Search found 32 matches

by dirac80
2012.09.10 13:29
Forum: Mixtures and Flexible Systems
Topic: EOM Results
Replies: 6
Views: 3808

Re: EOM Results

No, I didn't invert the sequence. Do you think this is the problem?
by dirac80
2012.09.07 11:07
Forum: Mixtures and Flexible Systems
Topic: EOM Results
Replies: 6
Views: 3808

Re: EOM Results

Excuse me, but I must add another oddity. If I run EOM with the monomer's sequence (2300aa), I didn't have any problem, infact EOM ran correctly. In your opinion, why does EOM operate correctly with a monomer sequence while not with "dimer sequence"?
by dirac80
2012.09.07 09:33
Forum: Mixtures and Flexible Systems
Topic: EOM Results
Replies: 6
Views: 3808

Re: EOM Results

Thank you Giancarlo. I attached protein sequence, EOM fit, Ranch and Gajoe log files. But please consider that the online version of EOM does not support dimer unless you consider your protein as a unique big chain. I consider my protein as a unique big chain infact I inserted the complete sequence ...
by dirac80
2012.09.06 18:29
Forum: Mixtures and Flexible Systems
Topic: EOM Results
Replies: 6
Views: 3808

EOM Results

Hi All, I have a problem with EOM. I ran EOM with some high resolution protein domain (10) and the protein sequence. My protein is a dimer and , obviously, I inserted the sequence of the dimer (high number of aa - about 4600). I've obtained a strange result, indeed EOMs' fit is good (low chi-square)...
by dirac80
2012.06.22 16:37
Forum: Rigid Body Modelling
Topic: BUNCH with multiple curves
Replies: 1
Views: 2014

BUNCH with multiple curves

Hi all, I have some questions about the program BUNCH. I have a long protein (about 230kDa - 2350 aa). I measured its I(q) spectra and by means of BUNCH I have built the 3d structure. Next, I measured a mixture composed by this long protein and a small peptide (about 4kDa - 40 aa). I would like to b...
by dirac80
2012.05.31 14:59
Forum: Ab Initio Shape Determination
Topic: GASBOR refinement?
Replies: 3
Views: 2824

Re: GASBOR refinement?

The protein is composed by 1600aa. The protein MW is 184kDa. I read that the GASBOR limit is 600kDa (ATSAS on-line). Is it true? The high value of Dmax is due to presence of a few aggregates. As to refinement what can you say me?
by dirac80
2012.05.30 18:45
Forum: Ab Initio Shape Determination
Topic: GASBOR refinement?
Replies: 3
Views: 2824

GASBOR refinement?

Hi all, I measured a bacterial protein as a four temperature function (T=20, 25, 30, 37). I analyzed the SAXS data and I obtained four different p(r) (see attached file) with differents giration radius which it grows with the temperature increases. In a attempt of obtaining a 3d low-resolution struc...
by dirac80
2011.11.14 18:57
Forum: Ab Initio Shape Determination
Topic: DAMMIN_error_starting_guess_PDB
Replies: 3
Views: 6174

DAMMIN_error_starting_guess_PDB

Hi all,

I'm trying to refine a DAMAVER structure, as suggested by a Svergun's review, by using DAMMIN. When I ran DAMMIN with simmetry, I obtained this error:

DAMSYM --W-: Atom# 1 does not have simmetry mate
by dirac80
2011.11.12 23:24
Forum: Rigid Body Modelling
Topic: SASREF, BUNCH, CORAL average
Replies: 1
Views: 2093

SASREF, BUNCH, CORAL average

Hi all,

Do I need to average the SASREF, BUNCH or CORAL models by using DAMAVER as DAMMIN, GASBOR and MONSA?
by dirac80
2011.11.04 20:49
Forum: Mixtures and Flexible Systems
Topic: EOM limits?
Replies: 10
Views: 6372

You should estimate MW using Porod volume. Btw, your data looks aggregated - what does AutoRg say? I estimated MW using autoPorod. It is 630kDa. I attached autoRg. As you are seeing the protein isn't aggregated or at least AutoRg said this. 8x 900aa = 7200aa and you say a dimer is ~4772aa. By the w...
by dirac80
2011.11.04 15:47
Forum: Mixtures and Flexible Systems
Topic: EOM limits?
Replies: 10
Views: 6372

Are you sure about the size? Yes, I performed protein purity and size by using SDS-PAGE, Dot blot and ELISA. The results showed the protein was a dimer (~4772aa). What concentrations did you use for the measurements? Solutions with protein concentrations between 0.7 and 1mg/ml were measured. Due to...
by dirac80
2011.11.03 16:14
Forum: Mixtures and Flexible Systems
Topic: EOM limits?
Replies: 10
Views: 6372

Excuse me, but I didn't remember that the figure is so much big...I apologize for the inconvenience...
by dirac80
2011.11.03 16:04
Forum: Mixtures and Flexible Systems
Topic: EOM limits?
Replies: 10
Views: 6372

Hi Giancarlo, thank you very much for your reply. I used both ATSAS 2.4.1 and on-line ATSAS. I think that my protein is partially folded with linker domains (see Kratky plot). It's known that this protein exists only as dimeric form. Now, I'm trying to reconstruct 3d-model by using BUNCH because som...
by dirac80
2011.11.02 15:50
Forum: Mixtures and Flexible Systems
Topic: EOM limits?
Replies: 10
Views: 6372

EOM limits?

Hi all, I'm trying to use EOM with a dimer protein. I inserted only the complete sequence of my protein (4776 aminoacids) and experimental data, no pdb files. The results are very bizarre because the program found only one PDB structure with an Rg (19nm) don't compare with Guinier-Rg (9nm). There ar...
by dirac80
2011.10.28 11:40
Forum: Rigid Body Modelling
Topic: CORAL subunit and chain limitations
Replies: 6
Views: 3693

Hi Alex,

what's the new version of ATSAS? Is it ATSAS 2.4.1 (xp-version)? Thanks for your reply.