Dear Amr, I am using Coot 0.7.1 and here the problem is that the atom placed at pointer is by default added to a new molecule. So if you don’t change “new molecule” to your current molecule in the place atom window, the added atom will be lost and the water will remain.
Concerning the red patches, this typically happens when ones tries to refine a partially occupied ion with full occupancy. To compensate for the lower electron density in the center, the refinement program will inflate the temperature factor, increasing the apparent size of the ion, leading to too much model electron density around the center. Refining the occupancy of the metal ions should take care of this problem. Good luck! Herman Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von Roger Rowlett Gesendet: Donnerstag, 23. Oktober 2014 19:37 An: [email protected] Betreff: Re: [ccp4bb] Adding zink and coper by COOT There is a bug in version 0.7.2 Coot that causes metal ions added via the "place atom at pointer" to be a water. However, if you add the metal ions through the "Get Monomer" dialog I think it will work OK. _______________________________________ Roger S. Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [email protected]<mailto:[email protected]> On 10/23/2014 1:32 PM, amro selem wrote: Dear ccp4bb Community , i hope this email finds you well, i am trying to do add Zink and Copper to my Superoxid dismuase Enzyme by Coot , i encountered two problems. 1- after adding Zink and copper by place atom at pointer << other <<< writing ZN OR CU then running Refmac5 , both atom is turned to water 2- i traied to added atom and merge the atoms with coordinate file out side the coot. the atoms are added but i see red patches arround them. i also added calcium instead then i replaced them bz editing the PDB file. 3- the Rfactor 16 and R free is 22.1 so my question how can i add zink and copper in right way. second what is the red patches mean? thank you in advance Amr
