Clarisa,
Depending on what you want to do with the file, you may not need to save
a new PDB at all.
You could for example,
* Issue the command symexp xxxx,xxxx,(all),4.0 to generate nearby
symmetry mates, then remove the objects you don't need to form the
proper dimer. (xxxx is your PDB file object)
* The select File...Save Molecule and select all the objects to save
using shift-clicks. (but this may be unnecessary--see below)
When you do this both chains will have the same chain identifers (e.g.
chain A) This could be clumsy later if you are doing further
manipulations of the structure and you save the molecule as a single PDB
with two identical chain identifiers. In this case, every selection you
made would be a double selection (one in both chains.) You can change
the chain identifier for the symmetry chain easily enough in a text
editor, I suppose, but this is an extra step.
Alternatively, if you simply want to work with your new dimer structure
in Pymol, there is no need to alter the chain numbers after doing the
proper symmetry expansion. Rather, you can select individual items in
one chain or the other by selecting the original or symmetry object.
This might be useful, for example, if you want to highlight one active
site and its interaction with the neighboring chain. I usually assign
object names to the two monomers as "achain" and "bchain" to make
manipulation of the structure easier. So, for example,
* "Select asite, resi 42+44+98 and achain" might select active site
residues from the original chain
* "Select otherres, resi 33 and bchain" might select interactigin
residues form your symmetry expanded chain.
* No need to save the molecule as a separate PDB. Just save the
session file.
Cheers,
_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu
On 10/7/2015 11:00 AM, Clarisa Alvarez wrote:
Hello everyone:
I need help because I have a pdb of a monomer but I know that it is a
dimer by crystallographic symmetry, how can I make a new molecule of
it? because I could make it by generate/symmetry mate...but I could
not save it...any help will be great!
Thanks in advance!
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