Search found 350 matches

by SaxsMax
2008.02.25 20:59
Forum: Working with Models
Topic: shell size
Replies: 1
Views: 3938

The shell width is indeed a fixed parameter in Crysol, however in most of applications only the product of the shell width and the shell contrast matters. So, one could try to vary the density of the shell instead of changing its width. Also the use of tentative detergent molecules around the protei...
by SaxsMax
2008.02.13 22:09
Forum: Ab Initio Shape Determination
Topic: MONSA - control and master files
Replies: 1
Views: 3589

The first phase is the part of the protein corresponding to the fragment dat. Then the second phase is the rest. The volumes in MASTER file were evaluated using Primus (Porod Button) and DAMMIN. I put the volume and RG from the fragment and the protein. This should be the volumes of the two parts an...
by SaxsMax
2008.02.13 21:53
Forum: Rigid Body Modelling
Topic: Defining starting configuration SASREF
Replies: 1
Views: 3523

Yes, and this is even the default option,
i.e. if you do not shift and rotate the subunits on purpose.
by SaxsMax
2008.01.25 13:56
Forum: Ab Initio Shape Determination
Topic: DAMMIN/MONSA for natively or partially unfolded protein
Replies: 1
Views: 3870

EOM package seems to be the most suitable for the case
by SaxsMax
2008.01.25 13:54
Forum: Rigid Body Modelling
Topic: Bunch and clashes
Replies: 3
Views: 4649

You could run Bunch in the expert mode and increase the weight of
cross penalty (by an order let say)
by SaxsMax
2008.01.25 13:48
Forum: Rigid Body Modelling
Topic: SANS - Bunch and other programs
Replies: 4
Views: 5141

No, due to the same reason
by SaxsMax
2008.01.24 15:25
Forum: Ab Initio Shape Determination
Topic: envelope functions
Replies: 5
Views: 13484

SASHA is the only program (somewhat old though) i know to generate the envelope function directly from the data. I would use Dammin/Dammif for shape determination and then if you really need the envelope, it can be done from the resulting bead model using Crysol or directly in Rasmol as described ab...
by SaxsMax
2008.01.24 15:12
Forum: Rigid Body Modelling
Topic: SANS - Bunch and other programs
Replies: 4
Views: 5141

The present version of Bunch contains only DR formfactors for the X-ray case, therefore it is not recommended to use Bunch with SANS data. Better option would be to generate (randomly or with the help of bioinformatics servers) templates for the loops and use them as additional bodies in SASREF (of ...
by SaxsMax
2007.12.11 16:29
Forum: Ab Initio Shape Determination
Topic: envelope functions
Replies: 5
Views: 13484

MASSHA can display the envelope represented by *.flm file
(which can be generated by CRYSOL)
by SaxsMax
2007.12.11 16:12
Forum: Mixtures and Flexible Systems
Topic: contacts in BUNCH
Replies: 6
Views: 7328

By the way, the tutorial contacts.cnd file for the gst-dhfr should be changed accordingly to 1 and 1, as that is a single chain multidomain example
No, that is right. There is two-fold symmetry and therefore there are two chains
by SaxsMax
2007.11.23 12:44
Forum: Mixtures and Flexible Systems
Topic: contacts in BUNCH
Replies: 6
Views: 7328

Hm, this is strange. What is your operating system? Do you use the answers file from the bunch package (gd01.ans) Just in case (though it is not relevant), there is a difference between the sasref and bunch contacts files: for sasref the first and the fourth numbers are the subunit #, for bunch they...
by SaxsMax
2007.11.23 12:27
Forum: Working with Models
Topic: CRYSOL: displaced solvent volumes and radii of heteroatoms
Replies: 1
Views: 4841

The radii is a consensus from several sources: Radii from Fraser et al., http://www.sicyon.com/ http://www.webelements.com/ C CH CH2 CH3 N NH NH2 NH3 O OH 1.577,1.73,1.85,1.97,0.84,1.22,1.45,1.62,1.30,1.50, S SH P FE CU CA MG MN ZN NHH NHM* 1.68,1.81,1.11,1.24,1.28,1.97,1.60,1.30,1.33,1.22,1.22, MO ...
by SaxsMax
2007.11.21 22:30
Forum: Rigid Body Modelling
Topic: Modelling homodimers with SAXS data
Replies: 3
Views: 5030

Hello Jon,
did you do an AUTORG analysis of the curve?
It is recommended to cut the very beginning of the data
up to the first point in Guinier plot according to AutoRG (if it is not #1)

Globsymm should be a better program than dimfom
by SaxsMax
2007.11.21 22:25
Forum: Mixtures and Flexible Systems
Topic: contacts in BUNCH
Replies: 6
Views: 7328

could you post your cnd file?
What is the error?
by SaxsMax
2007.11.20 12:51
Forum: Rigid Body Modelling
Topic: Curve fitting of BUNCH
Replies: 3
Views: 5265

The scattering curves are computed slightly different
in Crysol and Bunch. Still if the model yields a good fit by Bunch,
it should normally also be fitted well by Crysol