m: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Kevin Cowtan
Sent: Tuesday, September 07, 2010 12:54 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fd-3m with pdbset
George M. Sheldrick wrote:
> Perhaps I should mention that with the SHELX method of specifying the
> spac
George M. Sheldrick wrote:
Perhaps I should mention that with the SHELX method of specifying
the space group symmetry using the symmetry operators, alternative
settings, specified in IT or not, cause no problems. But then we
would not have had this thread (or the H3/R3 and P21221 threads).
W
half 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 :&#
chreu...@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
del
I was going to say that we could adopt the convention that the
default setting of a centrosymmetric space group is the one with the
origin on an inversion centre, since this is assumed by all programs
that I am aware of, thus making ':2' for 'second setting' unnecessary
and keeping the name to 11
It seems that it's the new addition of ':n' which has pushed it over
the limit of the 11 char field. Has this been thought through? I
can see that the ':n' qualifier is necessary to disambiguate alternate
origins. Without the redundant formatting spaces 9 chars would be
sufficient even for 'P 4
> > There seem to be a few CCP4 Fortran files that have character spgnam*10
> > from the good old days ...
>
> What good old days were those? The Cryst1-format for PDB-files in the ccp4
> documentation says
> 56-66Space group symbol, left justified (not used)
> which is eleven characters. Were
On Mon, Sep 06, 2010 at 02:45:49PM +0100, Martyn Winn wrote:
>
> Yes, I can reproduce this, and I think I have found the bug.
> It is simply that PDBSET dimensions the spacegroup name to 10
> characters. Increasing that to 20 allows you to use either
>
> spac 'F d -3 m :1'
> or
> spac 227
>
> Ho
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 ce
Yes, I can reproduce this, and I think I have found the bug.
It is simply that PDBSET dimensions the spacegroup name to 10
characters. Increasing that to 20 allows you to use either
spac 'F d -3 m :1'
or
spac 227
However, it still won't recognise 'F d -3 m' because this is not in the
syminfo file
ect 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: CCP4B
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 list
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