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 = 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: [email protected]
> [mailto:[email protected]] On Behalf Of
> Dr. Daniel James White PhD
> Sent: Tuesday, April 06, 2004 6:22 AM
> To: [email protected]
> Subject: [PyMOL] save all not working for multiple objects
> from split_states?
>
> Hi all,
>
> I opened a "biological unit" pdb file of a viral capsid
> protein containing the 60 "states" or "models" making up the
> whole viral capsid structure.
>
> I did
> split_states
> to get all 60 molecules as individual objects
>
> sweet!
>
> then I deleted the ones I didnt want, leaving 15 molecules
> around one of the 5 fold symmetry axes.
>
> now I want to save these molecules to a pdb file.
>
> so I did
>
> save 5fold.pdb, all
>
> this gave no errors, but the pdb file written only contains
>
> END
>
> what am I doing wrong? I expect it is my simple mistake?
>
> cheers
>
> Dan
>
>
> Dr. Daniel James White BSc. (Hons.) PhD
> Cell Biology
> Department of biological and environmental science PO Box 35
> University of Jyväskylä Jyväskylä FIN 40014 Finland
> +358 14 260 4183 (work)
> +358 468102840 (new mobile)
> NEW PHONE NUMBER!!!
>
> http://www.chalkie.org.uk
> [email protected]
> [email protected]
>
>
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