Search found 346 matches

by SaxsMax
2019.09.27 16:35
Forum: Working with Models
Topic: cryson output.fit
Replies: 1
Views: 47

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: 2239

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: 1659

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: 2380

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: 2380

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: 1929

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: 3431

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: 2941

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: 5988

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: 5988

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: 5988

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
by SaxsMax
2017.08.24 12:10
Forum: Mixtures and Flexible Systems
Topic: how to fix an interface in EOM ?
Replies: 1
Views: 1356

Re: how to fix an interface in EOM ?

One can simply fix domains 1 and 4 in EOM, so that the desired interface is maintained
by SaxsMax
2017.08.24 12:08
Forum: Mixtures and Flexible Systems
Topic: Which program should I use to model protein and DNA complex
Replies: 2
Views: 1627

Re: Which program should I use to model protein and DNA comp

You could use Crysol to compute the fit from "6. Simulated protein and DNA complex" to "1. SAXS profile of protein and DNA complex" If the resulting fit is not good Sasref can be applied to arrange "4. Simulated DNA helix in pdb format" and "5. Crystal structure of the protein" to fit "1. SAXS profi...
by SaxsMax
2017.08.23 13:08
Forum: Rigid Body Modelling
Topic: Coral distance conditions
Replies: 1
Views: 2766

Re: Coral distance conditions

Please note just in case that in the Coral contact conditions one should refer to the chain number, not domain number. Further, the current Coral version concatenates all the chains into one master chain and uses GLY as DR name identifier. The clarity of the output should be improved in the future r...
by SaxsMax
2017.06.19 12:47
Forum: Working with Models
Topic: Obtaining Profiles With Explicit Waters
Replies: 2
Views: 3733

Re: Obtaining Profiles With Explicit Waters

One can change "WAT" to "H2O" for example and then use "-eh" and "-dro=0" keywords in the command line