I showed you pdbset .. Find the centre of mass for your assembly. Move it where you will
pdbset xyzin mow.pdb end Find CoM 0.7 1.3 -0.2 Hmm - a little thought - centre at 1 -1 0 say pdbset yzin now.pdb xyzout changed.pdb symgen x , y-2, z end New CoM 0.7 -0.7 -0.2 Eleanor On 18 December 2017 at 00:19, Edward A. Berry <ber...@upstate.edu> wrote: > Neat idea! > And do you have a 1-line command for setting all the coordinates to 1,1,1? > or 0.1,0.1,0.1 if I still want it near the origin but biased toward the > inside of the positive-going cell? > eab > > > On 12/14/2017 07:23 PM, James Holton wrote: > >> What I usually do for this is make a copy of the PDB file and change all >> the atom x-y-z positions to "1.000". Then I use something like reforigin >> or my "origins.com" script to shift the original coordinates via allowed >> symmetry operations, origin shifts, or perhaps indexing ambiguities until >> it is as close as possible to the "reference", which is at 1,1,1. I use >> 1,1,1 instead of 0,0,0 because there are generally at least two >> symmetry-equivalent places that are equidistant from the origin. Declaring >> the reference to be a bit off-center breaks that ambiguity, and also biases >> the result toward having all-positive x,y,z values. >> >> >> In case it is interesting, my script is here: >> >> http://bl831.als.lbl.gov/~jamesh/scripts/origins.com >> >> >> You need to have the CCP4 suite set up for it to work. Run it with no >> arguments to get instructions. >> >> >> -James Holton >> >> MAD Scientist >> >> >> On 12/13/2017 5:50 AM, Kajander, Tommi A wrote: >> >>> >>> Hello, >>> >>> If someone could point this out would be very helpful... Wasnt there a >>> simple script somewhere that would transfer coordinates close to origin - >>> if they for some reason are not? Just cant find anything right away. Sure i >>> have done this before... >>> >>> >>> Thanks, >>> >>> Tommi >>> >>> >>> >>
