Dear Sergey,
>From looking at your PDB file, I don't think PyMOL supports exactly what you
want. I believe that in order for all_states to show atoms properly, they
have to be in all of the states (all MODELs). So, you could do something
like the following, but it feels a little clunky to me. Also, I have found
it difficult to show changing CONECT records in different states. I hope
it's helpful in some way. I just put the atoms you don't want to see in
each frame off camera (at 999).
=========== PML file =================
load tmp2.pdb
set_view (\
0.000000000, 0.000000000, 1.000000000,\
0.000000000, 1.000000000, 0.000000000,\
1.000000000, 0.000000000, 0.000000000,\
0.000000000, 0.000000000, -160.000000000,\
170.746078491, 17.884912491, 31.797996521,\
-322.770446777, 1235.630004883, -20.000000000 )
hide everything
show sticks
show spheres
set sphere_scale, 0.5
color black, elem z
show sticks
===================================
============= PDB file ==================
MODEL 1
HETATM 1 O 999.000 999.000 999.000
HETATM 2 O 999.000 999.000 999.000
HETATM 3 O 999.000 999.000 999.000
HETATM 4 O 999.000 999.000 999.000
HETATM 5 O 999.000 999.000 999.000
HETATM 13 N 999.000 999.000 999.000
HETATM 14 C 999.000 999.000 999.000
HETATM 15 C 999.000 999.000 999.000
HETATM99985 Z 0.000 0.000 0.000
HETATM99986 Z 50.000 0.000 0.000
HETATM99987 Z 0.000 50.000 0.000
HETATM99988 Z 50.000 50.000 0.000
HETATM99989 Z 0.000 0.000 50.000
HETATM99990 Z 50.000 0.000 50.000
HETATM99991 Z 0.000 50.000 50.000
HETATM99992 Z 50.000 50.000 50.000
CONECT9998599986
CONECT9998599987
CONECT9998599989
CONECT9998699988
CONECT9998699990
CONECT9998799988
CONECT9998799991
CONECT9998899992
CONECT9998999990
CONECT9998999991
CONECT9999099992
CONECT9999199992
ENDMDL
MODEL 2
HETATM 1 O 24.000 46.000 39.000
HETATM 2 O 24.000 47.000 39.000
HETATM 3 O 24.000 47.000 38.000
HETATM 4 O 25.000 47.000 38.000
HETATM 5 O 25.000 47.000 39.000
HETATM 13 N 11.000 43.000 8.000
HETATM 14 C 12.000 43.000 8.000
HETATM 15 C 13.000 43.000 8.000
HETATM99985 Z 999.000 999.000 999.000
HETATM99986 Z 999.000 999.000 999.000
HETATM99987 Z 999.000 999.000 999.000
HETATM99988 Z 999.000 999.000 999.000
HETATM99989 Z 999.000 999.000 999.000
HETATM99990 Z 999.000 999.000 999.000
HETATM99991 Z 999.000 999.000 999.000
HETATM99992 Z 999.000 999.000 999.000
ENDMDL
===================================
On Mon, Jan 10, 2011 at 9:38 AM, Sergey Ivanov <icegood1...@gmail.com>wrote:
> Have pdb file with pseudobeads:
> MODEL 2
> HETATM 1 O 24.000 46.000 39.000
> HETATM 2 O 24.000 47.000 39.000
> HETATM 3 O 24.000 47.000 38.000
> HETATM 4 O 25.000 47.000 38.000
> HETATM 5 O 25.000 47.000 39.000
> HETATM 6 O 25.000 46.000 39.000
> HETATM 7 O 25.000 45.000 39.000
> HETATM 8 O 25.000 45.000 40.000
> HETATM 9 O 26.000 45.000 40.000
> HETATM 10 O 26.000 45.000 39.000
> HETATM 11 O 26.000 45.000 38.000
> HETATM 12 O 25.000 45.000 38.000
> HETATM 13 N 11.000 43.000 8.000
> HETATM 14 C 12.000 43.000 8.000
> HETATM 15 C 13.000 43.000 8.000
> HETATM 16 C 13.000 44.000 8.000
> HETATM 17 N 0.000 5.000 29.000
> HETATM 18 C 49.000 5.000 29.000
> HETATM 19 C 48.000 5.000 29.000
> HETATM 20 C 47.000 5.000 29.000
> HETATM 21 N 23.000 30.000 17.000
> HETATM 22 C 22.000 30.000 17.000
> HETATM 23 C 21.000 30.000 17.000
> HETATM 24 C 20.000 30.000 17.000
> ENDMDL
> MODEL 1
> HETATM99985 Z 0.000 0.000 0.000
> HETATM99986 Z 50.000 0.000 0.000
> HETATM99987 Z 0.000 50.000 0.000
> HETATM99988 Z 50.000 50.000 0.000
> HETATM99989 Z 0.000 0.000 50.000
> HETATM99990 Z 50.000 0.000 50.000
> HETATM99991 Z 0.000 50.000 50.000
> HETATM99992 Z 50.000 50.000 50.000
> CONECT9998599986
> CONECT9998599987
> CONECT9998599989
> CONECT9998699988
> CONECT9998699990
> CONECT9998799988
> CONECT9998799991
> CONECT9998899992
> CONECT9998999990
> CONECT9998999991
> CONECT9999099992
> CONECT9999199992
> ENDMDL
>
> Want to picture BOTH models, not second one only. How to do that
> WITHOUT splitting into one model? "WITHOUT" because it's just test
> data for real structures more than 100000 beads.
>
> --
> Kind regards,
> Sergey Ivanov
>
>
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--
Michael Zimmermann
Ph.D. student in Bioinformatics and Computational Biology
Department of Biochemistry, Biophysics and Molecular Biology
Iowa State University
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