Thank you for your response. That might be the case but for my purpose, I need the DNA to be fixed (treated as a rigid body) in both the complexes and the modelling to be done irrespective of that. I came across an automodel feature " nonstd_restraints(aln) " ( http://salilab.org/modeller/manual/node69.html) but I do not know how to use it - I added a.nonstd_restraints(aln) in the model-ligand.py file but got an error saying that nonstd_restraints() expects 2 arguments, of which 1 is given. If someone knows how to use these automodel features, please guide.
On Wed, Mar 28, 2012 at 9:30 PM, Ashish Runthala ashishr@bits-pilani.ac.inwrote:
> Dear Sumedha, > You are being confused with the assessment results, but they are correct. > As you have stated, you modelled protein with, without DNA(using as a > ligand) and got the RMSD difference between the models as 0.5A' in RMSd, > when screened against the selected template. But this is obvious. The > model with 0.1RMSD has probably better localized topology spanned over the > 9bases of DNA. Check out the TM-Score of the two models against the > template. As you have not provided further details about the protein > length, the two models, and the template, it is difficult to precisely > conclude something. TM-Score will answer your query the best. > > Ashish Runthala, > Lecturer, Structural Biology Cell, > Biological Sciences Group, > BITS, Pilani > Rajasthan, INDIA > > ----- Original Message ----- > From: "modeller usage-request" modeller_usage-request@salilab.org > To: "modeller usage" modeller_usage@salilab.org > Sent: Wednesday, March 28, 2012 4:02:12 PM GMT +05:30 Chennai, Kolkata, > Mumbai, New Delhi > Subject: modeller_usage Digest, Vol 11, Issue 35 > > Send modeller_usage mailing list submissions to > modeller_usage@salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > modeller_usage-request@salilab.org > > You can reach the person managing the list at > modeller_usage-owner@salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. mutate_selection.py (ARVIND PAL) > 2. Re: mutate_selection.py (Modeller Caretaker) > 3. Re: Regarding protein 3D structure modeling (Modeller Caretaker) > 4. DNA-protein complex modelling discrepancy!! (Sumedha Roy) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 26 Mar 2012 12:49:18 +0530 > From: ARVIND PAL arvind.sbt@gmail.com > To: modeller_usage@salilab.org > Subject: [modeller_usage] mutate_selection.py > Message-ID: > <CAMw18pPwUrHq13ZNb5Pu_fqe6ms4Nmg6z9cH7igxmM99w6E+TA@mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Dear sir > when i am running the > *mutate_selection.py< > http://salilab.org/modeller/9.9/examples/commands/mutate_selection.py%3E > command i got the error selection contains no atom. what does it means. > plz help me. > * >