Dear all, Im interested to create a rough model of a quadruplex molecule using a specific sequence. One possibility could be to load a pdb structure of a quadruplex and « mutate » each nucleotide with the correct one. Is this feasible with Chimera ? Alternative suggestions are appreciated as well. Thanks for your help, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 www.rete29aprile.it ---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it
Dear Marco, There is a "swapna" command for mutating nucleic acids: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapna.html> The results may be fairly rough, with some nonoptimal geometries and/or steric clashes, but you could try this and see if it meets your needs. There is also a Minimize Structure tool (in menu under Tools... Structure Editing) or "minimize" command, but it has limited ability to clean up a structure. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 25, 2014, at 1:00 AM, sette@uniroma2.it wrote:
Dear all, I’m interested to create a rough model of a quadruplex molecule using a specific sequence. One possibility could be to load a pdb structure of a quadruplex and « mutate » each nucleotide with the correct one. Is this feasible with Chimera ? Alternative suggestions are appreciated as well. Thanks for your help, Marco
Hi Elaine, this is very useful :) Many thanks!!! Marco Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Dear Marco, There is a "swapna" command for mutating nucleic acids: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapna.html>
The results may be fairly rough, with some nonoptimal geometries and/or steric clashes, but you could try this and see if it meets your needs. There is also a Minimize Structure tool (in menu under Tools... Structure Editing) or "minimize" command, but it has limited ability to clean up a structure.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 25, 2014, at 1:00 AM, sette@uniroma2.it wrote:
Dear all, I'm interested to create a rough model of a quadruplex molecule using a specific sequence. One possibility could be to load a pdb structure of a quadruplex and « mutate » each nucleotide with the correct one. Is this feasible with Chimera ? Alternative suggestions are appreciated as well. Thanks for your help, Marco
Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 www.rete29aprile.it ---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it
You're welcome! I forgot to mention that for RNA (not DNA), there is a nice modeling/refinement plugin, Assemble2, developed by Fabrice Jossinet at University of Strasbourg: <http://bioinformatics.org/assemble/index.html> It interfaces with web services for RNA structure prediction and refinement. Elaine On Jun 26, 2014, at 11:02 AM, sette@uniroma2.it wrote:
Hi Elaine,
this is very useful :) Many thanks!!! Marco
Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Dear Marco, There is a "swapna" command for mutating nucleic acids: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapna.html>
The results may be fairly rough, with some nonoptimal geometries and/or steric clashes, but you could try this and see if it meets your needs. There is also a Minimize Structure tool (in menu under Tools... Structure Editing) or "minimize" command, but it has limited ability to clean up a structure.
On Jun 25, 2014, at 1:00 AM, sette@uniroma2.it wrote:
Dear all, I'm interested to create a rough model of a quadruplex molecule using a specific sequence. One possibility could be to load a pdb structure of a quadruplex and « mutate » each nucleotide with the correct one. Is this feasible with Chimera ? Alternative suggestions are appreciated as well. Thanks for your help, Marco
participants (2)
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Elaine Meng -
sette＠uniroma2.it