Re: [modeller_usage] Per-residue RMSD

śr., 20 kwi 2022 o 07:04 Oscar Conchillo-Solé <">> napisał(a):

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

ZjQcmQRYFpfptBannerStart

This Message Is From an External Sender

This message came from outside your organization.

ZjQcmQRYFpfptBannerEnd
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: " target="_blank">
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
_______________________________________________
modeller_usage mailing list
" target="_blank">
https://salilab.org/mailman/listinfo/modeller_usage