[COOT] SMILES all trans

2008-10-01 Thread Giles Robertson 

Dear folks,

Just wanted to point out that in version 0.5 (and older) the cis trans  
isomerism gets messed up when reading in the smiles code for a small  
molecule.  For example C/C=C/C looks the same as C/C=C\C.   Although  
it is possible to edit the .cif file manually, I just thought, you  
know feed back, that kind of thing.


Enjoying the 0.5 OSX binary by the way,

Cheers,

Giles

Re: [COOT] SMILES all trans

2008-10-01 Thread Paul Emsley 

Giles Robertson wrote:

Dear folks,

Just wanted to point out that in version 0.5 (and older) the cis trans 
isomerism gets messed up when reading in the smiles code for a small 
molecule.  For example C/C=C/C looks the same as C/C=C\C.   Although 
it is possible to edit the .cif file manually, I just thought, you 
know feed back, that kind of thing.


Dear Giles,

First off, thank you.

I'd like to point out that there is no cleverness at all in Coot about 
SMILES.  The merit for that should be to Alexei Vagin and his LIBCHECK.


I will inform him of your note.

Regards,

Paul.