Search found 347 matches

by SaxsMax
2007.11.13 20:49
Forum: Rigid Body Modelling
Topic: contact conditions across symmetry mates in BUNCH
Replies: 4
Views: 6661

Could you please specify the residue ranges in the fixed and the flexible
parts and how does your contacts file look ?
by SaxsMax
2007.11.13 20:43
Forum: Working with Models
Topic: can't get to help menu in supcomb13
Replies: 1
Views: 4115

Hi,
To show the help menu of supcomb you need to type in the command line:
supcomb13 /h

In order to run damaver,
all executables from damaver package (and also supcomb)
should be either in the directory on the system path
or in the folder with the pdb files to average.
by SaxsMax
2007.10.30 12:07
Forum: Ab Initio Shape Determination
Topic: DAMMIF resolution limits
Replies: 2
Views: 3899

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: 3689

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: 5649

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: 4402

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: 4402

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: 5649

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: 3519

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: 3454

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: 9799

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: 6661

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: 4200

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: 9799

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: 4075

Did Monsa complain that the s_max value is too small?