Search found 101 matches

by Hayds
2011.08.10 11:04
Forum: Mixtures and Flexible Systems
Topic: Guinier Rg vs Rg distribution from GAJOE (EOM)
Replies: 15
Views: 9610

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
by Hayds
2011.08.09 22:22
Forum: Mixtures and Flexible Systems
Topic: Guinier Rg vs Rg distribution from GAJOE (EOM)
Replies: 15
Views: 9610

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...
by Hayds
2011.06.28 09:18
Forum: Mixtures and Flexible Systems
Topic: Guinier Rg vs Rg distribution from GAJOE (EOM)
Replies: 15
Views: 9610

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...
by Hayds
2011.06.27 09:51
Forum: Mixtures and Flexible Systems
Topic: Guinier Rg vs Rg distribution from GAJOE (EOM)
Replies: 15
Views: 9610

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...
by Hayds
2011.06.27 08:16
Forum: Mixtures and Flexible Systems
Topic: Guinier Rg vs Rg distribution from GAJOE (EOM)
Replies: 15
Views: 9610

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...
by Hayds
2011.06.27 07:52
Forum: Mixtures and Flexible Systems
Topic: Guinier Rg vs Rg distribution from GAJOE (EOM)
Replies: 15
Views: 9610

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...
by Hayds
2011.06.24 14:13
Forum: Mixtures and Flexible Systems
Topic: Guinier Rg vs Rg distribution from GAJOE (EOM)
Replies: 15
Views: 9610

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...
by Hayds
2011.03.31 21:06
Forum: Literature
Topic: SAXS and Shannon Channels Paper
Replies: 1
Views: 5633

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 ...
by Hayds
2011.02.02 04:39
Forum: Rigid Body Modelling
Topic: Bunch keeping oligomer organisation
Replies: 8
Views: 5562

CORAL manual

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 ...
by Hayds
2011.01.20 09:50
Forum: Rigid Body Modelling
Topic: Bunch keeping oligomer organisation
Replies: 8
Views: 5562

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...
by Hayds
2010.12.24 12:46
Forum: Rigid Body Modelling
Topic: Bunch keeping oligomer organisation
Replies: 8
Views: 5562

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...
by Hayds
2010.12.24 12:18
Forum: Ab Initio Shape Determination
Topic: radius of DR in Gasbor22pqw
Replies: 9
Views: 5101

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 ...
by Hayds
2010.12.24 00:37
Forum: Ab Initio Shape Determination
Topic: radius of DR in Gasbor22pqw
Replies: 9
Views: 5101

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...
by Hayds
2010.12.21 12:49
Forum: Primary Data Processing
Topic: Data range issues in GNOM
Replies: 2
Views: 2364

Hi Justin, I'm not familiar with the error myself, but if it is related to the experimental errors you can replace the third column (assuming your background subtracted data file is of aformat like: Q, I(Q), ERR) with uniform errors as a test. Also, maybe try a 10% error. I assume you have removed t...
by Hayds
2010.12.20 22:36
Forum: Rigid Body Modelling
Topic: Bunch keeping oligomer organisation
Replies: 8
Views: 5562

Hi Lionel,

When you take the extracted monomer and read this into MASSHA, then generate P6 does the hexamer look ok?

Haydyn