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, [email protected] 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:[email protected]] On Behalf Of > Tim Gruene > Sent: Monday, September 06, 2010 1:38 PM > To: [email protected] > 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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