[PyMOL] Orient every sidechain and make a movie

2018-06-15 Thread Murpholino Peligro
Dear PyMOL users... Is there a way to orient every sidechain and take a picture to produce a movie? Idea: By aligning the pdbs and maps and having them in the grid mode, with this movie I could f take a quick look at how well my electron density fits to all my models... Thanks --

Re: [PyMOL] Orient every sidechain and make a movie

2018-06-15 Thread Murpholino Peligro
Dear PyMOL users.. I found this bb_inspector at https://pymolwiki.org/index.php/MovieSchool_4 It kinda does what I want, so I tweak it little bit ... (*.pml attached) If you run the script and play the movie you'll see that sometimes the sidechain is a little bit obscured by some density/atoms

Re: [PyMOL] Structure and map comparison like Phenix

2018-06-15 Thread Murpholino Peligro
"The bug" is currently being fixed by the phenix developers. And also I found out that there's a way to superpose maps in PyMOL. Look at the second example in https://pymolwiki.org/index.php/Matrix_Copy :) 2018-06-14 17:34 GMT-05:00 Murpholino Peligro : > Dear PyMOL users... > Have you tried t

Re: [PyMOL] Orient every sidechain and make a movie

2018-06-15 Thread Thomas Holder
Hi Murpholino, How about an interactive version instead of a fix-speed movie? The attached script maps the F1 key to advance to the next residue, and F2 to go back. It also colors atoms by density fit (red if they don't fit into the 1.2 sigma shell). It will only show sticks for the current res

Re: [PyMOL] Orient every sidechain and make a movie

2018-06-15 Thread Murpholino Peligro
Wow. I like it. Thanks. I got 8 structures with their respective maps. So in order to view them all at once, interactively, I think I only need to merge my code with yours and ...add a ramp for every map? I am gonna try that now. Here's my code (pml attached) If you want to have my maps and pdbs

Re: [PyMOL] Orient every sidechain and make a movie

2018-06-15 Thread Murpholino Peligro
resending... I hope you can see the link to the screenshots in my gdrive Here is the code merged. It works ...but the F1 key now zooms farther away from the residues. :P ​ firstF1.png ​​ ma