Re: [Chimera-users] chemical structure
Dear Dr. Meng, thank you for your immediate and detailed reply. it is greatly appreciated. does your e-facility supports siRNA (short-interfering RNA) structures. as you know siRNA have special biochemical features in comparison to common RNA molecules, independently the sequence. is there any specific option for siRNA and /or to add chemical modifications? yours, christos -------------------------------------------- Στις Παρ., 15/04/16, ο/η Elaine Meng <meng@cgl.ucsf.edu> έγραψε: Θέμα: Re: [Chimera-users] chemical structure Προς: "kotakis xristos" <kotakisx@yahoo.gr> Κοιν.: chimera-users@cgl.ucsf.edu Ημερομηνία: Παρασκευή, 15 Απρίλιος 2016, 20:59 Dear Dr. Christos Kotakis, You probably meant PDB (not PDF), which you can save from the Chimera File menu or with the “write” command after creating the structure. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> To create the structure in Chimera, I can think of 3 general ways: (1) for a completely regular, idealized double helix, you can use Build Structure (in menu under Tools… Structure Editing), the Start Structure section, open “helical DNA/RNA”, choose “RNA,” enter sequence, etc. However, if there are unpaired bases on the ends or you expect the structure should be irregular rather than a perfect helix, you may need to use one of the other methods. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start> (2) there is an “Assemble2” plugin to Chimera that does all kinds of RNA structural modeling. It is quite fancy… one can draw the 2D diagram of the desired RNA and then calculate possible 3D structures. You have to get the plugin separately from <http://bioinformatics.org/assemble/index.html> <http://www.bioinformatics.org/assemble/downloads.html> (3) if there is a 3D structure already available for a similar siRNA duplex (i.e., you expect your duplex to have similar 3D structure), you can open that structure in Chimera and then try “mutating” the bases to your sequence with the “swapna” command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapna.html> I hope this helps, Elaline ----- 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 15, 2016, at 9:15 AM, kotakis xristos <kotakisx@yahoo.gr> wrote:
Dear Sir/Madam, I have a siRNA duplex (21nt) of a given sequence and I would like to generate the chemical structure of that in a single file (e.g. pdf)
What do you suggest?
looking forward to your response thanks in advance,
yours,
Dr. Christos Kotakis _
Dear Christos, Nothing specifically, but you could either (1) use Build Structure, the Modify Structure section to manually build atom-by-atom <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html> or (2) superimpose modified bases from other crystal structures onto the corresponding positions in your structure, write out the superimposed coordinates (File… Save PDB, “relative to” your structure), then manually in a text-editor (not in Chimera) substitute the coordinates of the atoms from the modified base for the unmodified base in your PDB file. Both of these require a fair amount of manual labor and are not easy or simple. Maybe the Assemble2 plugin has some features for building these modified bases, but I haven’t tried it, so I’m not sure. You would have to check the manual for that plugin. Best, 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 18, 2016, at 7:55 AM, kotakis xristos <kotakisx@yahoo.gr> wrote:
Dear Dr. Meng,
thank you for your immediate and detailed reply. it is greatly appreciated. does your e-facility supports siRNA (short-interfering RNA) structures. as you know siRNA have special biochemical features in comparison to common RNA molecules, independently the sequence. is there any specific option for siRNA and /or to add chemical modifications?
yours, christos -------------------------------------------- Στις Παρ., 15/04/16, ο/η Elaine Meng <meng@cgl.ucsf.edu> έγραψε:
Θέμα: Re: [Chimera-users] chemical structure Προς: "kotakis xristos" <kotakisx@yahoo.gr> Κοιν.: chimera-users@cgl.ucsf.edu Ημερομηνία: Παρασκευή, 15 Απρίλιος 2016, 20:59
Dear Dr. Christos Kotakis, You probably meant PDB (not PDF), which you can save from the Chimera File menu or with the “write” command after creating the structure. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>
To create the structure in Chimera, I can think of 3 general ways:
(1) for a completely regular, idealized double helix, you can use Build Structure (in menu under Tools… Structure Editing), the Start Structure section, open “helical DNA/RNA”, choose “RNA,” enter sequence, etc. However, if there are unpaired bases on the ends or you expect the structure should be irregular rather than a perfect helix, you may need to use one of the other methods. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start>
(2) there is an “Assemble2” plugin to Chimera that does all kinds of RNA structural modeling. It is quite fancy… one can draw the 2D diagram of the desired RNA and then calculate possible 3D structures. You have to get the plugin separately from <http://bioinformatics.org/assemble/index.html> <http://www.bioinformatics.org/assemble/downloads.html>
(3) if there is a 3D structure already available for a similar siRNA duplex (i.e., you expect your duplex to have similar 3D structure), you can open that structure in Chimera and then try “mutating” the bases to your sequence with the “swapna” command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapna.html>
I hope this helps, Elaline ----- 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 15, 2016, at 9:15 AM, kotakis xristos <kotakisx@yahoo.gr> wrote:
Dear Sir/Madam, I have a siRNA duplex (21nt) of a given sequence and I would like to generate the chemical structure of that in a single file (e.g. pdf)
What do you suggest?
looking forward to your response thanks in advance,
yours,
Dr. Christos Kotakis _
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
-
Elaine Meng -
kotakis xristos