It seems that the experimental data are in inverse angstroems,
but 1/nm is given as the input. Try to rerun with proper units.
Search found 340 matches
- 2018.12.03 14:49
- Forum: Rigid Body Modelling
- Topic: Assembly a multi-domain protein from available mono-domain?
- Replies: 5
- Views: 1024
- 2017.11.02 15:49
- Forum: Mixtures and Flexible Systems
- Topic: EOM input bug (shell version)?
- Replies: 2
- Views: 1027
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: 2735
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: 2735
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) ?
- 2017.08.24 13:24
- Forum: Rigid Body Modelling
- Topic: Coral Restrains chain ID problem
- Replies: 9
- Views: 2735
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
dist 5.0
1 41 41 2 262 262
dist 5.0
1 62 62 2 238 238
- 2017.08.24 12:10
- Forum: Mixtures and Flexible Systems
- Topic: how to fix an interface in EOM ?
- Replies: 1
- Views: 1012
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
- 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: 1194
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...
- 2017.08.23 13:08
- Forum: Rigid Body Modelling
- Topic: Coral distance conditions
- Replies: 1
- Views: 1037
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...
- 2017.06.19 12:47
- Forum: Working with Models
- Topic: Obtaining Profiles With Explicit Waters
- Replies: 2
- Views: 1787
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
- 2017.05.31 13:49
- Forum: Working with Models
- Topic: Volumes used by crysol
- Replies: 5
- Views: 2145
Re: Volumes used by crysol
Please note that the formfactors are still computed from Gaussian spheres, not solid spheres
- 2017.05.31 13:43
- Forum: Working with Models
- Topic: Volumes used by crysol
- Replies: 5
- Views: 2145
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.
The present version of Crysol supports 108 atom and atomic groups (e.g. CH)
whose Wan-der-Waals volumes seem to work well.
- 2017.05.31 12:18
- Forum: Working with Models
- Topic: Atomic form factors and incoherent scattering in Cryson
- Replies: 1
- Views: 1272
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.
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.
- 2017.05.10 11:45
- Forum: Working with Models
- Topic: Volumes used by crysol
- Replies: 5
- Views: 2145
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 ...
- 2017.03.14 11:31
- Forum: Rigid Body Modelling
- Topic: Coral Restrains chain ID problem
- Replies: 9
- Views: 2735
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?
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?
- 2017.02.02 13:24
- Forum: Rigid Body Modelling
- Topic: Slit smearing in SASREF and BUNCH
- Replies: 4
- Views: 3861
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.