Ah, right! I see. Sure. I added hydrogen bond calculation outside of the
context of PDB files, and then I forgot to enable the menu item for that.
OK. This is fixed for Jmol 12.3.15 and 12.2.15.
See http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
On Sat, Jan 28, 2012 at 12:57 AM, j
Ah, right. Definitely not a protein!
On Mon, Jan 30, 2012 at 2:37 PM, johannes.per...@edumendo.fi <
johannes.per...@edumendo.fi> wrote:
> Here is an example file.
>
> Johannes
>
>
> 30.1.2012 17:03, Robert Hanson kirjoitti:
>
> I'm guessing that MOL2 file does not include proper 3-letter PDB gro
Here is an example file.
Johannes
30.1.2012 17:03, Robert Hanson kirjoitti:
I'm guessing that MOL2 file does not include proper 3-letter PDB group
names in columns 61-63. Please send me a copy of the problem file.
I'm guessing that MOL2 file does not include proper 3-letter PDB group
names in columns 61-63. Please send me a copy of the problem file.
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Thank you Ángel for your research. This works. I can show my students
that hbonds feature works in the pop-up menu with pdb files and if they
use mol2 files, it can be done via console.
I think we continue with mol2 format because of the partial charge data
and electrostatic potential surfaces
Well, I have done a little research and yes, I can confirm Johannes'
observation.
Jmol 12.2.2 has also disabled the popup menu "calculate Hbonds" for MOL2 files,
but not for PDB files. However, the ability to calculate is there in the script
console.
These "feature" is by design, since that po
Hello Johannes
As you may know, H-bond calculation in Jmol is limited to certain situations
(mostly proteins) and has evolved (expanded) during the last years.
I am not sure about your problem, first I thought it may be related to the file
format not being pdb. But since you say that you can d
Dear all Jmol users.
Is there a reason why I can't calculate hbonds using pop-up menu?
When I select Style --> Hydrogen bonds --> Calculate function is not
active.
I use the newest version of Jmol and I tried to calculate hbonds for
mol2 -file format.
I can always calculate them via command l
> Dear all Jmol users.
>
> Is there a reason why I can't calculate hbonds using pop-up menu?
> When I select Style --> Hydrogen bonds --> Calculate function is not
> active.
> I use the newest version of Jmol and I tried to calculate hbonds for
> mol2 -file format.
>
> I can always calculate th
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