Thanks Paul for the quick reply! I wasn't aware of Coot's Transform Map by LSQ Fit function, I'll definitely try it out. Is there a command-line equivalent of this that I could use for batch processing multiple structures/maps that I want to align to a single reference? I'm using Pymol now because it was recommended to me, but clearly there are better solutions...
________________________________ From: Paul Emsley <[email protected]> Sent: Friday, October 2, 2020 11:44 PM To: Jade <[email protected]>; [email protected] <[email protected]> Subject: Re: PyMol-exported CCP4 maps not being read correctly in Coot On 02/10/2020 23:30, Jade wrote: > I'm trying to use PyMol's matrix_copy command to align some PDB/CCP4 map > pairs, and I ran through the first example outlined here: > https://pymolwiki.org/index.php/Matrix_Copy, which fetches two PDBs/maps, > 1rx1 and 3dau, aligns the 1rx1 PDB to 3dau, and then matrix_copy's the 1rx1 > map to the aligned 1rx1 PDB. > > The resulting maps look well-aligned in Pymol, but when I save these maps as > .ccp4 files and load them into Coot, Coot doesn't seem to register the > movement of the 1rx1 map. I chatted with Schrodinger about this and they > suspect that Coot is not reading the skew transformation flags SKWMAT and > SKWTRN that are written by Pymol, so the map stays in its original, unaligned > position. I was wondering if anyone has run into this same issue, and whether > there is an easy fix. This is the reference that I'm using for CCP4/MRC maps: https://www.ccpem.ac.uk/mrc_format/mrc2014.php It doesn't mention skew. After a bit of googling: http://legacy.ccp4.ac.uk/html/maplib.html This doesn't mention skew - but I've only just discovered it. So yes, Coot does ignore the skew. It would be nice to have - I'll try to get it done for 0.9.2. So that answers your question. But... I must ask... why are you even using PyMOL at all? Why not just use the map transformation tool built into Coot? Calculate -> Map Tools -> Transform Map by LSQ fit Here, I did that example. (It doesn't do SSM superposition via the gui - you'd have to cut and paste the matrix) Paul. ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
