Dear Paul, it is pleasure to receive the message from you.
if I understood correctly, just forget about the rotation and translation. First I have to make copies myself, just what I did before. (edit the pdb file, copy the atoms and change the chain ID). second, translate and rotate these monomers into the right position in the map one by one manually. then using the NCS Ghost function. edit one chain (master chain), apply the changes to the rest chains. I have another question, probably it is not about Coot, that is how to display the map as it is? for example, the density map size is 100x100x100, now I extract the center section of 100x100x20, then display it in Coot, while Coot will generate the copies of the extracted density map and show them together. I think it bases on the space group which is P1 (default, I think). is there any way to avoid this happen? Best wishes Yao-Wang Li School of Life Science, Tsinghua University Room 255, New Biology Building, Beijing, China, 100084 From: Paul Emsley Date: 2018-06-11 15:40 To: COOT Subject: Re: rotation and translation when building model in cryo-em map On 11/06/2018 04:15, [email protected] wrote: > > > this is my first thread here, and I am not sure this topic was discussed or > not, please tell me if it was. It was not! Not to my memory at least. > > Coot I thought is originally for density map of crystal, it can work on the > cryo-em map too. I have a > cryo-em map of helical filament congratulations. > and try to build a model. good for you > I can build a model based on the monomer, but I am > not sure how to generate the copies based on the symmetry. I think the key > problem is how to determine the > rotation center which based on the map, then the rotation center together > with the known helical parameters > can do it. You do not need to know the rotation centre. You do need to know the rotation and translation. Coot could make this easier for you. I will work on this at some stage... but for now... > > suppose we got the rotation center, how to implement these operations in Coot? > > Certainly, there is a stupid way which I already did, that is to copy the > refined monomer multiple times and > fit them all together, This is in fact the regular practice here (amongst my colleagues). The idea is to build make 5 copies, A,B,C,D,E and fix up the C chain in coot and then copy over the differences/updates to A,B,D,E. > later were refined using the Phenix. > OK. > another way is try to edit the pdb file directly. rotate and translate the > monomer, later change the chain ID. > > But I want to do it simply in Coot, could it possible? Draw -> NCS Ghost Control -> NCS Master Chain -> C -> OK Extensions -> NCS -> Copy NCS Chain -> C -> OK Paul. ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
