Subject: | | Re: Fd-3m with pdbset |
From: | | [log in to unmask] |
Reply-To: | | [log in to unmask][log in to unmask], 7 Sep 2010 09:10:34 +0200906_ISO-8859-1 Dear colleagues,
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Date: | | Mon, 6 Sep 2010 14:43:34 +0200 |
Content-Type: | | text/plain |
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Hi Tim,
The string 'Fd-3m:1' is recognized by pdbset, but still produces 'F d -3
m :'. I did a test with a single small ligand with coot and if you
delete the ':' from the CRYST1 card to make 'F d -3 m' coot happily
accepts it and seems to produce the correct symmetry mates. I hope that
this way you are able to display your molecule. I agree that there must
be a bug somewhere.
Best,
Herman
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
Tim Gruene
Sent: Monday, September 06, 2010 1:38 PM
To: [log in to unmask]
Subject: [ccp4bb] Fd-3m with pdbset
Hello,
I tried to assign a cell with space group F d -3 m to a PDB file using
pdbset.
Since it did not recognize the string 'F d -3 m' (nor 'F d -3 m :1') , I
used the space group number 227. This resulted in the space group string
'F d -3 m :'
in the PDB-file instead of 'F d -3 m :1' as it is listed in syminfo.lib,
and hence coot refused to display the symmetry mates for the molecule.
When I add the missing '1' in the resulting PDB-file, coot does display
the cell, but when I ask to display the symmetry mates, coot chokes and
consumed all my cpu power (for 8 molecules present in the unit cell...)
until I killed it.
I was wondering if this is a known bug in syminfo.lib (and/or the
dependent
programs) and if there is a way around it (without using
phenix.get_me_out_of_here, I could of course use xp instead of coot for
such a small molecule).
Kind regards, Tim
P.S.: The bug in pdbset persits also in pdbset from ccp4-6.1.3
--
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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