Inconvenient fading of 3D display

User 25d107bd42

29-11-2010 15:52:49

Hi, having now Marvin 5.4.0.0 there is a new "feature":


The display of 3D structures in MarvinSketch is now fading into the background, see attached screenshot. Question: Where is the nitrile group of the displayed amygdalin ?


Is this display usable for beamer presentations ?


Is there a possibilty to switch this fading off, as in the former versions of Marvin ?


And: The default should be: Off = no fading.


Regards, Hans-Ulrich

ChemAxon 990acf0dec

30-11-2010 09:58:28

Hi Hans-Ulrich,


The implementation of the display option to switch off the fog-effect (or fading as you refer to it) is on the way; probably comes in the next patch release.


But I think the default should remain "On", because it helps understanding what is closer and what is farther on the screen. Actually, I don't understand your question "Where is the nitrile group". Could you please refrase it?


Thanks and best regards,


Akos

User 25d107bd42

01-12-2010 15:07:41

Hi Akos, thank you for your answer.


Corresponding to the nitrile question I have attached another screenshot image,one produced with Marvin 5.4.0.0 (upper) and the other with Marvin 5.3.8 (lower). The nitrile group of mandelic acid, which is the essential part of the glucoside amygdalin, is nearly hidden by the fog. Using 5.3.8 it is displayed and signified by the triple bonds.


Please implement the switcher as early as possible. And, if you cannot decide to set the default to "Off", please save the option in the setting file when the user changes this option. So the user must not always switch when using 3D display.


(F.e. , you have done this option saving for the Clean 3D Cleaning Methods some Marvin versions ago and this was a very good implementation).


Best regards, Hans-Ulrich

User 25d107bd42

01-12-2010 16:08:34

Hi, here one example more:


Doing some tests for my other topic about allene and C3H4 compounds I found the attached images for propnye. There is no possibilty to show all hydrogen atoms without critical fading.


Regards, Hans-Ulrich

ChemAxon 990acf0dec

01-12-2010 17:11:46

Hi Hans-Ulrich,


I see the point, but if you rotate the structure to have the nitrile group in the front, then it is visible very well.


Anyway, we are going to implement the optional switch off, and it will be "remembered", so it will be still switched off upon the next startup.


Best regards,


Akos

User 25d107bd42

01-12-2010 17:28:41

Hi Akos, two comments more:


"if you rotate the structure to have the nitrile group in the front, then it is visible very well"


Of course, but first I have to know where it is.


And for the propyne example, I didn't find a rotated position to see all four hydrogens very well.


But it's good to read this option will be "remembered".


Thank you and best regards, Hans-Ulrich

ChemAxon 990acf0dec

01-12-2010 17:32:20

Yes, we could also increase the visibility of the farthest atoms and bonds a bit. We try to improve that as well.


The original purpose of this feature was to somehow visualize the distances between the z coordinate, e.g. during the rotation of 3D structures, and I still think it is good for that purpose. To take an example from your snapshots: can you tell me which hidrogen is closer and which one is farther on your last snapshots (5.3.8, on the right)? Is the bond to the rightmost hydrogen really collinear with the triple bond on the left? On that snapshot it looks like it is ;-)


Best regards,


Akos

User 25d107bd42

01-12-2010 18:02:13

Hi Akos,


"we could also increase the visibility of the farthest atoms and bonds a bit"


that's a good idea. So we will have the advantage of both representations


Best regards, Hans-Ulrich

ChemAxon 990acf0dec

21-03-2011 15:47:13

Hi Hans-Ulrich,


 


As you might have found it already, we introduced an option in version 5.4.1 to be able set the strength of the fog effect or switch it off completely. (Edit > Preferences, Display tab.)


In the upcoming 5.5 release we would like to modify the setting for the Automatic fog-effect, and I would like to ask your opinion on it:


- What do you think the default fog effect strength should be on a 0-100 scale? (0: no fog-effect, 100: maximum fog-effect)


- Do you think it would be good to have different fog-effect settings (changable in the View menu) optimized for: A. Monitor, B. Projector, C. Printer?


 


Thank you for your feedback in advance.


 


Best regards,


 


Akos

User 25d107bd42

21-03-2011 17:46:20

Hi Akos, here some answers to your questions:


1) The option setting is a little bit inconsistent. As you see in the screenshot 01 having "Automatic fog effect" set to [ON], but there is no fog effect. And I cannot scale the effect ??


