Re: [COOT] symmetry operator generation on COOT
For the record/archive I'd like to conclude this thread. It recognizes the spacegroup as P 1 21/c 1. Is seems that Coot indeed does display symmetry correctly for this spacegroup, but not in the way that other programs (e.g. Mercury or Swiss PDB Viewer) do. coot (show-spacegroup 0) P 1 21/c 1 If I then ask coot to show-symmetry I get the following coot (show-symmetry 0) Backtrace: In current input: 8: 0* (show-symmetry 0) unnamed port:8:1: In expression (show-symmetry 0): unnamed port:8:1: Unbound variable: show-symmetry ABORT: (unbound-variable) You followed the instructions in the manual. I am sorry to say that there is a error there, it should have (and now does) read: (get-symmetry imol) Thanks, Paul.
[COOT] symmetry operator generation on COOT
Hi all, I am running Coot 0.5.2 on an intel Mac 10.5.6. I am trying to visualize the symmetry related molecules for a small inorganic molecule in spacegroup P 21/C. If I load the file into swiss PDB viewer or Mercury, the symmetry operators show that I have 4 molecules in my unit cell and a pretty orderly looking packing scheme. Coot, however, does not seem to like the P 21/C spacegroup. I changed the CRYST1 line to read CRYST1 25.0006.082 11.308 90.00 100.04 90.00 P 1 21/c 1 If I go to Draw-cell and symmetry- master switch: show symmetry related atoms- yes I get a very cramped unit cell with many more than just 4 molecules within. I tried to ask coot what it thinks my spacegroup and symmetry operators were to reconcile this result with those of mercury and swiss viewer. It recognizes the spacegroup as P 1 21/c 1. coot (show-spacegroup 0) P 1 21/c 1 If I then ask coot to show-symmetry I get the following coot (show-symmetry 0) Backtrace: In current input: 8: 0* (show-symmetry 0) unnamed port:8:1: In expression (show-symmetry 0): unnamed port:8:1: Unbound variable: show-symmetry ABORT: (unbound-variable) Am I doing something dumb here? Thank you in advance. -Jennifer
Re: [COOT] symmetry operator generation on COOT
Hi Jennifer, Doebbler wrote: I am running Coot 0.5.2 on an intel Mac 10.5.6. I am trying to visualize the symmetry related molecules for a small inorganic molecule in spacegroup P 21/C. If I load the file into swiss PDB viewer or Mercury, the symmetry operators show that I have 4 molecules in my unit cell and a pretty orderly looking packing scheme. Coot, however, does not seem to like the P 21/C spacegroup. I changed the CRYST1 line to read CRYST1 25.0006.082 11.308 90.00 100.04 90.00 P 1 21/c 1 Indeed. That is what I would have done. The space group symbol in the PDB file should match the xHM symbol in syminfo.lib If I go to Draw-cell and symmetry- master switch: show symmetry related atoms- yes I get a very cramped unit cell with many more than just 4 molecules within. Well that is a surprise. You should definitely only see 4. Cramped as in crowded I presume you mean. I imagine that Coot at least got the cell correct. (I presume (because of your scripting competence) that it wasn't something trivial like inadvertently displaying the symmetry for other molecules also) I tried to ask coot what it thinks my spacegroup and symmetry operators were to reconcile this result with those of mercury and swiss viewer. It recognizes the spacegroup as P 1 21/c 1. coot (show-spacegroup 0) P 1 21/c 1 As it should be. If I then ask coot to show-symmetry I get the following coot (show-symmetry 0) Backtrace: In current input: 8: 0* (show-symmetry 0) unnamed port:8:1: In expression (show-symmetry 0): unnamed port:8:1: Unbound variable: show-symmetry ABORT: (unbound-variable) :-( There is no command to output the symmetry operators. I'll make a note to add one. I'm stumped - I don't know what is going on. If you have a shelx .ins file for this molecule, I'd be curious to know if it was displayed correctly. Paul.
