Background color and Hydrogen display in MSpace

Hi, I have two inconveniences which are connected.




1) After opening a molecule in MSketch I can display it directly in MSpace, using "View-Open MSpace". It's a fine feature, see the upper screenshot bf0078.


But the background is black. This is very bad if you want to take a screenshot and put it in a paper. And I found no option to change the color of this background.




2) So I have to save the molecule and to open it in MSpace seperately. Then I can change the background to white and can do the desired screenshot or save the image. OK.


But, when I start MSpace once more, the background is black once more. The background setting is not stored. So you have to change it each time you start MSpace.




Looking in the file ~/.chemaxon/marvin.properties I find the lines


"saveGUIproperties=false" and "readGUIproperties=false", see screenshot bf0079.


Do these lines belong to the context in 1) and 2) ?




Is there a workaround editing this file?




BTW: It is interesting to look in this file. The second [...] corresponds to a very long list of items. I have edited it, to short the file for the screenshot.




Regards, Hans-Ulrich

Dear Hans-Ulrich,

Quote:

1) After opening a molecule in MSketch I can display it directly in MSpace, using "View-Open MSpace". It's a fine feature, see the upper screenshot bf0078. But the background is black. This is very bad if you want to take a screenshot and put it in a paper. And I found no option to change the color of this background.

We are planning to launch a full-featured MSpace from msketch/mview. This probably will be included in 5.1.3. Upon release this feature we will inform You in this topic.

Quote:

But, when I start MSpace once more, the background is black once more. The background setting is not stored. So you have to change it each time you start MSpace.

Currently MSpace does not store bacground or other view settings. As far as I know implementing this feature is not scheduled in the imminent future.








Regards,


Gabor

Dear Gabor,


OK.


But one tiny modification could be easily done: After opening a molecule in MSketch you can display it directly in MSpace and the background is black.


Why is it not white ? This could easily done by changing one line in the JAVA code using "Color.white".


As I have argued above, white would give an easy possibilty to use the display via screenshot, without separately starting MarvinSpace.





Regards, Hans-Ulrich

Dear Gabor,


and here more comments about MarvinSpace.





While evaluating the MarvinSpace option "Save screen as..." I found a super feature: Saving the screen in PNG format produces a picture without background, i.e. with a transparent background, see the screenshot. So you can handle the molecules in a picture separately and compose impressive demonstrations and the color of the original screen is arbitrary. Super !





Caution, this is only possible in PNG format. In JPG transpareny is not implemented.





But there is also another thing: Using "Export image..." in PNG format does not produce a transparent background. This should be equal to the option "Save screen as...".





Regards, Hans-Ulrich

Dear Hans-Ulrich,

Quote:

But one tiny modification could be easily done: After opening a molecule in MSketch you can display it directly in MSpace and the background is black. Why is it not white ? This could easily done by changing one line in the JAVA code using "Color.white".

Since traditionally white background is associated to the 2D sketching/viewing and black to 3D view, it is supposed to use black by default in MSpace. However as i mentioned above, we plan to allow change GUI settings of MSpace launched from msketch.

Quote:

But there is also another thing: Using "Export image..." in PNG format does not produce a transparent background. This should be equal to the option "Save screen as...".

Currently image export has two different implementations: "Save screen as..." exports the image as displayed (graphics settings, 2D labels, etc) while "Export image ..." allows higher resolution but no transparency. As far as i know converging these two exports into single is nor scheduled yet.





Regards,


Gabor

Dear Gabor, to the first point: OK.





But to the second:

Quote:

"Export image ..." allows higher resolution but no transparency. As far as i know converging these two exports into single is not scheduled yet.

Yes, the higher resolution is a good feature. My wish is not to converge these two exports, but to export to PNG with transparency in both procedures. If someone wants to have a colored background, each pixel program can do it. But it is very difficult to erase a background color. Normally you erase some colored parts of the objects/molecules, too.





If you want to have a colored background, you can export in JPG and you have one.





To bring it out once more: Saving/exporting images with transparent background with high resolution would be a super feature. I don't know other programs (besides GIMP of course) which can do that. And I see no problem to program the export option in the same way as the save option.





I am so glowing about the transparent background that I must attach a second example, see below. (If you look accurately, you can see all atoms of vitamin C).





Regards, Hans-Ulrich.

Dear Hans-Ulrich,





I am sorry for being ambiguous about the image export: it is clear that image export functionality can accommodate further improvements, however currently we are not planning to allocate developer resources for this task in the near future.

Quote:

I am so glowing about the transparent background that I must attach a second example, see below. (If you look accurately, you can see all atoms of vitamin C).

Thank you. Btw, some times it is nice to add a slight "Drop Shadow" in Gimp to such an image with transparent shadow. As far as I know OpenOffice.org's Impress presentation software is able to handle the non fully transparent alpha channel for displaying it (see the attached images)

Dear Gabor,





OK. I agree there are more important topics.





