The online version of Coral uses the default weight of cross penalty. Apparently it is not enough for your samples.
For the time being could you please run local version of Coral in the expert mode and try to increase the cross penalty weight.
Search found 351 matches
- 2020.08.13 09:35
- Forum: Mixtures and flexible systems
- Topic: CORAL output pdb model
- Replies: 4
- Views: 1321
- 2020.03.05 14:57
- Forum: Ab initio shape determination
- Topic: Chi-Squared Values
- Replies: 14
- Views: 10924
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?
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?
- 2020.03.05 09:57
- Forum: Ab initio shape determination
- Topic: Chi-Squared Values
- Replies: 14
- Views: 10924
Re: Chi-Squared Values
Could you please attach the resulting fit file?
- 2020.03.03 14:28
- Forum: Ab initio shape determination
- Topic: Chi-Squared Values
- Replies: 14
- Views: 10924
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.
deviations, 3% relative error is assigned.
In practice, the third column in the resulting *.fit file is the used error value.
- 2019.11.11 10:54
- Forum: ATSAS package in general
- Topic: ATSAS release 3.0 is available
- Replies: 6
- Views: 4248
Re: ATSAS release 3.0 is available
Hi Thiago, so far there is no publication dedicated to FlexBin
- 2019.09.27 16:35
- Forum: Model evaluation and manipulation
- Topic: cryson output.fit
- Replies: 1
- Views: 1681
Re: cryson output.fit
Cryson automatically fits the background, so the deviation from the experimental data is simply a constant
- 2019.08.21 19:20
- Forum: Mixtures and flexible systems
- Topic: Oligomer online error - zipped pdb archive
- Replies: 2
- Views: 7573
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
- 2019.05.13 09:59
- Forum: Model evaluation and manipulation
- Topic: Unexpected behavior of CRYSOL
- Replies: 1
- Views: 4398
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
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
- 2019.04.27 11:45
- Forum: Model evaluation and manipulation
- Topic: CRYSOL error: Fortran run-time error
- Replies: 4
- Views: 6209
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 ...
- 2019.04.25 14:46
- Forum: Model evaluation and manipulation
- Topic: CRYSOL error: Fortran run-time error
- Replies: 4
- Views: 6209
Re: CRYSOL error: Fortran run-time error
Hi Anthony,
Could you please attach the PDB file causing the error?
Could you please attach the PDB file causing the error?
- 2019.03.21 11:25
- Forum: Model evaluation and manipulation
- Topic: User control of hydration layer contrast in crysol 3.0
- Replies: 1
- Views: 4847
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
It can be enabled in the future Atsas releases
- 2018.12.03 14:49
- Forum: Rigid body modelling
- Topic: Assembly a multi-domain protein from available mono-domain?
- Replies: 5
- Views: 7915
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.
but 1/nm is given as the input. Try to rerun with proper units.
- 2017.11.02 15:49
- Forum: Mixtures and flexible systems
- Topic: EOM input bug (shell version)?
- Replies: 2
- Views: 5932
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
and neither of the input PDB files is a multimer?
In such a case eom requires that a contacts file is provided
- 2017.09.25 12:54
- Forum: Rigid body modelling
- Topic: Coral Restrains chain ID problem
- Replies: 9
- Views: 12005
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?
Could you post the input files to check?
- 2017.08.31 15:03
- Forum: Rigid body modelling
- Topic: Coral Restrains chain ID problem
- Replies: 9
- Views: 12005
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) ?
What is the resulting chi^2 and the contact penalty (in the header of the generated PDB file) ?