I hope you all are well and had a lovely holiday. I have a couple questions. I was able to measure the inner volumes through the directions Tom had given me a couple months ago:

open 1lp3

open alphafold prediction

matchmaker #2 to #1

sym #2 symmetry #1 copies true

molmap #3 12

volume #4 level 0.07

choose "blob", right click to color it

surface splitbycolor #4.1

view position #5 sameAs #4

hide #4,5.1 model

measure volume #5.2

For some reason, on one of my AAVs it is giving me a different volume that is not accurate. The AAV3B inner volumes seems correct since the sequence for VP4 is shorter, therefore has more space in the inside:

AAV3B VP3 only: 2.348 X 10^6

AAV3B VP4 only: 2.488 x 10^6

However, the AAV8 is showing the opposite with VP4 having less space compared to VP3, and the sequences are very similar between AAV3B and AAV8. I am hoping you may know why? or was curious if this may be a bug? And how can I fix it to reflect the data given to me?

AAV8 VP3: 2.558 x 10^6

AAV8 VP4: 2.478 x 10^6

I also attached an MSA to help show that the sequences are very similar length wise, so they should come out to be close in inner volume measurements. 

Last question, I am still learning but is there a way to use the Chimera and ChimeraX through a command prompt with the computer or is the command line the only thing available? I thought maybe I could try to see where the error is coming from using a prompt, but I do not know how to access this.

Thank you, and I hope to hear from you soon.