O(+)(v1)
User 870ab5b546
23-11-2008 00:56:36
Hi,
When we show a molecule in MarvinView that has a monovalent O+ atom, MarvinView shows (v1) next to the O. We already show implicit H atoms on heteroatoms, so the O atom would show as OH2+ if it were not monovalent, so the (v1) designation is redundant. On top of that, it confuses students because it is not standard notation. I suggest you do not show valence numbers for atoms all of whose implicit H atoms are set to display.
-- Bob
User 25d107bd42
24-11-2008 11:39:25
Hi Bob,
could you please post an example for such a formula ?
The best would be a mrv-file.
Regards, Hans-Ulrich
User 870ab5b546
24-11-2008 14:18:17
[O+][C-]1CCCC1
User 25d107bd42
24-11-2008 14:31:46
Is this meant as one of the resonance formulas of cyclopentanone ?
User 870ab5b546
24-11-2008 14:33:58
Yes, a very bad one, obviously.
The same "(v)" notation occurs whenever a heteroatom is unexpectedly electron-deficient.
User 25d107bd42
24-11-2008 14:46:44
Yes, the (v) notation is really confusing.
ChemAxon 990acf0dec
27-11-2008 12:32:51
Hi Bob and Hans-Ulrich,
What about a display option to switch off the display of non-standard valences? Would it help?
User 870ab5b546
27-11-2008 15:42:39
Yes, that would help.
User 25d107bd42
29-11-2008 17:01:27
I agree, and the option should be off by default.
What is the usage of "v0" "v1" ... described in the help documentation ?
ChemAxon 990acf0dec
02-12-2008 16:14:02
Hi Hans-Ulrich,
It is an atom property, and means an explicit valence (total bond order):
http://www.chemaxon.com/jchem/doc/user/query_features.html#atprop
It is usually used as a query property, and therefore I don't think it should be off by default (because then it cannot be recognized that it is set).
Best regards,
Akos
User 25d107bd42
03-12-2008 08:20:12
Hi Akos,
does that mean the MarvinSketch GUI and the command line tools use the same settings?
Regards, Hans-Ulrich
ChemAxon 990acf0dec
03-12-2008 09:48:34
Hi Hans-Ulrich,
I don't understand your question exactly. The display option is available only in the GUI, but the valence setting is part of the molecule, so it is available also in the command line tools.
Best regards,
Akos
User 25d107bd42
05-12-2008 13:12:07
Hi Akos,
I meant "the display option" should be off by default.
I think this option is not used by cxcalc, or is it used ?
Does cxcalc etc. use any options stored in the directory .chemaxon ?
Regards, Hans-Ulrich
User 870ab5b546
05-12-2008 13:33:00
For myself, I don't think it matters much whether it is off by default or not. It's easy enough to turn it off in the Web app.
But, if you want to be really subtle about it, I suggest turning it off when display of implicit H atoms on heteroatoms is turned on, and turn it on when display of implicit H atoms on heteroatoms is turned off. The (v) notation is necessary only when the display of implicit H atoms on heteroatoms are off.
On a related matter: I would like an option to turn on valence error display (underlining atoms with improper valences in red) in MarvinView. Is it available?
ChemAxon 990acf0dec
08-12-2008 10:18:37
Dear Hans-Ulrich,
Display options are not used in cxcalc, only in molconvert (and even there they are used only for image generation purposes).
I have created a feature request task for this display option, but I don't think we will have capacity for this before 5.2.
Dear Bob,
To switch this option on/off together with the display of implicit hydrogens is a good idea; I added this to the above mentioned feature request task.
Regarding the valence error display in MView please read the description of the valenceErrorVisibleInView parameter on the following page:
http://chemaxon.com/marvin/help/developer/viewman.html
I hope it helps.
Best regards,
Akos
User 870ab5b546
08-12-2008 13:15:36
Yes it does, thanks. From which version does this option date?
ChemAxon 5433b8e56b
08-12-2008 16:10:16
Dear Bob!
Refer to our
forum it seems this feature is available since Marvin 5.0.1 is out.
Best regards,
Istvan
ChemAxon 990acf0dec
08-12-2008 16:10:29
I have not planned yet... after closing 5.2 we start the planning of 5.2.x versions, and it will be available in one of those.
ChemAxon 990acf0dec
08-12-2008 16:20:37
So we are mixing two options here:
- MView valence error display option - available since 5.0.1
- Explicit valence display option - coming in 5.2.x
User 25d107bd42
06-02-2009 14:54:51
Hi,
I have a question here:
How can I produce [O+][C-]1CCCC1 using the MarvinSketch canvas GUI ?
Using the toolbar tool "Increase charge" or "Charge +1" and "Remove implicit hydrogen" always produces [OH2+][C-]1CCCC1 after saving.
Regards, Hans-Ulrich
User 870ab5b546
06-02-2009 14:59:25
Convert it to a divalent radical after giving it a + charge.
User 25d107bd42
06-02-2009 15:47:25
Hi Bob,
thank you for your speedy answer.
I used this procedure, but in the next post Akos showed another way to do it. So I deleted the result here.
Regards, Hans-Ulrich
ChemAxon 990acf0dec
07-02-2009 16:00:40
Hi Hans-Ulrich,
Set the valence of the oxygen to 1 (type .v1 on the canvas, then click on the atom, or on the Query tab of the Periodic system select the .v+ or .v- tools and click on the atom consequtively until the valence is set to 1).
Best regards,
Akos
User 25d107bd42
07-02-2009 17:20:44
Hi Akos,
OK, that's a good way to produce this formula. And I found now the description in the User's Guide, see screenshot.
Marvin has many good tools. Super!
Thank you and best regards, Hans-Ulrich