RE: [PyMOL] save all not working for multiple objects from split_states?

[Warren D. <wa...@de...>]

Dan,

	That's the not expected result, but indeed you have a problem --
each of those subunits will have identical atoms.  To resolve this, =
assign a
unique segment identifier to each subunit:

load 1c8e.pdb1, 1c8e
split_states 1c8e
delete 1c8e
alter all, segi =3D model[-4:]
rewind
save test.pdb, all

dele all
load test.pdb

The reason why you were getting a PDB file with just END is that you =
didn't
return the viewer ro frame/state 1 after moving all of the data to state =
1.

After the above, you'll now be able to address each subunit indepently =
as:

hide
show ribbon
color red, segi 0001
zoom segi 0001

http://delsci.com/img/1c8e-subunit.jpg

Cheers,
Warren


> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Dr. Daniel James White PhD
> Sent: Tuesday, April 06, 2004 6:22 AM
> To: pym...@li...
> Subject: [PyMOL] save all not working for multiple objects=20
> from split_states?
>=20
> Hi all,
>=20
> I opened a "biological unit" pdb file of a viral capsid=20
> protein containing the 60 "states" or "models" making up the=20
> whole viral capsid structure.
>=20
> I did
> split_states
> to get all 60 molecules as individual objects
>=20
> sweet!
>=20
> then I deleted the ones I didnt want, leaving 15 molecules=20
> around one of the 5 fold symmetry axes.
>=20
> now I want to save these molecules to a pdb file.
>=20
> so I did
>=20
> save 5fold.pdb, all
>=20
> this gave no errors, but the pdb file written only contains
>=20
> END
>=20
> what am I doing wrong? I expect it is my simple mistake?
>=20
> cheers
>=20
> Dan
>=20
>=20
> Dr. Daniel James White BSc. (Hons.) PhD
> Cell Biology
> Department of biological and environmental science PO Box  35=20
> University of Jyv=E4skyl=E4 Jyv=E4skyl=E4 FIN 40014 Finland
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