Search found 339 matches

by SaxsMax
2017.11.02 15:49
Forum: Mixtures and Flexible Systems
Topic: EOM input bug (shell version)?
Replies: 2
Views: 364

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: 1935

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: 1935

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: 1935

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: 468

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: 442

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: 510

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: 1124

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
by SaxsMax
2017.05.31 13:49
Forum: Working with Models
Topic: Volumes used by crysol
Replies: 5
Views: 1436

Re: Volumes used by crysol

Please note that the formfactors are still computed from Gaussian spheres, not solid spheres
by SaxsMax
2017.05.31 13:43
Forum: Working with Models
Topic: Volumes used by crysol
Replies: 5
Views: 1436

Re: Volumes used by crysol

Fraser et al. (1978) lists observed volumes for just four atoms.
The present version of Crysol supports 108 atom and atomic groups (e.g. CH)
whose Wan-der-Waals volumes seem to work well.
by SaxsMax
2017.05.31 12:18
Forum: Working with Models
Topic: Atomic form factors and incoherent scattering in Cryson
Replies: 1
Views: 620

Re: Atomic form factors and incoherent scattering in Cryson

In Cryson the form factors for individual atoms are constants equal to the corresponding scattering lengths
but for the atomic groups (like CH) the formfactors are computed using the Debye formula and therefore depend on s.

Incoherent scattering is not taken into account in prediction mode.
by SaxsMax
2017.05.10 11:45
Forum: Working with Models
Topic: Volumes used by crysol
Replies: 5
Views: 1436

Re: Volumes used by crysol

Dry volume is simply computed from the molecular weight as V=1.21*MW where MW is in Dalton and V is in A^3. Displaced volume is the sum of the Van-der-Waals volumes of individual atomic groups, (i.e. it serves as V0 in formula). Excluded volume is the adjusted value (V in the formula, in prediction ...
by SaxsMax
2017.03.14 11:31
Forum: Rigid Body Modelling
Topic: Coral Restrains chain ID problem
Replies: 9
Views: 1935

Re: Coral Restrains chain ID problem

Hi,

Internally Coral puts all the input proteins into one "superchain",
therefore the reported numbering is different from the dist.cnd.
Have you checked that the conbdition is fulfilled in the resulting model?
by SaxsMax
2017.02.02 13:24
Forum: Rigid Body Modelling
Topic: Slit smearing in SASREF and BUNCH
Replies: 4
Views: 3284

Re: Slit smearing in SASREF and BUNCH

The smearing is done according to the equation (9.26) from Feigin&Svergun book, page 295 with W(t)=2*Smax (i.e. constant) corresponding to an infinite slit.
by SaxsMax
2017.01.13 18:02
Forum: Working with Models
Topic: Using Crysol for non-biological systems
Replies: 2
Views: 755

Re: Using Crysol for non-biological systems

If PDB file contains standard atoms, one can use Crysol in the same way as for biological molecules