Hi Warren,
OK, that works just as you say it does.
however, what I really need is each chain to have a unique chain
identifier in the pdb file written out.
I see there might be a problem here as there are 60 molecules, and only
24 letters in the alphabet....
I actually only want to have 15 of them in my model, so we could get
round it that way, by deleting the ones I dont want....
but then how to give them unique pdb chain identifiers?
I want to load the 15 molecule model in Bodil to do my actual modelling.
cheers
Dan
On 6 Apr 2004, at 21:36, Warren DeLano wrote:
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: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Dr. Daniel James White PhD
Sent: Tuesday, April 06, 2004 6:22 AM
To: pymol-users@lists.sourceforge.net
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
d...@chalkie.org.uk
wh...@cc.jyu.fi
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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
d...@chalkie.org.uk
wh...@cc.jyu.fi
