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 >