thesisandpapers

Firstly, save your movie as png images. You can set_view/get_view to have the right orientation. To save scenes go to > scene > store > F 1/2/3... then > Movie > Program > Scene Loop I use usually: Nutate > 30 deg. over 4 sec. > file > save movie as png images then for 300 images you can easily use http://gifmaker.me/ (quite slow even with highest speed) or https://ezgif.com/maker up to 2000 files (delay time 1 makes a nice speed) or it's easy to find some png to gif conventer online

Sometimes I'm googling stuff. How to do something.. And I'm forgetting then. Or writing on paper. But better to keep it on-line, so other googlers can find it, too ;) Thanks for  http://randomthesisstuff.blogspot.co.uk/  useful! Another great one -  http://www.keepcalmandpublishpapers.com/ So PyMOL,  alternative conformation . It makes messy some of my calculations to keep alternative conformations, so to remove it, simply type: PyMOL>remove not (alt ''+A) PyMOL>alter all, alt='' But it's choosing conformation A, not that with higher occupancy! See here -  https://pymolwiki.org/index.php/Property_Selectors#Alternate_Locations Alternatively in  Phenix  - Model tools - pdb tools - options - remove alternate conformers, but it gave me the same output as PyMOL, conformation A, not higher occupancy. You can do it in  Coot , but then (probably?) have to go from residue to residue (with double occupancy), I didn't find how to do it for...