Re: [ccp4bb] Coot 0.6.2 CRYST1 problems ?

2010-12-17 Thread Bosch, Juergen 
Sorry,

I should have specified that this happens to all PDB files. I first thought 
it's the particular one which O downloaded, but when I then downloaded my own 
to manually adjust the CRYST card on the "broken" entry I realized no PDB works 
at all. You can pick any random PDB code and it will not work. Since it's also 
effecting Pymol I'm not sure what's going on if a central library from CCP4 is 
broken.

The system I'm running on is OS X Snow leopard 10.6.3

Try 2PC4 as an example. On a second machine which I have not upgraded yet 
through fink I have no problem generating symmetry mates.

I did not try pdbset, but there's nothing obviously wrong in the header. I'll 
send a screenshot of the error message shortly.

Jürgen

-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-3655
http://web.mac.com/bosch_lab/

On Dec 17, 2010, at 7:31 AM, Tim Gruene wrote:

Dear Juergen,

this is difficult to answer without
- knowing the exact error message coot issues
- knowing the CRYST1 card of the PDB-file. maybe it got scrambled, the space
 group was left out or corrupted or...

Did you run the PDB file through pdbset to reset space group and cell
dimensions.

Cheers, Tim

On Thu, Dec 16, 2010 at 06:07:24PM -0500, Bosch, Juergen wrote:
Dear  BB,
I finked my MacPro (Snow Leopard)ti the latest and greatest version of Coot
0.6.2-pre-1 (revision 3290)  [with guile 1.8.7 embedded] [with python 2.7.1 
embedded]
and found out that I can not display any symmetry related molecules anymore.
Coot complains about a problem in the CRYST card.

Is this a feature or a know bug ?

Any help Paul ?

Thanks,

Jürgen

-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-3655
http://web.mac.com/bosch_lab/


--
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

phone: +49 (0)551 39 22149

GPG Key ID = A46BEE1A

Re: [ccp4bb] Coot 0.6.2 CRYST1 problems ?

2010-12-17 Thread Tim Gruene 
Dear Juergen,

this is difficult to answer without 
- knowing the exact error message coot issues
- knowing the CRYST1 card of the PDB-file. maybe it got scrambled, the space
  group was left out or corrupted or...

Did you run the PDB file through pdbset to reset space group and cell
dimensions.

Cheers, Tim

On Thu, Dec 16, 2010 at 06:07:24PM -0500, Bosch, Juergen wrote:
> Dear  BB,
> I finked my MacPro (Snow Leopard)ti the latest and greatest version of Coot
> 0.6.2-pre-1 (revision 3290)  [with guile 1.8.7 embedded] [with python 2.7.1 
> embedded]
> and found out that I can not display any symmetry related molecules anymore.
> Coot complains about a problem in the CRYST card.
> 
> Is this a feature or a know bug ?
> 
> Any help Paul ?
> 
> Thanks,
> 
> Jürgen
> 
> -
> Jürgen Bosch
> Johns Hopkins Bloomberg School of Public Health
> Department of Biochemistry & Molecular Biology
> Johns Hopkins Malaria Research Institute
> 615 North Wolfe Street, W8708
> Baltimore, MD 21205
> Phone: +1-410-614-4742
> Lab:  +1-410-614-4894
> Fax:  +1-410-955-3655
> http://web.mac.com/bosch_lab/
> 

-- 
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

phone: +49 (0)551 39 22149

GPG Key ID = A46BEE1A



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[ccp4bb] Coot 0.6.2 CRYST1 problems ?

2010-12-16 Thread Bosch, Juergen 
Dear  BB,
I finked my MacPro (Snow Leopard)ti the latest and greatest version of Coot
0.6.2-pre-1 (revision 3290)  [with guile 1.8.7 embedded] [with python 2.7.1 
embedded]
and found out that I can not display any symmetry related molecules anymore.
Coot complains about a problem in the CRYST card.

Is this a feature or a know bug ?

Any help Paul ?

Thanks,

Jürgen

-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-3655
http://web.mac.com/bosch_lab/