Strange behaviour of pdf and color: monochrome ?

I wanted to save my reaction mechanism in monochrome for printing in black/white, which looks better if no colors need to be converted by the printer. Most colors (including the common red of oxygen) are printed as gray.

I set "View - colors - monochrome" and the structure showed the desired effect on the molecule: see msketch.png.

But as I told MarvinSketch to save it as a pdf it still showed the colors: see pdf.pdf.

Is there a way to tell MSketch to do the molecules completely in black when saving as a pdf?

 

Best Regards, jube

 

Edit: apparently the forum doesn't allow pdfs as attachements. I added it as a png, which kind of defeats the purpose of uploading a pdf...

Dear Jube, 

 

Thank you for your report. Unfortunately you can't export to pdf in monochrome color mode. I'm investigating this issue, and you'll receive my proper answer soon. Thank you for your patience.

 

Best Regards:

 

János Papdeák
software developer
Chemaxon Ltd.

Dear Jube,

We've found the solution for this issue. It will be fixed in Marvin 5.10. which will be released before the end of Q2 2012. Thank you for your report.

 

Best regards:

János

Thank you very much!

 

Unfortunately, I have found another issue with the export to pdf: If, in text mode, a 3 in HNO3 is written in subscript, it moves it somewhere else in the pdf.

moved3.png shows a screenshot of the canvas in MSketch, moved3-1.png shows a screenshot of the pdf.

Also, the number under the molecule shows a line break.

It strangely doesn't show this behaviour when testing with only the HNO3 on an otherwise clear canvas. I'm not sure if this movement happened because I used align and distribute?

Best Regards, jube

Dear Julia,

The original bug is fixed and it will be in Marvin 5.9.3  (it will be released in a week).

Although, I cannot reproduce the second bug could you send me the original mrv file please!

Thank you,

Efi

Thank you for fixing the bug, it works perfectly now!

And I think I found the problem with the linebreak in the text: If, in text mode, no window of a certain size is opened and MarvinSketch is allowed to choose the size of the text-field itself, it makes it a small bit too short.

I enlarged the field on the right border and now it works fine.

Perhaps there could be added a bit more space to the bordering?

I am glad that it works.

Thank you for fixing the color problem, but the second problem is still there. Did you note this problem and is it going to be fixed in a future release?

 

I will add two more pictures which once again show the error. This molecule is a problem that came up on the weekend.

canvas.png shows a molecule where letters are added to refer to the atoms for a NMR-spectrum discussion.

pdf.png shows the pdf output, where the letters are far away from the position where they should be.

The spacing from the text to the border should be bigger for text fields. I had to manually enlarge every single text field to solve this.

I found another bug with the export to pdf:

A file is saved as a pdf, and, at a later time, after changes are made, it is saved as a pdf again (same filename) and overwrites the old one (MarvinSketch asks if it should be overwritten).

But MSketch doesn't actually overwrite the file.pdf, the old file is still there. Deleting the pdf and saving it again solves this, but it is bothersome.

 

Best Regards, jube

Hi, 

I've moved the topic to the appropriate forum.

My colleges will answer you soon.

Regards, 

Peter

Dear Jube,

Thank you reporting this bug, we will fix it.

Best Regards,

Efi

The problem of the first post reappeared in Marvin 6.0:

If the color sceme is set to monochrome, it only is monochrome on the canvas. As soon as the molecule is saved as .pdf, the colors are back.

 

Best Regards,

Julia

I'll add my problem here, as it seems to be related: Marvin 6.0 (didn't test the older versions) does ignore custom coloring (via Right-Mouse-Click, Document Style, Apply Changes For Selected ...) when exporting PDF.

It does however work with (all?) the other exports!

I have the same problem.

Dear All!

   The coloring bugfix will be available in our next patch (6.0.1).

Regards:
Balázs 

Hello!

The color PDF bug seems to back in version 6.0.2 (Mac). At least I could't figure out how to save as a b/w PDF.

Best Regards,

Markus

Hi Markus,

unfortunatelly, you are right. We are checking what could happened, and fix the issue again soon.

Sorry for the inconvenience. We will improve also our QA process, after we found out how this issue could occure again.

Thank you for the report, if we know further details we will notify you in this topic.

Regards,
Istvan 

The problem of exporting colored pdf-files even though the coloring in the Marvin window is set to monochrome is still there. When will there be a fix for that?

Edit: Marvin 6.2.0

Best Regards, Julia

Dear Julia!

   Please could you check whether "Save / Load Gui settings (.mrv, .pdf format)" is selected in Edit-> Preferences -> Saev / Load (tab)? It works for me with this.

Regards:
Balázs

Dear Balázs,

The box was not checked, thank you very much, the export works now.

Is this the default setting, or not? I use a freshly installed Marvin. I didn't mess with these options.

If it is not the default setting, could this be implemented?

Best Regards, Julia

Dear Julia!

   Gui settings for MRV and PDF needs other defaults. Until these two features can not be separated I can not promiss any change. However I will pop up this request to our product owner.

Regards:
Balázs 

Dear Julia,

I am asking your patience on this issue, our decision maker (the product owner) is sick and she will be available possibly mid next week, you should expect the answer after she is back. I hope you are fine with the workaround Balazs gave you until we are able to improve Marvin and solve this issue.

Regards,
Istvan 

Hi Julia,

I understand your request and made a task in our issue tracking system; however I cannot promise to implement it in the near future.

Best Regards,

Efi