Re: [COOT] symmetry molecules in H32
Paul Emsley wrote: James Whittle wrote: Hi- I'm trying for the first time to work with a structure in spacegroup H32. Coot reads the CRYST card, but when I build a helix, or look at a H32 PDB entry, the symmetry mates appear squished. I know there is some discussion about handling this spacegroup: do I need to change the CRYST line to get the structure to display correctly? chuckle what timing :-) OK, so the answer is that Coot does not support such a spacegroup symbol. You need to specify it as R 3 2 :H. Paul Paul - you have to fix this - until such time as PDB depositions return such a symbol. At the moment they have H32 E
Re: [COOT] symmetry molecules in H32
Doesn't mmdb read the 'old' lines from syminfo.lib? In which case, H 3 2 should work. H32 without spaces clearly won't, and I don't think such a symbol would be present in a modern (remediated) PDB file. symbol ccp4 155 symbol Hall ' R 3 2' symbol xHM 'R 3 2 :H' symbol old 'H 3 2' Eleanor Dodson wrote: Paul Emsley wrote: James Whittle wrote: Hi- I'm trying for the first time to work with a structure in spacegroup H32. Coot reads the CRYST card, but when I build a helix, or look at a H32 PDB entry, the symmetry mates appear squished. I know there is some discussion about handling this spacegroup: do I need to change the CRYST line to get the structure to display correctly? chuckle what timing :-) OK, so the answer is that Coot does not support such a spacegroup symbol. You need to specify it as R 3 2 :H. Paul Paul - you have to fix this - until such time as PDB depositions return such a symbol. At the moment they have H32 E
Re: [COOT] symmetry molecules in H32
Eleanor Dodson wrote: Paul Emsley wrote: James Whittle wrote: Hi- I'm trying for the first time to work with a structure in spacegroup H32. Coot reads the CRYST card, but when I build a helix, or look at a H32 PDB entry, the symmetry mates appear squished. I know there is some discussion about handling this spacegroup: do I need to change the CRYST line to get the structure to display correctly? chuckle what timing :-) OK, so the answer is that Coot does not support such a spacegroup symbol. You need to specify it as R 3 2 :H. Paul Paul - you have to fix this - until such time as PDB depositions return such a symbol. At the moment they have H32 Actually, at the moment they have H 3 2. For example, I tried 1B41 and that displays symmetry just fine, as Kevin suggests. James, name an accession code that appears to have squished symmetry (you are using the latest stable version, I take it). Fitting a helix is a different story though, I get a pdb file with a rhombohedral spacegroup but hexagonal cell (which makes a mess of the symmetry related coordinates of course). Both cell and spacegroup for a Fit Helix molecule should be picked up from the map/MTZ file - so I don't know what is going on there. Paul.
Re: [COOT] symmetry molecules in H32
I'm sorry to have ignited more controversy. As seems somehow always inevitable, I now find I can't recreate the problem I saw before: the PDB file that yesterday looked squished (1a4x) now displays fine, so it's likely there is no problem with how your code handles pdb entries. It's rather embarrassing. I'm using 0.5.1-pre-1. As far as building, using R 3 2 :H allows me to place helices whose symmetry mates display correctly. I was taking Se sites from SHARP, so it's likely coot was reading the symmetry from that PDB, rather than the map. I may have stumbled on an obscure way to screw this up. --James On Oct 29, 2008, at 5:46 AM, Paul Emsley wrote: Eleanor Dodson wrote: Paul Emsley wrote: James Whittle wrote: Hi- I'm trying for the first time to work with a structure in spacegroup H32. Coot reads the CRYST card, but when I build a helix, or look at a H32 PDB entry, the symmetry mates appear squished. I know there is some discussion about handling this spacegroup: do I need to change the CRYST line to get the structure to display correctly? chuckle what timing :-) OK, so the answer is that Coot does not support such a spacegroup symbol. You need to specify it as R 3 2 :H. Paul Paul - you have to fix this - until such time as PDB depositions return such a symbol. At the moment they have H32 Actually, at the moment they have H 3 2. For example, I tried 1B41 and that displays symmetry just fine, as Kevin suggests. James, name an accession code that appears to have squished symmetry (you are using the latest stable version, I take it). Fitting a helix is a different story though, I get a pdb file with a rhombohedral spacegroup but hexagonal cell (which makes a mess of the symmetry related coordinates of course). Both cell and spacegroup for a Fit Helix molecule should be picked up from the map/MTZ file - so I don't know what is going on there. Paul.
