cryson output.fit

Cryson automatically fits the background, so the deviation from the experimental data is simply a constant
by SaxsMax
2019.08.21 19:20
Forum: Mixtures and Flexible Systems
Topic: Oligomer online error - zipped pdb archive
Replies: 2
Views: 6667

Re: Oligomer online error - zipped pdb archive

The possible problem is that the zip file contains a folder with pdb files, whereas they should be in the root of the zip. If this condition is fulfilled and still there are complaints, then could you please send the zip for testing
by SaxsMax
2019.05.13 09:59
Forum: Working with Models
Topic: Unexpected behavior of CRYSOL
Replies: 1
Views: 3793

Re: Unexpected behavior of CRYSOL

1. Crysol not only evaluates the element, but rather an atomic group,
e.g. C, CH, CH2, CH3. For this the complete atomic name is needed.

2. Only the ions that are in close vicinity to the RNA should be kept
by SaxsMax
2019.04.27 11:45
Forum: Working with Models
Topic: CRYSOL error: Fortran run-time error
Replies: 4
Views: 5037

Re: CRYSOL error: Fortran run-time error

Hi Anthony, I've been able to run the following command on Win 10, Atsas 2.8.4 without any problems crysol K16Abilayer_no_metal_optimized_SPC_frame150_exported_watersdeleted_Cldeleted_unboundHdeleted.pdb -sm 2.0 -ns 201 Which platform/Atsas version do you use? Try maybe to shorten the pdb file name ...
by SaxsMax
2019.04.25 14:46
Forum: Working with Models
Topic: CRYSOL error: Fortran run-time error
Replies: 4
Views: 5037

Re: CRYSOL error: Fortran run-time error

Hi Anthony,
Could you please attach the PDB file causing the error?
by SaxsMax
2019.03.21 11:25
Forum: Working with Models
Topic: User control of hydration layer contrast in crysol 3.0
Replies: 1
Views: 4206

Re: User control of hydration layer contrast in crysol 3.0

Indeed it is currently not possible to provide the User-defined contrasts of the hydration shell(s) in Crysol 3.0.
It can be enabled in the future Atsas releases
by SaxsMax
2018.12.03 14:49
Forum: Rigid Body Modelling
Topic: Assembly a multi-domain protein from available mono-domain?
Replies: 5
Views: 6479

wrong angular units

It seems that the experimental data are in inverse angstroems,
but 1/nm is given as the input. Try to rerun with proper units.
by SaxsMax
2017.11.02 15:49
Forum: Mixtures and Flexible Systems
Topic: EOM input bug (shell version)?
Replies: 2
Views: 5293

Re: EOM input bug (shell version)?

Could it be that your construct contains multiple chains
and neither of the input PDB files is a multimer?

In such a case eom requires that a contacts file is provided
by SaxsMax
2017.09.25 12:54
Forum: Rigid Body Modelling
Topic: Coral Restrains chain ID problem
Replies: 9
Views: 9726

Re: Coral Restrains chain ID problem

Given that the penalty is zero, the contacts restraints should be fulfilled.
Could you post the input files to check?
by SaxsMax
2017.08.31 15:03
Forum: Rigid Body Modelling
Topic: Coral Restrains chain ID problem
Replies: 9
Views: 9726

Re: Coral Restrains chain ID problem

It might be that the dimer is not consistent with the SAXS data.

What is the resulting chi^2 and the contact penalty (in the header of the generated PDB file) ?
by SaxsMax
2017.08.24 13:24
Forum: Rigid Body Modelling
Topic: Coral Restrains chain ID problem
Replies: 9
Views: 9726

Re: Coral Restrains chain ID problem

You could try the following conditions:

dist 5.0
1 41 41 2 262 262
dist 5.0
1 62 62 2 238 238