sorry, how i move the mtz into the transformed pdb for the question in my previous email?
| | Smith Liu | | 邮箱：smith_liu...@163.com | 签名由 网易邮箱大师 定制 在2017年12月18日 23:37，Smith Liu 写道： thanks. i may mean something other. for example, if i rotate the pdb by 30 degree (or 29.5 degree), or i shift the pdb along x-axis by something for example 0.123*a, then how i move the mtz map correspondingly for the fitting of mtz into the transformed map? | | Smith Liu | | 邮箱：smith_liu...@163.com | 签名由 网易邮箱大师 定制 在2017年12月18日 21:58，herman.schreu...@sanofi.com 写道： Dear Smith, The map extends through the whole crystal. What happens is that the map is calculated around the atom you clicked on during centering. So by centering on your transformed pdb, you will sample the same map at a different position. Just load your transformed pdb and untransformed mtz and try. If the transformed pdb does not fit the map, something went wrong during the transformation of your pdb. If you have applied an origin shift (is not equal to applying a crystallographic symmetry operation), you have to recalculate the mtz, e.g. by running another round of refinement. I hope this is clear so. Herman Von: Smith Liu [mailto:smith_liu...@163.com] Gesendet: Montag, 18. Dezember 2017 14:52 An: Schreuder, Herman /DE Betreff: [EXTERNAL] Re: [ccp4bb] AW: Re: [ccp4bb] coordinate transformation you mean the mtz map will transform simutaneously? | | Smith Liu | | 邮箱：smith_liu...@163.com | 签名由 网易邮箱大师 定制 在2017年12月18日 21:26，herman.schreu...@sanofi.com写道： If you use coot with on the fly map calculation (e.g. you load an mtz and not a map file), you do not need to transform the map. Otherwise I would recommend to run one more round of refinement and produce a new map your usual way. This will also get rid of any rounding errors due to the transformation. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Smith Liu Gesendet: Montag, 18. Dezember 2017 14:16 An:CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] coordinate transformation Dear All, If I have a set of PDB with the corresponding density map, after I transform the PDB based on the suggestion of everybody, is any way to transform the map so that the map will be fit with the transformed PDB? Smith At 2017-12-18 18:39:34, "Eleanor Dodson" <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: 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
