Dear all, Here is a PDB file of a DNA portion. It contains only the atoms of the backbone chain trace. Is there a way to rebuild the remaining parts (sugar,...)? Many thanks for your help Damien
Dear Damien, Sorry, Chimera does not have automated methods for building all-atom models from chain traces, either protein or DNA. Chimera's Build Structure tool (under Tools... Structure Editing) enables manual, step-by-step building, but it is not guided by an input backbone trace, and it would be far too tedious for such long chains anyway. I haven't done much building in other programs, but I try to keep track of useful web servers. For protein CA traces, there is a Maxsprout server, but for nucleic acid building, I only know of one web server (make-na) and I believe it just builds the whole thing from scratch and cannot be guided by a chain trace. <http://structure.usc.edu/make-na/> <http://www.ebi.ac.uk/Tools/maxsprout/> Sorry I couldn't help more -- maybe someone else on the list will know of a suitable program. 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 Apr 13, 2011, at 9:46 AM, Damien Larivière wrote:
Dear all, Here is a PDB file of a DNA portion. It contains only the atoms of the backbone chain trace. Is there a way to rebuild the remaining parts (sugar,...)? Many thanks for your help Damien <DNAdeformed.pdb>_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
May be you can try here http://rutchem.rutgers.edu/~xiangjun/3DNA/ Marco Def. Quota "Elaine Meng" <meng@cgl.ucsf.edu>:
Dear Damien, Sorry, Chimera does not have automated methods for building all-atom models from chain traces, either protein or DNA. Chimera's Build Structure tool (under Tools... Structure Editing) enables manual, step-by-step building, but it is not guided by an input backbone trace, and it would be far too tedious for such long chains anyway.
I haven't done much building in other programs, but I try to keep track of useful web servers. For protein CA traces, there is a Maxsprout server, but for nucleic acid building, I only know of one web server (make-na) and I believe it just builds the whole thing from scratch and cannot be guided by a chain trace.
<http://structure.usc.edu/make-na/> <http://www.ebi.ac.uk/Tools/maxsprout/>
Sorry I couldn't help more -- maybe someone else on the list will know of a suitable program. 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 Apr 13, 2011, at 9:46 AM, Damien Larivière wrote:
Dear all, Here is a PDB file of a DNA portion. It contains only the atoms of the backbone chain trace. Is there a way to rebuild the remaining parts (sugar,...)? Many thanks for your help Damien <DNAdeformed.pdb>_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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 ---------------------------------------------------------------- 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 Elaine, Dear Marco Many thanks for your message and suggestion. Marco, I took contact with Xian-Jun Lu who is in charge of 3DNA. I'm waiting for his answer. I will give a feedback here. Elaine, I keep in mind the idea of Maxsprout for protein rebuild from trace. About the DNA, since I have the initial DNA portion, not deformed and complete, I tried to make a morph between the complete DNA and its deformed trace. But only the trace of the original structure morphed. A colleague is going to make something using Yasara. Wait and see. Thanks Damien Le 14/04/2011 09:19, sette@uniroma2.it a écrit :
May be you can try here
http://rutchem.rutgers.edu/~xiangjun/3DNA/
Marco
Def. Quota "Elaine Meng"<meng@cgl.ucsf.edu>:
Dear Damien, Sorry, Chimera does not have automated methods for building all-atom models from chain traces, either protein or DNA. Chimera's Build Structure tool (under Tools... Structure Editing) enables manual, step-by-step building, but it is not guided by an input backbone trace, and it would be far too tedious for such long chains anyway.
I haven't done much building in other programs, but I try to keep track of useful web servers. For protein CA traces, there is a Maxsprout server, but for nucleic acid building, I only know of one web server (make-na) and I believe it just builds the whole thing from scratch and cannot be guided by a chain trace.
<http://structure.usc.edu/make-na/> <http://www.ebi.ac.uk/Tools/maxsprout/>
Sorry I couldn't help more -- maybe someone else on the list will know of a suitable program. 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 Apr 13, 2011, at 9:46 AM, Damien Larivière wrote:
Dear all, Here is a PDB file of a DNA portion. It contains only the atoms of the backbone chain trace. Is there a way to rebuild the remaining parts (sugar,...)? Many thanks for your help Damien <DNAdeformed.pdb>_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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
---------------------------------------------------------------- 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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Yes -- as you found, Chimera's morphing only includes the atoms that are present in both the starting and ending structures. Elaine On Apr 14, 2011, at 10:38 AM, Damien Larivière wrote:
Elaine, I keep in mind the idea of Maxsprout for protein rebuild from trace. About the DNA, since I have the initial DNA portion, not deformed and complete, I tried to make a morph between the complete DNA and its deformed trace. But only the trace of the original structure morphed.
participants (3)
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Elaine Meng -
sette＠uniroma2.it