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
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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)
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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.pyhttp://salilab.org/modeller/9.9/examples/commands/mutate_selection.py command i got the error selection contains no atom. what does it means. plz help me. *