Dear Jeff, I have an utility which can apply any operator, specified by the user as e.g. -y,x+1/2,z-2/3 etc. You could use it to build your "crystal". Your molecule should of course have the right starting position and you have to figure out the correct operators yourself. If you are interested, I can send it.
For the visualization: if you use the "multi-chicken" option in coot with 10-20 contour levels, you can get images which resemble EM-images. Best, Herman -----Original Message----- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Jeffrey D Brodin Sent: Sunday, November 28, 2010 8:31 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] generating 2D projections The diffraction from the TEM experiments seems to inidicate that the unit cell is not the same as in the crystal structure and that there is only one screw axis. Because of this, I'd like to essentially start from a single protein molecule and build the unit cell based on symmetry seen in the diffraction pattern. Is there a feasible way to do this? Thanks, Jeff On Nov 28, 2010, at 1:53 AM, Nicholas M Glykos wrote: > > Hi Jeff, > >> I'm currently working on a project where we are attempting to compare >> a single crystal X-ray structure with 2D crystals we've imaged with >> TEM. I have nice 2D cyrstals and low dose cryo images. >> >> My question is whether there is a program in ccp4 that will let you >> input a model and then generate a 2D projection using different plane >> groups. We are pretty sure, based on electron diffraction, that the >> 2D crystals contain a screw axis, as did the X-ray structure. Also, >> after generating the images, is there another program that will >> calculate structure factors and a diffraction pattern? > > Since you have an X-ray structure, the easiest (?) way would be to > obtain structure factors for the X-ray structure, select zone axis > reflections for the sought projection, Fourier transform them, and > then use maprot to prepare a map with the projection down the > sectioning axis. You can then directly compare your projections. > > Nicholas > > > > -- > > > Dr Nicholas M. Glykos, Department of Molecular Biology > and Genetics, Democritus University of Thrace, University Campus, > Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) > +302551030620, > Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/ >
