Hi,
thanks for your efforts Otis! What I want is not as fancy as Bob guessed. Let
me try to reformulate what I want to achieve: "Use the mouse to rotate an
arbitrary set of atoms around its geometric center.".
I set up a page with some comments (also attached below) to clarify things,
hopeful
Alex,
That's what I needed. We will need a new parameter:
set rotateSelectedAtoms
It will be in Jmol 12.1.21, to be released later today.
Bob
On Tue, Nov 9, 2010 at 4:20 AM, Alexander Rose
wrote:
> Hi,
>
>
> thanks for your efforts Otis! What I want is not as fancy as Bob guessed.
> Let me tr
Make that...
version=12.1.21_dev
# new feature: set allowMoveAtoms
#-- allows rotation/dragging of atoms regardless of bonding
#-- automatically sets/unsets allowRotateSelected and dragSelected
#-- ALT-left --> rotates selected set
#-- ALT-SHIFT-left --> drags selected set
On Tu
Alex,
Yeah, that is the "icky" case. PLM is bonded to the protein chain. You
can break that sulfur bond and then play with PLM independently (using
model kit mode). You can also rotate it about that bond (using model kit
mode). For complete independent movement while attached, Bob obviously
h
Bob,
I think the following are two correct SMILES for 3-methyl benzaldehyde:
c12=cc=cc(C)=c2.C1=O
c1(c=O)=cc=cc(C)=c1
With the first being generated by the current model window and the
second coming from a database, the following fails:
var cks = {*}.find('SMILES','c1(c=O)=cc=cc(C)=c1');echo
OK, so after a couple of silly symptoms, I sort of decided that the
system was mad betond reason. I have therefore applied the "master
method for troubleshooting": uninstall Java, check that there are no
java files left behind, and reinstall. The problem has gone. One more
mistery on the list,
what's with the lower case (c=O)?
On Tue, Nov 9, 2010 at 11:03 AM, Otis Rothenberger wrote:
> Bob,
>
> I think the following are two correct SMILES for 3-methyl benzaldehyde:
>
> c12=cc=cc(C)=c2.C1=O
>
> c1(c=O)=cc=cc(C)=c1
>
> With the first being generated by the current model window and the
>
was surprised by the result:
>>
>> {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15}
>>
>> I take it that the elements and the "=" are being matched (found) - not
>> the dot??
>>
>>
not the dot ? What's being found here are atoms. I see, you mean we
aren't matching 10-12? I will have to look into that
Bob,
That's clearly my mistake. A lot of the kekule aromatic entries in my
database came from JME, and I hand edited JME's upper case aromatic "C"
to lower case aromatic "c" for Jmol comparison. I clearly hand edited a
non-aromatic here. I'll check the isoprene again to see if there is
anythi
Grrr...
Isoprene was another hand editing issue. I had:
"smiJ": "C/C/1=C.C\1=C", "smiR": "CC(=C)C=C",
It should have been:
"smiJ": "C/C/1=C.C\\1=C", "smiR": "CC(=C)C=C",
The smiles strings are handed to Jmol script via JavaScript, so the
database has to store \\ for \.
I now have Jmol scri
On Tue, Nov 9, 2010 at 11:03 AM, Otis Rothenberger wrote:
> One more question, probably naive: With the FIND that worked above, I
> was surprised by the result:
>
> {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15}
>
>
Jmol is missing three H atoms; I will check that out.
>
>
>
> ---
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