Dear Chimera
I am sorry to interrupt your busy schedule.
My name is Matsui, and I am a second-year master's student at a Japanese
university.
Thank you for taking time out of your busy schedule to respond to my
question the other day.
We are investigating the buried surface area to see the magnitude of the
interaction between protein and ligand.
For this purpose, I calculated the solvent accessible area of the ligand.
However, the value is 9955, which shows the entire surface area of the
protein.
What should I do? I am not in a hurry for answers , so I would appreciate a
reply when you have the time.
In this case, the ligand was in the binding pocket of the protein, so I
would like to calculate the ligand's solvent contact area = buried surface
area.
I tried to check and tried , but it did not work.
1.See
https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003521.html
2.Try to use measure blob using chimera X.
Reference:
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea
However, I didn't know how to solve this command.
Command ;ui mousemode right "pick blobs
Reference; https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html
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Kenji Matsui
Graduate School of Tokyo University of Agriculture and Technology M2
2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
Hello,
my intention is to plot RMSD chart for only Pd,Cl,Cl,C atoms (their numbers
are 1,2,3,4). But I couldn't find a way to do it.Also II want to plot
dihedral RMSD for all atoms except C,H,Cl,P atoms.How can I do that?
Thank you
Dear Chimera users,
How can I generate an image with the intermediate steps in a morphing session (of an atomic structure between its two conformations).
The image of intermediate states can appear 'lighter' than the original and final states.
Stay safe & Regards
Anindito Sen. Ph.D
Microscopy and Imaging Center
Texas A&M University
301 Old Main Dr
College Station, TX 77843-2257
Office: ILSB Room 1133
<http://microscopy.tamu.edu/>Tel. 979-458-9881
fax: 979-847-8933
http://microscopy.tamu.edu<http://microscopy.tamu.edu/>
