Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 35
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. *
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. > * >
participants (2)
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Ashish Runthala -
Sumedha Roy