On Tuesday 30 January 2007, Francesco Pietra wrote:
> Let me say that a package dealing with molecules that
> does not place hydrogens correctly is of no use
> professionally. I must add that I am strongly
> disappointed, and back to my old MM package, which
> places the hydrogens correctly, like t
On Wednesday 31 January 2007, Bob Hanson wrote:
> When we met in Cologne last August, Egon and I agreed that Jmol -- at
> least in our hands -- won't be in the business of doing quantum chem or
> molecular mechanics calculations. Of course, anyone who wants can
> implement whatever they can with Jm
Hi Frederick,
You missed a discussion of this topic 2-3 days ago on this list. The
subject line of much of it contained:
[Jmol-users] adding hydrogens
I just did a Google search for this subject line and did not come up
with the posts, so I guess sourceforge has not yet published them. I
Hi,
I found nothing about my problem in the documentation, so i dare asking here.
Is there a way to add Hydrogens to a PDB-Structure in Jmol like there is in
Pymol with H_add() ?
And is there a way to extract the molecule into my Java environment, so i
can work with it in my applet? I want to c
When we met in Cologne last August, Egon and I agreed that Jmol -- at
least in our hands -- won't be in the business of doing quantum chem or
molecular mechanics calculations. Of course, anyone who wants can
implement whatever they can with Jmol, but we are more interested, as
Angel describes,
Here is Bob Hanson's reply, from late October, to my inquiry regarding
Jmol's ability to sprout hydrogens as was possible within Chime. (My
knowledge is not sophisticated enough to know whether this line of pursuit
might meet your needs, but here it is.) There was little feedback from
others so I b
On Mon, January 29, 2007 6:16 pm, Francesco Pietra wrote:
> Let me say that a package dealing with molecules that
> does not place hydrogens correctly is of no use
> professionally.
If Jmol was a MM program or even a molecular-editor you might have reason
to have such a view. But, Jmol is a molecu
On 29 Jan 2007 at 15:16, Francesco Pietra wrote:
> Let me say that a package dealing with molecules that
> does not place hydrogens correctly is of no use
> professionally. I must add that I am strongly
> disappointed, and back to my old MM package, which
> places the hydrogens correctly, like the
Let me say that a package dealing with molecules that
does not place hydrogens correctly is of no use
professionally. I must add that I am strongly
disappointed, and back to my old MM package, which
places the hydrogens correctly, like the nonvolatiles.
How do you start a quantum mechanical computa
Another option for adding hydrogen atoms to pdb files is the
excellent Molprobity web site:
http://molprobity.biochem.duke.edu/
Frieda
///
Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
/
I am opening two new threads for Paul questions in his last post to "
loading jmol file from open babel"
On 29 Jan 2007 at 10:44, H. Paul Benton wrote:
> To all the other uses I have one more question to ask
> "If a file was loaded with no Hydrogens how can I get
> Jmol to put them on?".
Jmol
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