[ccp4bb] generating 2D projections
Hi all, 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? Thanks in advance for the help, Jeff Brodin
Re: [ccp4bb] generating 2D projections
Assuming that your 2d crystals are membrane proteins and are truly 2d (one layer thick), how can there be a screw axis? JPK On Sat, Nov 27, 2010 at 12:02 PM, Jeffrey D Brodin jbro...@ucsd.edu wrote: Hi all, 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? Thanks in advance for the help, Jeff Brodin
Re: [ccp4bb] generating 2D projections
Sorry, my question probably was not complete enough. The crystals aren't a membrane protein and in most cases are probably more than one layer thick. They are however quite thin and we can get nice TEM images and diffraction patterns. The fact that they aren't one layer may cause more problems later, but for now I'd like to come up with projection images of a hypothetical unit cell and the corresponding diffraction patterns. Since the crystals lay flat on the grids the beam is essentially aimed directly down one unit cell axis. Thanks, Jeff From: Jacob Keller [j-kell...@fsm.northwestern.edu] Sent: Saturday, November 27, 2010 5:45 PM To: Jeffrey D Brodin Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] generating 2D projections Assuming that your 2d crystals are membrane proteins and are truly 2d (one layer thick), how can there be a screw axis? JPK On Sat, Nov 27, 2010 at 12:02 PM, Jeffrey D Brodin jbro...@ucsd.edu wrote: Hi all, 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? Thanks in advance for the help, Jeff Brodin
Re: [ccp4bb] generating 2D projections
Jacob Keller wrote: Assuming that your 2d crystals are membrane proteins and are truly 2d (one layer thick), how can there be a screw axis? I think you can have 2-fold screw axes in the plane of a single-layer membrane- in fact I understand P2(1)2(1) is fairly common, with rows of alternately up- and down- facing molecules along the x and y axes. JPK On Sat, Nov 27, 2010 at 12:02 PM, Jeffrey D Brodinjbro...@ucsd.edu wrote: Hi all, 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? Thanks in advance for the help, Jeff Brodin My ideas, perhaps naive- keep the plane constant and parallel to the x-y plane (EM grid?), but rotate the assembly of protein, using pdbset, to sample different projections. Construct a 3-D cell around the assembly by choosing an arbitrary-length c-axis perpendicular to a, b; and calculate structure factors with ccp4's sfall. select the h,k,0 reflections and these will be the transform of the projection on the x-y plane, I think. eab
[ccp4bb] Coot density fit analysis with mtz from PHENIX 1.6.4
Dear CCP4BB, Has anyone encountered the following problem when using Coot (coot-0.6.2pre) validate density fit analysis with an mtz file calculated using phenix.refine (1.6.4)? All of the density fit values are exactly 0.0 (all bars same height and red) when using a 2Fo-Fc map calculated from an mtz file output by PHENIX Version: 1.6.4, Release tag: 486, Platform: intel-linux-2.6 redhat-e5.5. Density fit analysis worked fine when I was using mtz files from PHENIX Version: 1.6.2, Release tag: 432, Platform: intel-linux-2.6 redhat-e5.5. Thus, it appears to be an issue with the new version of phenix. I should mention that the maps from 1.6.4 mtz files display fine in Coot and real space refinement against those maps in Coot works fine too. It is just the density fit analysis utility that seems to be problematic. Thanks, Jack Tanner -- John J. Tanner Professor of Chemistry and Biochemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-2754 Email: tanne...@missouri.edu http://www.chem.missouri.edu/TannerGroup/tanner.html
Re: [ccp4bb] Coot density fit analysis with mtz from PHENIX 1.6.4
Dear all, I noticed the same problem on Mac OSX (snow leopard) . Seems to be an issue for all phenix installation packages for current release. Cheers, Albert Guskov, Dr rer nat Medical Structural Biology, Nanyang Technological University, Singapore On Sunday, November 28, 2010, Tanner, John J. tanne...@missouri.edu wrote: Dear CCP4BB, Has anyone encountered the following problem when using Coot (coot-0.6.2pre) validate density fit analysis with an mtz file calculated using phenix.refine (1.6.4)? All of the density fit values are exactly 0.0 (all bars same height and red) when using a 2Fo-Fc map calculated from an mtz file output by PHENIX Version: 1.6.4, Release tag: 486, Platform: intel-linux-2.6 redhat-e5.5. Density fit analysis worked fine when I was using mtz files from PHENIX Version: 1.6.2, Release tag: 432, Platform: intel-linux-2.6 redhat-e5.5. Thus, it appears to be an issue with the new version of phenix. I should mention that the maps from 1.6.4 mtz files display fine in Coot and real space refinement against those maps in Coot works fine too. It is just the density fit analysis utility that seems to be problematic. Thanks, Jack Tanner -- John J. Tanner Professor of Chemistry and Biochemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-2754 Email: tanne...@missouri.edu http://www.chem.missouri.edu/TannerGroup/tanner.html
