Search found 346 matches

by SaxsMax
2008.01.25 13:54
Forum: Rigid Body Modelling
Topic: Bunch and clashes
Replies: 3
Views: 4337

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: 4734

No, due to the same reason
by SaxsMax
2008.01.24 15:25
Forum: Ab Initio Shape Determination
Topic: envelope functions
Replies: 5
Views: 12571

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: 4734

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: 12571

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: 6879

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: 6879

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: 4547

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: 4641

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: 6879

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: 4896

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
by SaxsMax
2007.11.20 12:46
Forum: Ab Initio Shape Determination
Topic: supcomb13 and symmetry
Replies: 2
Views: 3466

Hi
Did you specify in supcomb13 that the symmetry is P3?
by SaxsMax
2007.11.14 17:22
Forum: Rigid Body Modelling
Topic: SASREF / Globsymm
Replies: 1
Views: 3563

Hi, Let me start with Sasref: actually sasref6 should be the appropriate program in your case and it asks for the symmetry only once. If still you prefer to use Sasref7, you need to put P2 three times: the highest overall symmetry, the symmetry of the only curve and the symmetry of the only subunit....
by SaxsMax
2007.11.13 20:52
Forum: Rigid Body Modelling
Topic: contact conditions across symmetry mates in BUNCH
Replies: 4
Views: 6587

P.S. The simplest condition to make the P2 structure interconnected would be:
dist 7.0
1 1 0 2 1 0
by SaxsMax
2007.11.13 20:49
Forum: Rigid Body Modelling
Topic: contact conditions across symmetry mates in BUNCH
Replies: 4
Views: 6587

Could you please specify the residue ranges in the fixed and the flexible
parts and how does your contacts file look ?