Search found 353 matches

by SaxsMax
2021.08.26 09:43
Forum: Mixtures and flexible systems
Topic: CORAL output pdb model
Replies: 6
Views: 1877

Re: CORAL output pdb model

One could increase the penalty weight until the fit gets worse. Please note that only C-alpha (and phosphor atoms in case of nucleic acid) are taken into account for the cross penalty. What is the oligomeric state of your sample? The clashes may point to (partial) dissociation in case of multimeric ...
by SaxsMax
2021.04.26 10:27
Forum: Mixtures and flexible systems
Topic: EOM on short peptides
Replies: 0
Views: 382

EOM on short peptides

Warning: When running EOM on short peptides it is recommended to use fixed size ensemble with 50 curves per ensemble and disallow repetitions. For details see A. Sagar, C.M. Jeffries, M.V. Petoukhov, D.I. Svergun and P. Bernado (2021) Comment on the Optimal Parameters to Derive Intrinsically Disord...
by SaxsMax
2020.08.13 09:35
Forum: Mixtures and flexible systems
Topic: CORAL output pdb model
Replies: 6
Views: 1877

Re: CORAL output pdb model

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.
by SaxsMax
2020.03.05 14:57
Forum: Ab initio shape determination
Topic: Chi-Squared Values
Replies: 14
Views: 12335

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: 12335

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: 12335

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: 7
Views: 5168

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: Model evaluation and manipulation
Topic: cryson output.fit
Replies: 1
Views: 1979

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: 7951

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: Model evaluation and manipulation
Topic: Unexpected behavior of CRYSOL
Replies: 1
Views: 4688

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: Model evaluation and manipulation
Topic: CRYSOL error: Fortran run-time error
Replies: 4
Views: 6747

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: Model evaluation and manipulation
Topic: CRYSOL error: Fortran run-time error
Replies: 4
Views: 6747

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: Model evaluation and manipulation
Topic: User control of hydration layer contrast in crysol 3.0
Replies: 1
Views: 5135

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: 8555

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: 6258

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