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

Hi Murpholino, This should be the correct selection expression: sele = '(sc. or name CA) and i. {}'.format(stored.x) Cheers, Thomas > On Jun 20, 2018, at 3:11 PM, Murpholino Peligro wrote: > > I have waters and ions in my structures. > > If I add the "sc." it works for non-glycine

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

Thanks. It works perfect this time. 2018-06-20 15:00 GMT-05:00 Thomas Holder : > Hi Murpholino, > > This should be the correct selection expression: > > sele = '(sc. or name CA) and i. {}'.format(stored.x) > > Cheers, > Thomas > > > On Jun 20, 2018, at 3:11 PM, Murpholino Peligro >

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

I have waters and ions in my structures. If I add the "sc." it works for non-glycine residues. (The error is "ExecutiveWindowZoom-Warning: selection doesn't specify any coordinates.") How to tweak it so that F1 works for all my residues? Ps I was thinking to include the alpha carbon in the

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

> It works ...but the F1 key now zooms farther away from the residues. :P Are there other atoms with residue number 1? Ligands? Solvent? I had removed the "sc." selector, so that it works on Glycine as well. You can add it back to the sele string in the zoomnext function. sele = 'sc.

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

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 ​​

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

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

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

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

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

[PyMOL] Orient every sidechain and make a movie

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