BODIES manual?

[Guðmundsdóttir]

Dear ATSASers,

I noticed that there are new body types in BODIES: liposome and memebrane (membrane?) protein!
How can I use these? Does anyone have examples? There is nothing in the BODIES manual about liposome and membrane protein. Whatever a-b-c-d-e-f values I enter for liposome I always get an empty dat file as output.

Thank you in advance for any help.

[franke]

The parameters for the liposome are
- a (positive)
- b (less than a)
- c (less than b)
- d to f (positive)

a, b, c are the semi-axis of the outer ellipsoid, while d, e, f are the semiaxis of the inner ellipsoid.

The parameters for the membrane protein are:
- Rmemb (positive)
- Rtail (greater than Rmemb)
- Rhead (greater than Rtail)
- delta (positive)
- zcorona (positive)

See Manalastas-Cantos et al. (2021) Figure 5 for details on these parameters.

That said, you might be disappointed if you are after the scattering - that's not implemented. However, you can use DAM mode to generate a model and run the models through crysol (only in ATSAS 3.1 or later!). That should give you an approximation. HTH.

[Guðmundsdóttir]

When I try to run my generated model through Crysol (from ATSAS 3.2.1) it crashes:

crysol test1.pdb

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x7fb3bc6f1d21 in ???
#1 0x7fb3bc6f0ef5 in ???
#2 0x7fb3bc35708f in ???
#3 0x55b81bdd83c6 in ???
#4 0x55b81bdd9f02 in ???
#5 0x55b81bdd56f9 in ???
#6 0x55b81bdd371e in ???
#7 0x7fb3bc338082 in ???
#8 0x55b81bdd374d in ???
#9 0xffffffffffffffff in ???
Segmentation fault


The model was generated like this:

bodies
Operation mode? Select one of: (f) fit, (p) predict, (d) dam, (v)
search volume (default: fit) ......................................... : d
Body type? Select one of: (1) ellipsoid, (2) rotation-ellipsoid, (3)
cylinder, (4) elliptic-cylinder, (5) hollow-cylinder, (6)
parallelepiped, (7) hollow-sphere, (8) dumbbell, (9) liposome, (10)
memebrane protein (default: ellipsoid) ............................... : 9
Value of parameter 'a' [Angstrom]? ................................... : 100
Value of parameter 'b' [Angstrom]? ................................... : 90
Value of parameter 'c' [Angstrom]? ................................... : 80
Value of parameter 'd' [Angstrom]? ................................... : 70
Value of parameter 'e' [Angstrom]? ................................... : 60
Value of parameter 'f' [Angstrom]? ................................... : 50
Value of parameter 'scale'? .......................................... : 1
Number of dummy atoms? (default: 2000) ............................... :
DAM output file name? ................................................ : test1.pdb

[franke]

Ouch. Indeed. Thanks for the report!

Two ways to workaround: (1) use mmCif as output format, e.g. test1.cif, or if you have to use PDB for another application, (b) open the PDB file and remove all trailing whitespace in the REMARK section, those after the values. This should also work (bad parser being thrown off by extra whitespace, ups).

HTH