[chimerax-users] Blob measurement question?

[Noriega, Heather]

Hello,

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.

Thank you,

Heather Noriega
PhD-Pharmaceutical Science student
Howard University
heather.noriega at bison.howard.edu
520-203-1883
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