Re: [PyMOL] Slice

Hi Divya, I can confirm that slices don't work properly with some map formats (those which define a transformation matrix). What's the file format (file extension) of your map? Cheers, Thomas > On Aug 15, 2018, at 7:38 PM, Divya Kaur Matta > wrote: > > Dear all, > > > I would like to us

Re: [PyMOL] Slow loading of protein structures with Pymol

Hi Gianpiero, Loading each of your files takes 5-10 seconds for me on my MacBook. Most of that time is for surface generation. The files have defined very high surface quality (surface_quality=1), which is always slow. Cheers, Thomas > On Aug 2, 2018, at 2:46 PM, Gianpiero Landolfi > wrote

Re: [PyMOL] Serine phosphorylation

Hi Wei, Phosphorylating a serine with the builder works fine for me. 1) click "Builder" button -> opens panel and should automatically switch to "3-Button Editing" mouse mode 2) click on the serine's OG atom -> should create "pk1" selection 3) click "P=O3" button on the Builder panel To change

Re: [PyMOL] Slice

Hi Divya, Try to output a .phi file with delphi, that format should work fine with slices. In your delphi .param file: out(phi,file=phimap.phi,format=0) Cheers, Thomas > On Aug 17, 2018, at 4:28 PM, Divya Kaur Matta > wrote: > > Dear Thomas, > > It’s phimap.cube file. ( .cube is an extens

Re: [PyMOL] Slice

Dear Thomas , Thank you so much for your suggestion. I will try this. I appreciate your help. Best Regards Divya Get Outlook for iOS From: Thomas Holder Sent: Friday, August 17, 2018 11:05 AM To: Divya Kaur Matta Cc: pymol-users@lists.sou

Re: [PyMOL] Slice

Dear Thomas, It’s phimap.cube file. ( .cube is an extension). These cube files are from Delphi. ( Poisson Boltzmann solver). Thank you , Best Regards Divya Get Outlook for iOS From: Thomas Holder Sent: Friday, August 17, 2018 4:51 AM To:

[PyMOL] unable to produce publication quality images

Hi! I have been using pymol since 2015. I was able to make publication quality images back then. However, I can no longer use the ray command. I have pymol for eucational use. Looking forward to your kind help! Regards, Raag Saluja -