2) In the second screenshot 02 the fog effect is set to "Strong". Do you see the carbonyl group of mifegyne. There is no need to have "Strong".


3) In screenshot 01 I have changed the arrangement of the MarvinView and the MarvinSketch options. So it is clear which option belongs to which program.


My suggestions are:


4) There is no need to have a 0-100 scale. To much options are counterproductive: "Which one to choose?" Three options are enough: No - Middle - On, with the setting "Weak" -> "Middle" and "Middle" -> "On" and "Strong" deleted.


5) Do have different fog effect settings is very problematic: There are many different monitors. Projectors have different light intensity and different contrast. Projection screens are also very different. Which option to choose planning a presentation in an other university? No, there are other problems of MarvinSketch to be solved.


Sometimes simplicity is better.


Best regards, Hans-Ulrich

User 870ab5b546

21-03-2011 18:34:23

My two cents:  


I don't think you need different settings for Monitor, Projector, Printer.  Let the user figure out what is best for him or her.


I think the Automatic fog effect checkbox is redundant.  The slide is sufficient.  Where you have set the default is fine, and I think the labels on the slide are fine as they are.  

ChemAxon 990acf0dec

23-03-2011 18:23:21

Hi Bob and Hans-Ulrich,

Thanks to both of you for the suggestions.

I think a little explanation is needed (I just realized, that the documentation is not perfect; we will improve that as well):

Automatic means that the fading of the bonds and atoms happens according to the changes of the Z coordinate in 3D, so in smaller molecules the difference between the darkness of the colors of the neighboring atoms/bonds is bigger then in case of larger molecules, while the settings using the "slider" do not consider the Z coordinate.

Summarizing your suggestions, I think the following solution would be the best:

- Use the Z coordinate (molecule-size) dependent fading when setting the fog-effect factor with the slider, so it sets only the lightest color (or the darkest in case of a dark background)

- Rename the "Automatic" checkbox to "Default", or remove it completely (but then the default can only be retained together with the other settings on this tab, using the Restore Defaults button).

- There will be no custom settings for printer/projector, etc.

What do you think?

Best regards,


Akos

User 870ab5b546

23-03-2011 18:39:45










akospapp wrote:

Automatic means that the fading of the bonds and atoms happens according to the changes of the Z coordinate in 3D, so in smaller molecules the difference between the darkness of the colors of the neighboring atoms/bonds is bigger then in case of larger molecules, while the settings using the "slider" do not consider the Z coordinate.



I still don't understand.  How can the fog effect set by the slider not consider the Z coordinate?  Isn't the entire basis of the fog effect the displacement along the Z axis?

User 25d107bd42

24-03-2011 07:59:19

Hi,


"so in smaller molecules the difference between
the darkness of the colors of the neighboring atoms/bonds is bigger then
in case of larger molecules"


Otherwise there would be either no effect in small molecules or the effect would be too strong in large molecules. The fog effect gradient is inversely proportional to the "length" of the molecule in "z"-direction. For small molecules the gradient is higher than for large molecules.


Hans-Ulrich





ChemAxon 990acf0dec

24-03-2011 11:48:31

Hi,


Yes, correct Hans-Ulrich: if the automatic option is swithced on, the gradient is higher in case of smaller molecules, but when it is off, the there is no change in the gradient, so the use of the slider currently cannot work properly for both small and large molecules, but can be good if someone always work with similar-size molecules.


Best regards,


Akos

User 870ab5b546

24-03-2011 16:57:44

I see.  So the two options are, adjust gradient automatically to molecule size, or set gradient manually and have it operate regardless of molecule size.


But I can imagine someone wanting to have the gradient adjusted to the molecule size, but to have the greatest fog effect be smaller than what you would have set automatically.  

ChemAxon 990acf0dec

24-03-2011 21:36:39

Hi Bob,


Yes, this is why I suggested for the slider in my penultimate comment that "Use the Z coordinate (molecule-size) dependent
fading when setting the fog-effect factor with the slider, so it sets
only the lightest color (or the darkest in case of a dark background)".


And in this case we proably do not need the "automatic" option at all (except if we use this for retaining the original setting, but in this case we should call it "default" or so).



