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 <icegood1980@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