Search found 345 matches

by SaxsMax
2007.10.30 12:07
Forum: Ab Initio Shape Determination
Topic: DAMMIF resolution limits
Replies: 2
Views: 3810

There is such a question in dammif as well:
"Proportion of the curve to be fitted ? (0.0-1.0] (default: 1.00) ..... :"
However it is better to use limited data range already in Gnom
by SaxsMax
2007.10.30 12:04
Forum: Ab Initio Shape Determination
Topic: Chi square discrepancies ...
Replies: 1
Views: 3621

Averaged model does not necessarily yield the good fit to the data.
You can use the damstart.pdb for the "refinement" with dammin.
Also the computation of the fit from the bead model by Crysol is not
very accurate as it is designed for scattering calculation from atomic models
by SaxsMax
2007.10.12 18:49
Forum: Working with Models
Topic: CRYSOL search limits 2
Replies: 3
Views: 5575

Given the fact that the contrast of DNA is much higher than that of the protein, the hydration plays smaller role. Still the CRYSOL dro limits should be OK for nucleic acids
by SaxsMax
2007.10.10 21:16
Forum: Rigid Body Modelling
Topic: BUNCH segmentation error
Replies: 3
Views: 4301

Well, in fact it should be four, not three AA, sorry.
And then you need to cut out these residues from the
pdb files of the domains
by SaxsMax
2007.10.09 18:43
Forum: Rigid Body Modelling
Topic: BUNCH segmentation error
Replies: 3
Views: 4301

Did you try to run Bunch on another platform,
in other words does only l86 version crash?

Does the sequence have a gap between the two domains
(at least 3AA gap is required)?

Could you send your output from pre_bunch to
atsas_at_embl-hamburg.de to be checked?
by SaxsMax
2007.10.09 18:34
Forum: Working with Models
Topic: CRYSOL search limits 2
Replies: 3
Views: 5575

It is better to stay within CRYSOL limits to get reasonable results. If the sample is a bit aggregated/oligomerized it may be seen in the Guinier plot. Did you run AUTORG to find the Guinier range? The data at very low angles that are out of the Guinier range according to AUTORG should be cut out be...
by SaxsMax
2007.10.01 18:21
Forum: Ab Initio Shape Determination
Topic: Contrasts for MONSA
Replies: 1
Views: 3460

Hello, For SAXS it is reasonable to use contrast =1 for the protein and 2 for DNA/RNA In case of neutrons you can compute the contrast from arbitrary protein/nucleic acid by CRYSON and then use these numbers in Monsa assuming they are the same for your case. For lipids these values can be very diffe...
by SaxsMax
2007.10.01 18:15
Forum: Ab Initio Shape Determination
Topic: DAMMIN / GASBOR - command-line arguments
Replies: 1
Views: 3388

Yes, /SD is the only "hidden" key.
If the program does not recognize properly the angular units,
you need to run it manually or to prepare an answers file
by SaxsMax
2007.10.01 18:11
Forum: Ab Initio Shape Determination
Topic: DAMMIN - Fit Differs from GNOM
Replies: 8
Views: 9692

In the log file it should be written something like
"A constant was subtracted .............................. : 8.780e-2"

To see the fit to the original unsubtracted data you need to plot the *.fir file
by SaxsMax
2007.10.01 18:01
Forum: Rigid Body Modelling
Topic: contact conditions across symmetry mates in BUNCH
Replies: 4
Views: 6538

Format of the contacts file in Bunch is a little bit different than in Sasref:
Instead subunits # in Sasref, one should use the chain # in Bunch.
In case of P3 you have three chains and the residues ranges
should be given respectively the entire chain, not the individual domains.
by SaxsMax
2007.09.10 18:00
Forum: Mixtures and Flexible Systems
Topic: Contacts condition in Bunch
Replies: 2
Views: 4134

Hi, In new Bunch (version 8) it is possible to include contacts conditions as it is done in Sasref. Example: the condition dist 7.0 1 25 30 2 25 30 requires the 7A distance between the portions 25-30 in two symmetry related chains Alternatively, if the interface between the dimerization domains is k...
by SaxsMax
2007.09.10 17:50
Forum: Ab Initio Shape Determination
Topic: DAMMIN - Fit Differs from GNOM
Replies: 8
Views: 9692

Hi, Are you looking at the *.fir or *.fit file? In *.fit a constant is usually subtracted from the data to ensure the s^-4 decay (Porod behavior) What is the Final SQRT(Chi) against raw data (can be seen in the *.log or *.fir files)? Also the programs PRIMUS/SASPLOT can be used for visualizing the f...
by SaxsMax
2007.08.30 19:44
Forum: Ab Initio Shape Determination
Topic: MONSA: minimum s_max
Replies: 2
Views: 3997

Did Monsa complain that the s_max value is too small?
by SaxsMax
2007.08.30 19:41
Forum: Working with Models
Topic: CRYSON
Replies: 2
Views: 4765

Do you type "CR" or press the carriage return (enter button)?
In the latter case the program should happily continue...
If it does not, could you please send your pdb/dat files?
by SaxsMax
2007.08.22 17:34
Forum: Rigid Body Modelling
Topic: Modelling glycosylations
Replies: 2
Views: 3776

At the moment it seems there is no possibility to model flexible glycosylations.
On the other hand, the use of carbohydrates in the modelling could only be used
to facilitate the fitting but not to define their "exact" position/conformation from the SAS data