Best regards,


Akos

User 25d107bd42

25-03-2011 09:19:52

Hi, before suggesting new settings for the 3D fog effect here three tests.


Test # 1: The "Restore Defaults" setting [v] Automatic fog effect "On" doesn't show any fog effect. This bug I have already shown in an earlier post in this topic (Mon Mar 21, 2011, FadingDisplay01.png). But, as shown later, we don't need the "Automatic" option.


Test # 2: [ ] Automatic "Off" and using the default scale setting shows the stearat anion in a good display. The fading effect shows the long anion (24.9 A, according to the Marvin Geometry Tool) very fine.


Test #3: Here the fading effect is shown in two screenshots for two anions with different length (Not simultaniously). Top and end of the anions have the same grey color.


BTW: As already discussed in other topics, the "minus" should be larger. Please use a larger font size for the charge sign of ions.


In my next post I will give my answers to Akos' questions four days ago.


Regards, Hans-Ulrich

User 25d107bd42

25-03-2011 10:05:03

Hi,


here my suggestions for handling the 3D fog effect, please see the attached "manipulated" image. The example is cholesterol.


First some design changes:


1) The "Font Size" should be in the table on the left side, where it belongs.


2) The Option concerning MarvinView should not be intermixed in the MarvinSketch options. So it is now down in the table on the right side.


Now the changes to the fog effect:


3) The title line includes "3D". (for 2D representations the settings here are without effect).


4) The "Automatic fog effect" is totally deleted. We don't need it. The automatic setting is given by "Restore Defaults" and that's it.


5) The scale is in the old design and the default setting is "Medium". If someone wants to have weaker or stronger fog effects, here is the slider to change it.


6) The "No" fog effect option is clear enough for those who want the have no fog.


I think the intuitive design of GUIs is a very important thing. Many questions in this forum come from misunderstanding or disinformation of the user. And: Redundancy is a good thing !


And, as I have already given here: More simplicity and less options is often better.


Best regards, Hans-Ulrich

ChemAxon 990acf0dec

25-03-2011 11:30:13

Hi Hans-Ulrich,


Thank you for your suggestions on the Preferences dialog, and also for your deep investigation of the fog-effect.


- The Test1 in your previous message is clearly a bug, which must be related to the explicit hydrogens, but we don't know why yet. We will investigate it, and try to fix it still before the 5.5 beta release. (With the removal of the "Automatic fog effect" option it will be hidden anyway, but we have to find the source of it.)


- Your suggestions regarding the Display tab of the Preferences dialog are good, so we will redesign this tab of the dialog, but I don't think we have time for this before 5.5, so this will come in the next release I guess.


But:


You didn't tell if the molecule-size weighted fog-effect is a good think or not. I understand, that you might thought that the "automatic" option does not work at all, but if you try it without explicit hydrogens, you may understand its purpose: for bigger molecules a deeper fogging is used, so a lightest/darkest color is used for the back/front of the molecule. I think it should be applied on top of the strength setter.


Best regards,


Akos

User 25d107bd42

25-03-2011 12:53:58

Hi Akos,


OK, without hydrogen it works, see attached image.


But it is not worth to have a special option for it. If someone wants to change the display in this way, it can be done using the slider. And to change the lightest/darkest color used for the back/front of the molecule may look good, but is it worth the effort ? If I would really want to "design" such a display, then I am against "automatic" design, where I don't know the algorithm and the parameters. Then I need two sliders, one for the front and one for the back. So I would be able to design the carboxylgroup of these fatty acid anions with the same fading ... No. Let me stop here.


Sorry, if I repeat my argumentation: To have this additional option would lead to new questions etc. Possible misunderstanding will produce more problems. Do not include this "Automatic" option.


And also once more, to see the anion charge is much more important.


Best regards, Hans-Ulrich

ChemAxon e500b51457

07-04-2011 06:02:14

Hi Hans-Ulrich,

We have fixed the problem when fading disappeared after adding the explicit hydrogens and removed the automatic option.
The fix will be available in Marvin 5.5.

Regards,
Erika

User 25d107bd42

07-04-2011 08:57:28

Hi Erika,


thank you. Now I have a reason more to await eagerly Marvin 5.5.


Best regards, Hans-Ulrich