Hi
For that purpose I use a program call profit:
http://www.bioinf.org.uk/software/profit/
There is a function called "RESIDUE" which will give what you want.
You will have to read the manual in order to se choose the right
options for you (READALIGNMENT, LIMIT, ZONE, ATOMS, etc) but it will
give you what you want.
I hope this helps
OCS
Oscar Conchillo Solé
Computational Biology Group
Data Center Manager, Sysadmin and Bioinformatics
Institut de Biotecnologia i Biomedicina (UAB)
mail: ocs@bioinf.uab.es
telf:0034 93586 8939; 0034 93581 4431
On 15/4/22 19:48, Modeller Caretaker
wrote:
On
4/13/22 11:00 PM, Karolina Mitusińska (Markowska) wrote:
I would like to compare my predicted model
with a crystal structure. I know how to calculate RMSD between
these two models, but I would also like to have more detailed
information on the RMSD between corresponding atoms, for example
C-alphas.
Perhaps I am misunderstanding what you want to do here, but the
RMSD between a single pair of atoms is just the Cartesian
distance. So you can call superpose() to first fit the two models:
https://salilab.org/modeller/10.2/manual/node255.html
Then access the two Atom objects you're interested in and
calculate the distance in Python using their x,y,z coordinates:
https://salilab.org/modeller/10.2/manual/node383.html
If you mean you want the RMSD over *all* C-alphas or some other
subset, first do superpose() to fit the models, then select that
subset of atoms and do superpose() again with fit=False. This
won't change the superposition but will report the RMSD of the
subset.
Ben Webb, Modeller Caretaker