Re: [PyMOL] (no subject)
Hi Noloofar and Lina, >> I would like to calculate partial charges of my pdb. Is it possible to do it > > In pymol: > > Action-> compute -> partial charge sum this doesn't calculate partial charges, sorry. This does: Action -> generate -> vacuum electrostatics But better would be to use pdb2pqr: http://www.poissonboltzmann.org/pdb2pqr >> I have another question too, when aligning two structure in Pymol, there is >> a RMSD for the total structure, is there any command to calculate the RMSD >> for a specific region of the alignment. If the two structures have the same sequence (same atom identifiers) and you don't need an "alignment", you can use rms_cur. http://pymolwiki.org/index.php/Rms_Cur Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free "Love Thy Logs" t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Mutagenesis script
Hi Troels,
> cmd.(something) ALWAYS has to be in string format.
> So there is the cmd.frame wrong.
I'm sorry but this is not true, of course you can pass an integer to
cmd.frame
> Then you dont quit the mutagenesis wizard
which is not a problem as well.
> And you have a space in the cmd.save
I agree to avoid spaces between function name and parenthesis, but still
this is valid python syntax and works fine.
The full script posted by Rozaimi works fine for me by the way.
> cmd.set_wizard("done")
this doesn't quit the wizard, cmd.set_wizard() without arguments does.
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
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Re: [PyMOL] Mutagenesis script
So.
cmd.(something) ALWAYS has to be in string format.
So there is the cmd.frame wrong.
Then you dont quit the mutagenesis wizard
And you have a space in the cmd.save
*It total, try:*
#Initialize
fetch 1shr, async=0
create test, 1shr
cmd.wizard("mutagenesis")
cmd.do("refresh_wizard")
# Mutate
cmd.get_wizard().set_mode("HIS")
cmd.get_wizard().do_select("/test//B/36")
cmd.frame("1")
cmd.get_wizard().apply()
cmd.set_wizard("done")
# Save
cmd.save("kill.pdb")
or look at:
http://www.pymolwiki.org/index.php/Rotkit
import rotkit
*mutate test, chain=B, resi=36, target=HIS, mutframe=1*
2011/9/2 Rozaimi Razali
> Can someone please explain to me why my script is not working properly?
>
> #Initialize
> fetch 1shr, async=0
> create test, 1shr
> cmd.wizard("mutagenesis")
> cmd.do("refresh_wizard")
>
> # Mutate
> cmd.get_wizard().set_mode("HIS")
> cmd.get_wizard().do_select("/test//B/36")
>
> cmd.frame(1)
> cmd.get_wizard().apply()
>
> # Save
> cmd.save ("kill.pdb")
>
> Thanks!
>
>
> --
> Special Offer -- Download ArcSight Logger for FREE!
> Finally, a world-class log management solution at an even better
> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
> download Logger. Secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsisghtdev2dev
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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>
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price-free! And you'll get a free "Love Thy Logs" t-shirt when you
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Re: [PyMOL] (no subject)
On Sun, Sep 4, 2011 at 8:37 PM, niloofar niknam wrote: > > > Deal list, > I would like to calculate partial charges of my pdb. Is it possible to do it In pymol: Action-> compute -> partial charge sum > by Pymol? If not, Is anyone know any server > or software to do it? > I have another question too, when aligning two structure in Pymol, there is > a RMSD for the total structure, is there any command to calculate the RMSD > for a specific region of the alignment. > Any offer would be appreciated. > kind regards. > Niloofar > > -- > Special Offer -- Download ArcSight Logger for FREE! > Finally, a world-class log management solution at an even better > price-free! And you'll get a free "Love Thy Logs" t-shirt when you > download Logger. Secure your free ArcSight Logger TODAY! > http://p.sf.net/sfu/arcsisghtdev2dev > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Best Regards, lina -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free "Love Thy Logs" t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] (no subject)
Deal list, I would like to calculate partial charges of my pdb. Is it possible to do it by Pymol? If not, Is anyone know any server or software to do it? I have another question too, when aligning two structure in Pymol, there is a RMSD for the total structure, is there any command to calculate the RMSD for a specific region of the alignment. Any offer would be appreciated. kind regards. Niloofar -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free "Love Thy Logs" t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
