Saxier Forum

Hi ankitgpta,

one of the problems usually is not having a comment or blank line in the data files. MONSA is very picky about this. The rest of the set-up should be the same I think between the online and stand alone versions.

Cheers,

Haydyn

Hi James, in the MONSA manual http://www.embl-hamburg.de/biosaxs/manual_monsa.html you can define the "connected-ness" on line 4 of the master file: eg. Master file for PROT 55.0 21 0.0 0.0 -1.0 -1.0 0.0 0.0 0 1 0.0 0.0 'prot1_500pts.con' -1 'prot2_500pts.con' -1 This specifies that phase 2 (volume ...

Cheers Duncan,

I suspected perhaps a version issue. There were problems with older versions, some of which are covered here on the forum. Hopefully everyone is now using the latest ATSAS 2.4 package and will provide feedback for programs generating strange results.

Catchya,

Haydyn

Hi dmcg026, The average Rg is just calculated from the structures generated. This sounds a little strange. What was the average Rg from the selected ensemble generated (ie. from running crysol on each conformer in the PDB directory and taking the average)? I would certainly expect a range of differe...

Hi, both curves yield Kratky plots characteristic of an unfolded species. I think the reason for any discrepancy between the Rg from Guinier analysis and that from the selected ensemble in EOM is due to the break-down of the Guinier law for unfolded systems. In this case using the Debye Approximatio...

Hi again, this data set (28 C) is definitely an unfolded protein (this time there is a clear monotonic increase in intensity with increasing scattering angle). Do you have data at several concentrations for each temperature? I think we need to rule out inter-particle interference. What is the exclud...

Oops, sorry. The Kratky does not show a monotonic increase, don't know what I did there. It is indeed a strange plot. The saxs curve still looks suspiciously like an unfolded protein (due to the almost complete lack of features). Also. I don't think there is a reliable Guinier range. In a quick anal...

Hi Tia, the data is typical for an unfolded protein. If you look at the Kratky plot it shows the signature monotonic increase and no real evidence of "foldedness". Do you use any rigid bodies for EOM or just random chains? Other than that, the EOM fit is quite nice. Is the version of ranch13 from th...

Hi Tia, If the protein is about 700 residues, the Rg for a Gaussian chain (unfolded and flexible) would be ~ 92 A. Since you calculate Rg = 60 A, as you already mentioned it is most likely flexible with some residual domain structure. ~ 80 A is approaching the Rg expected for a highly flexible prote...

Hi Tom, a number of books and reviews discuss this, so I suppose it depends on exactly what you're after. A good one is the following: Koch MH, Vachette P, Svergun DI. Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution. Q Rev ...

Hi Tanya, at present we have no specific manual for CORAL. It is quite similar to both SASREF and BUNCH. (1) You need an input list of PDB files, a control file, eg called t.con nter 5 pdb1 link 10 pdb2 cter 5 the file then has the number of residues for linkers and termini and the actual pdb files ...

Hi Tanya, easiest way to do this is to open the pdb file in a text editor, then extract the relevant subunit (or delete the irrelevant parts) and save as a new file. If you need to generate symmetry mates later make sure you have the entire structure oriented correctly and at the origin before cutti...

Hi Lionel, maybe there is a slight difference between PYMOL and MASSHA in regards to the origin? I don't know. I think your plan sounds good, use the translation command to shift the hexamer to the origin in MASSHA, extract the monomer and use this as input for your P6 rigid body modeling. Cheers, H...

Hi Abhay, This is not an unusual case. In principle you should be able to generate a useful ab initio model to describe the entire construct. I would first use DAMMIN or DAMMIF to obtain a bead model (run 10 times and obtain an average model) and check that the volume is consistent with an expected ...

Hi Abhay, just wanted to highlight several things. In GASBOR, DR should be the number of known amino-acid residues in the protein. GASBOR uses an average form factor describing amino acids and thus the average dummy residue radius is fixed and should not be adjusted. For an improvement in the fit of...