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
Search found 103 matches
- 2011.12.19 06:42
- Forum: Ab initio shape determination
- Topic: quick monsa question
- Replies: 7
- Views: 8659
- 2011.12.19 03:11
- Forum: Ab initio shape determination
- Topic: MONSA online MONSA offline - Connectivity comparison
- Replies: 9
- Views: 7076
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 ...
- 2011.08.10 11:04
- Forum: Mixtures and flexible systems
- Topic: Guinier Rg vs Rg distribution from GAJOE (EOM)
- Replies: 15
- Views: 12616
- 2011.08.09 22:22
- Forum: Mixtures and flexible systems
- Topic: Guinier Rg vs Rg distribution from GAJOE (EOM)
- Replies: 15
- Views: 12616
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...
- 2011.06.28 09:18
- Forum: Mixtures and flexible systems
- Topic: Guinier Rg vs Rg distribution from GAJOE (EOM)
- Replies: 15
- Views: 12616
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...
- 2011.06.27 09:51
- Forum: Mixtures and flexible systems
- Topic: Guinier Rg vs Rg distribution from GAJOE (EOM)
- Replies: 15
- Views: 12616
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...
- 2011.06.27 08:16
- Forum: Mixtures and flexible systems
- Topic: Guinier Rg vs Rg distribution from GAJOE (EOM)
- Replies: 15
- Views: 12616
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...
- 2011.06.27 07:52
- Forum: Mixtures and flexible systems
- Topic: Guinier Rg vs Rg distribution from GAJOE (EOM)
- Replies: 15
- Views: 12616
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...
- 2011.06.24 14:13
- Forum: Mixtures and flexible systems
- Topic: Guinier Rg vs Rg distribution from GAJOE (EOM)
- Replies: 15
- Views: 12616
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...
- 2011.03.31 21:06
- Forum: Literature
- Topic: SAXS and Shannon Channels Paper
- Replies: 1
- Views: 9481
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 ...
- 2011.02.02 04:39
- Forum: Rigid body modelling
- Topic: Bunch keeping oligomer organisation
- Replies: 8
- Views: 7443
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 ...
- 2011.01.20 09:50
- Forum: Rigid body modelling
- Topic: Bunch keeping oligomer organisation
- Replies: 8
- Views: 7443
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...
- 2010.12.24 12:46
- Forum: Rigid body modelling
- Topic: Bunch keeping oligomer organisation
- Replies: 8
- Views: 7443
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...
- 2010.12.24 12:18
- Forum: Ab initio shape determination
- Topic: radius of DR in Gasbor22pqw
- Replies: 9
- Views: 7116
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 ...
- 2010.12.24 00:37
- Forum: Ab initio shape determination
- Topic: radius of DR in Gasbor22pqw
- Replies: 9
- Views: 7116
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...