Miguel wrote:
...
the property
ribbonedge on
which restores the original Jmol cartoon style had had only a short stay
during past Jmol versions, was this intended?
That was intended to stay. I will investigate.
sorry, I somehow missed the renaming to ribbonBorder as you explained in
an other mail
if bonds are added to a partial wireframe representation, they are
created invisible+
load pdb file
cpk off
wireframe off
select [PRO]
wireframe 70
# not 50
select protein and *.O
connect modify double (*.C and within(group, selected))
neither the visible bonds alter their style nor the invisible bonds get
visible. I think that every newly created/modified bond should be
visible as it gets created.
I think I disagre.
I don't think you do, I may not have been clear enough
You are modifying bonds that already exist.
You are modifying the order.
They retain their color and size.
but should alter their order (which didn't occur if I am using a
wireframe >63 command before)
If you create new bonds then they are displayed by default.
I agree, they should be displayed as they are created, but with the
script above, they do not show up.
Q: What do others think?
...
* exposure of 'bondcount' as an atom property:
select bondcount=2
how are double bounds counted? At the moment this a
connected atoms count (rename to boundedcount ?)
Correct. It is the connected atoms count.
It is not the sum of the bond orders.
If the names 'bondcount' and 'hbondcount' are going to be confusing then
should change them.
Q: Please recommend other names ... connectedAtomsCount ?
and only selects *.OG and *.SG (which
is correct, if not >C=O)
I do not understand this.
double bounded carbonyl oxygen, which I had generated above.
It is correct, you had explained that it is boundedAtomsCount.
select bondcount=3 and carbon
connect modify aromatic
the graph is a bit stochastic. I would prefer if either inner and outer
bonds regularly change in showing hbond style bond or only the inner
bonds are hbond style.
You are referring to the positioning of the dotted and solid lines in
'aromatic' bonds.
I wrote this code several years ago, to support aromatic rings. The code
was designed to find the inside of the ring.
it failed, the result looks stochastic
I was not aware of other applications where 'aromatic' would be used
outside of a 'ring'.
not necessary aromatic but unlocalized
|
o-c=o
c-c=c-c=c
but in any case inside would be right
If there are specific rules for placement of 'aromatic' bonds outside of a
ring context then we can investigate that after the 10.1 release.
While the 'aromatic' code is old, most people have never seen it ... so it
has not been subject to much review. So it is possible/likely that it will
make 'incorrect' decisions in ring or multi-ring contexts.
rotating such a graph often results in
Exception in thread "AWT-EventQueue-0"
java.lang.ArrayIndexOutOfBoundsException: 188856
at org.jmol.g3d.Graphics3D.plotPixelsClipped(Graphics3D.java:1260)
at
org.jmol.g3d.Circle3D.plot8FilledCircleCenteredClipped(Circle3D.java:133)
at
org.jmol.g3d.Circle3D.plotFilledCircleCenteredClipped(Circle3D.java:163)
at
org.jmol.g3d.Graphics3D.fillScreenedCircleCentered(Graphics3D.java:365)
This is somewhat disturbing.
This code has not changed in a long time.
I cannot reproduce this problem.
in my last session (4883) it occurred repeatedly, but now (4892) I can't
reproduce it.
Regards, Jan
Please try to produce a script with a specific molecule that causes the
problem.
Q: If anyone else has seen this type of problem please speak up.
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