Dear Herman,
thanks for the tip. Unfortunately it does not help with my version of coot
(linux, 0.6.1). Coot eats up all my memory (8GB RAM + 4GB swap) until it is
being terminated by the OS.
Which version of coot are you using? Could you send me your PDB-file that works
for you, please (you could even send it plain text to the bb to avoid an
attachment...) ?
The same happens when I read in an .ins-file which does not contain the space
group name or symbol, but provides the symmetry operators themselves.
Cheers, Tim
P.S.: I'll skip sending a copy to the coot-list since Paul is also reading this
one, I am sure.
On Mon, Sep 06, 2010 at 02:43:34PM +0200, [log in to unmask] wrote:
> 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
--
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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