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Molecule style & color [message #983] Wed, 08 July 2020 20:39 Go to next message
Paul is currently offline  Paul
Messages: 16
Registered: May 2019
Location: United States
Junior Member
Hello,

In version 5.02.01, the molecule style and color defaults for conformers have changed. How do I change the defaults back to ball and stick and color by atomic number?

Thanks,

Paul
Re: Molecule style & color [message #985 is a reply to message #983] Wed, 08 July 2020 22:09 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 646
Registered: June 2014
Senior Member
Hallo Paul,

with version 5.0.0 DataWarrior switched from JMol as 3D-molecule-viewer to FXMolViewer.
This involved many changes, e.g. instead of having a grid view 0f 3x3 conformers, all
conformers are now superpositioned in one view. A slider allows to separate the conformers.
The new viewer is much more flexible, has lots of features, which DataWarrior will use in
future updates and is based on the same cheminformatics library that DataWarrior itself uses,
this was an overdue and obvious change. However, you are right that the default molecule mode
changed from ball&sticks to sticks only, which seemed more appropriate for superpositioned
conformers. To better distinguish superposed conformers they have different colors. Nevertheless,
hetero atoms are shown in their native color (N=blue, O=red, etc).

Currently, DataWarrior does not use Settings of any kind. Would it help in your opinion, if you could
change all molecules to ball&sticks with a new popup menu item?

Thomas
Re: Molecule style & color [message #986 is a reply to message #985] Thu, 09 July 2020 00:42 Go to previous messageGo to next message
nbehrnd is currently offline  nbehrnd
Messages: 204
Registered: June 2019
Senior Member
Hello Paul,

if the window including the 3D representation is large enough, you may mark a bond or
an atom of the molecule displayed (left mouse click, turning the selected red) then
followed by a right click. This action opens a new menu with adjustable entries about
molecule style (including «Ball And Sticks») and molecule colour (with «By atomic No»).

index.php?t=getfile&id=230&private=0

This works equally well for the representation of single molecules (as shown in the
series of 01.png till 03.png, attached below), as well as for the simultaneous display
of conformers (04.png and 05.png). This menu may be closed by «Esc».

Norwid
  • Attachment: 01.png
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  • Attachment: 02.png
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  • Attachment: 03.png
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  • Attachment: 04.png
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  • Attachment: 05.png
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Re: Molecule style & color [message #989 is a reply to message #985] Thu, 09 July 2020 02:59 Go to previous messageGo to next message
Paul is currently offline  Paul
Messages: 16
Registered: May 2019
Location: United States
Junior Member
Thanks for the information (and the program in general).

Carbon and hydrogen atoms are displayed in the same color - 7fffd4. Nitrogen and oxygen atoms are their usual colors (blue and red).

It would be somewhat of an improvement if carbon were grey, dark grey or black. Or different from hydrogen.

I am able to use the right click menu to change molecule style and colors, on a per molecule basis.

When working with files of thousands of different molecules, the right click option is impractical.

Sticks versus balls and sticks is purely cosmetic, so I can live with just sticks, and might actually appreciate the benefits of superimposition of conformers.

I need to be able to differentiate carbon from hydrogen atoms, though.


Again, thanks!

Paul
Re: Molecule style & color [message #990 is a reply to message #989] Thu, 09 July 2020 09:57 Go to previous messageGo to next message
nbehrnd is currently offline  nbehrnd
Messages: 204
Registered: June 2019
Senior Member
Hello Paul,

a quick work-around could employ the platform independent Jmol.(1) It is possible to
save all of the conformers generated in one .sdf file in common -- just take care that
the export retains the 3D coordinates (which is not the default).

In Jmol running, the entry File -> Console opens the programs' own little terminal.
Then indicate Jmol the .sdf to read; it will recognize that the .sdf contains multiple
models, but by default will display only the first one. This is the chance to disable
the display of double / aromatic / triple bonds with more than one line (by the second
command), to adjust the diameter of the sticks and balls (third command) and eventually
display all models (here: all superimposed conformers) at once by the instruction of
model 0.

index.php?t=getfile&id=235&private=0

The scene may be exported like below.

index.php?t=getfile&id=236&private=0

The interaction with Jmol may be scripted (e.g., 2,3,4) thus you may reuse instructions
more than once. If the color of an atom type does not fit your needs, for example, you
could alter the representation by

select hydrogen
color gray

for all models load at once. You may return to the default color scheme by

select all
color cpk


Norwid

1) http://wiki.jmol.org/index.php/Main_Page
2) https://chemapps.stolaf.edu/jmol/docs/
3) https://earth.callutheran.edu/Academic_Programs/Departments/ BioDev/omm/jsmol/scripting/molmast.htm#V
4) Hanson, J.Appl.Cryst.(2010).43, 12501260, doi: 10.1107/S0021889810030256
Re: Molecule style & color [message #993 is a reply to message #990] Thu, 09 July 2020 18:52 Go to previous messageGo to next message
Paul is currently offline  Paul
Messages: 16
Registered: May 2019
Location: United States
Junior Member
Nice!

Thanks for the help.

I will need to explore these options.

Best Regards,

Paul
Re: Molecule style & color [message #995 is a reply to message #993] Fri, 10 July 2020 12:58 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 646
Registered: June 2014
Senior Member
Dear Paul,

I updated the behaviour. Hydrogen atoms of molecules, which are shown in a custom color,
are now painted in an intermediate color:

index.php?t=getfile&id=243&private=0

Thomas
  • Attachment: t.png
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Re: Molecule style & color [message #1004 is a reply to message #995] Mon, 13 July 2020 15:14 Go to previous message
Paul is currently offline  Paul
Messages: 16
Registered: May 2019
Location: United States
Junior Member
That works good, Thomas.

Now I can benefit from conformer superposition and recognize methyl branches.

Thanks,

Paul
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