Dear Herman, thanks for the PDB-file. I can confirm that there are no problems with this file at all. Paul has been in contact with me to work on the problem.
Tim On Tue, Sep 07, 2010 at 08:57:49AM +0200, herman.schreu...@sanofi-aventis.com wrote: > Dear bulletin board, > > Tim asked me for the pdb file I used for testing (coot version 0.6), > which I have attached here. It is a totally artifical pdb file with one > random small ligand in it. Using a symmetry radius of 50 Angstrom, one > can get an idea of the symmetry in 'F d -3 m'. If in Tim's case with a > real protein coot comes to a grinding halt, it looks to me more like a > question of memory management than a problem with the symmetry > definitions. > > Best, > Herman > > -----Original Message----- > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of > herman.schreu...@sanofi-aventis.com > Sent: Monday, September 06, 2010 2:44 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Fd-3m with pdbset > > 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:ccp...@jiscmail.ac.uk] On Behalf Of > Tim Gruene > Sent: Monday, September 06, 2010 1:38 PM > To: CCP4BB@JISCMAIL.AC.UK > 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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