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<mailto: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<mailto: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<https://urldefense.proofpoint.com/v2/url?u=http-3A__origins.com&d=DwMGbg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=kr4BAC6CGF8MkSeqVDxlDaQ3WprGVrjotZPIWrNrdts&s=RFDcNoPw6eYR8Aka4k3PWnf4_OIc98ZgWFd-LYwSoHo&e=>" 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<https://urldefense.proofpoint.com/v2/url?u=http-3A__bl831.als.lbl.gov_-7Ejamesh_scripts_origins.com&d=DwMGbg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=kr4BAC6CGF8MkSeqVDxlDaQ3WprGVrjotZPIWrNrdts&s=9dlreI0nRWqq1Feor3gq_OOcpIxVPjpdRl2KTg9fMqg&e=> 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
