Dear Modeller Users,
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. Is there a way I can have that in Modeller? Can you help me with some code?
Best regards, Karolina Mitusińska
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
Hi For that purpose I use a program call profit:
https://urldefense.com/v3/__http://www.bioinf.org.uk/software/profit/__;!!LQ...
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
Hi Oscar!
Thank you so much for suggesting ProFit - it does exactly what I wanted and is quite easy!
Best regards, Karolina
śr., 20 kwi 2022 o 07:04 Oscar Conchillo-Solé ocs@bioinf.uab.es napisał(a):
> Hi For that purpose I use a program call profit: > https://urldefense.com/v3/__http://www.bioinf.org.uk/software/profit/__;!!LQ... 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: > > https://urldefense.com/v3/__http://www.bioinf.org.uk/software/profit/__;!!LQ... > https://urldefense.com/v3/__http://www.bioinf.org.uk/software/profit/__;!!LQC6Cpwp!sn7-k0-rUIKbTzeomOPmR95389FIpAWYWpaROc18xU3RebOzhxI8ZuDA6dXV26kAw2g3zqVDA3uNuNR4B_btnA$ > > 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 > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >
-
Karolina Mitusińska (Markowska) -
Modeller Caretaker -
Oscar Conchillo-Solé