And thank you for the tip. The molecules look realy three dimensional using "Drop Shadow".





Regards, Hans-Ulrich

Dear Gabor,





the point I will mention here it not worth a new topic, but it has to do with MSpace. It is only a little bit annoying: About 90 percent of the computer programs use CTRL-Q to quit or exit the program, MSketch and MView, too. But MSpace uses ALT-X. I think many users have "left hand hard coded" this CRTL-Q. So when you are anyway optimising MSpace, this could be changed. Probably it's only two lines in the JAVA code.





Regards, Hans-Ulrich

Dear Hans-Ulrich,





Thanks for the suggestion.





Regards,


Gabor

gimre wrote:

Dear Hans-Ulrich, Quote: 1) After opening a molecule in MSketch I can display it directly in MSpace, using "View-Open MSpace". It's a fine feature, see the upper screenshot bf0078. But the background is black. This is very bad if you want to take a screenshot and put it in a paper. And I found no option to change the color of this background. We are planning to launch a full-featured MSpace from msketch/mview. This probably will be included in 5.1.3. Upon release this feature we will inform You in this topic.

Please be advised that a full-featured MSpace application opens from msketch (release in version 5.4.1).

  

Hi Miklos,

thank you for the information. It's good to have now the full-featured MSpace application directly inside MSketch. But the bugs and deficiencies of MSpace are also implemented. Please see the attached image, produced in the following way:

Drawing benzonitrile inside MSketch, using "Clean3D with Hydrogenize" and then "View - Open MarvinView 3D" or "View - Open View MarvinSpace". These produce the images shown. MarvinView 3D is OK, but MarvinSpace still does not show the aromatic bonds and the triple bond. (And the hydrogens are only shown using "Display - Draw Type - Ligand - Hydrogens").

You know: These are old problems:

 https://www.chemaxon.com/forum/ftopic6633.html

 https://www.chemaxon.com/forum/ftopic4210.html

I still have the old question: Why is it not possible to transport the code of MarvinView3D, which is able to show all bond types a molecule can have, to transport it into MarvinSpace ?

Regards, Hans-Ulrich

 

 

Please be advised that new release of mspace (in version 5.5, to be out soon) will display triple bonds as well as aromatic rings.

This does not mean however, that bond types will be identified properly in all cases.

Regards

Miklos

Dear Hans-Ulrich, 

Please note that since version 5.5 MarvinSpace supports the visualisation of triple bonds and aromatic rings. 

Suggestions are welcome.

Regards,

Miklos

Hi Miklos, you see, I'm active this weekend ...

Yes, now MarvinSpace is really included in MarvinSketch and it able to show aromatic rings and triple bonds. It's really a highlight of Marvin.

But to come back to the original title of this topic: The starting background is still black. Unusable for publications. So I have to do each time I'm using MarvinSpace six setting steps: Display - Options - Colors - Backgound Color - white - Apply OK. And this I must do each time starting MarvinSpace once more.

Please implement now saving the settings of MarvinSpace, too, just as MarvinSketch is doing it already in most cases.

Having now MarvinSpace really "inside" MarvinSketch (using Ctrl - Shift / M) the settings should be stored.

I have used the Amygdalin example to show another deficiency: To show the essential hydrogen at the benzyl-position of the benzaldehyde derivative I have to do four setting steps: Display - Draw Type - Ligand - Hydrogens ON. Now this essential hydrogen is shown and this chirality center can be assigned as (R). Of course MarvinSketch shows this assignment, but to learn and understand these definitions MarvinSpace is better. So I will repeat:

Please implement now saving the settings of MarvinSpace, also for displaying hydrogens.

But may be I will start a new topic on "Displaying Hydrogens in MarvinSpace".

BTW: For newcomers is not obvious to find the shown molecule in the option "Ligand" . I know, this comes from the usage of MarvinSpace for displaying proteins. And to omit the hydrogens in large proteins and peptides makes sense, of course. So the settings should be saved for the protein chemists, too.

Best regards, Hans-Ulrich

Hi Hans-Ulrich,

you see, I'm active this weekend ...

indeed! Thank you!

Please implement now saving the settings of MarvinSpace, also for displaying hydrogens.

I understand the importance of this feature. We will implement it at some stage but not now.

Miklos

 

Dear Miklos,

it seems to me, the problem is: MarvinSpace doesn't save any settings, i.e. the possibilty to save it is not programmed in MarvinSpace.

But, there would be another possibility to enhance the usage of Marvinspace:

Set the default of the background color to white and of the display of hydrogens to on.

The display of hydrogens may be a hindrance displaying large molecules such as proteins, but in the example displaying the hydrogens on white background is a good combination, see the attached image.

What do you mean ?

Best regards, Hans-Ulrich

Dear Hans-Ulrich,

I understand the need for saving setting, and we will add this feature to marvinspace sometime. This will enable you to save the required background colour. at present we do not consider to change the default background colour, but I personally do not exclude this possibility.

Regards,

Miklos