Formatting exported SVGs

User e3f03c303b

13-04-2015 00:42:29

Hi, 


I have noticed that SVGs made using MarvinSketch's export to image tool include six blank spaces in all atom labels. Is there any way of getting MarvinSketch to automatically not add these blank spaces to atom labels? 


Thanks for your time,


Brenton

ChemAxon f052bdfe3c

13-04-2015 16:12:31

Hi Brenton,


I was not able to reproduce this issue with our current (Marvin version 15.4.6. ) svg export, however we have fixed some svg related bugs recently. Could you check whether you see the blank spaces on the picture which I have generated and point out to them, please? Or can you send me an image on which these points are visible?


Thank you,


Efi

User e3f03c303b

13-04-2015 22:01:13

Here's the whitespace I'm talking about in your SVG. These spaces are why it's impossible for Inkscape to crop the SVGs that MarvinSketch produces as these spaces in the atom labels are interpreted as being part of the drawing.

ChemAxon f052bdfe3c

14-04-2015 12:33:18

Thank you. Now I could see the problem. I created a bug report in our issue tracking system, but unfortunately, I cannot promise a quick fix.


Best regards,


Efi

ChemAxon 4fa3cf533c

16-04-2015 14:13:33

Hi Brenton,


We haven't been able to identify the root cause - yet - but until then, I can provide a workaround for removing the extra spaces in the svg files. 


Open the svg file with some text editor, since svg is a simple xml formatted text file. 


Find the <text ...> </text>  tags, and inside them there will be an attribute called xml:space set to "preserve". Remove them, and the extra spaces will disappear.


I hope that his is a possible solution for you, and we will report back, when this issue has been solved.


 


Regards, 


Tamas Fazekas-Vígh

User e3f03c303b

17-04-2015 09:10:10

Thanks for your advice on how to correct this problem, sure beats removing these spaces manually in Inkscape. I was wondering if you might have a solution for the fact that MarvinSketch SVGs also has parts of it cut off (usually subscripts or hydrogens).  See the attached SVGs for examples of what I mean.


1st (Taurine.svg): notice how the H in the hydroxyl group is cut off. 


2nd (Glutamic acid (Glu, E).svg): notice how the 2 subscript is partially cut off. 

ChemAxon f052bdfe3c

17-04-2015 14:07:53

Hello,


I would like to ask which Marvin version do you use? The good news that I was not able to reproduce this cut-off with the developer  version which will be released next week *15.4.20). In the new version, margin can be set on the dialog which appears when you generate an  svg image.


Best regards,


Efi

User e3f03c303b

17-04-2015 14:42:55

Presently I'm using MarvinSketch 15.4.13. Ah that's good news, I've noticed this problem with versions back to the 6.x.x versions which was when I first started using ChemAxon software. Oh btw are there any plans on adding in-built updating capabilities for ChemAxon software (Marvin, JChem and Instant JChem included) such that the software can be set to automatically search for updates, download them and install them?

ChemAxon f052bdfe3c

17-04-2015 16:08:58

We certainly plan to have an auto updater in Marvin, I will ask the other teams.


Regards,


Efi

User e3f03c303b

21-04-2015 04:07:00

Hi, correct me if I'm wrong but isn't 15.4.20 meant to be released on 20 April 2015? If so it should have been released by now as it's presently 6 pm in Budapest (which as I understand it is where ChemAxon has its major headquarters) 21 April 2015. The other major headquarters of ChemAxon, as I understand it is on the East Coast of the U.S. where it just turned 12 pm 21 April 2015. 

ChemAxon f052bdfe3c

21-04-2015 09:11:08

We release the program weekly, the version number is always the data of the given Monday even if the actual release was on Friday.  Marvin 15.3.20 will be released today afternoon or tomorrow.


However, some doubt have arisen in the team whether we understand your workflow and problem correctly or not. Do you save the picture from MSketch UI or by Molconvert?  Do you modify the original Height and Width of the picture on the "Export of svg image" dialog? Or from code? ( It works properly with the default settings on my laptop. This leads to my next question: what kind of computer/OSX do you have?)


I am looking forward to your reply.


Efi

User e3f03c303b

21-04-2015 09:39:58

I use the GUI, not the command-line. My method & settings are shown in the screenshots. Ask if any additional info is desired. 


 


EDIT: Sorry, I didn't see your question about OS. My OS is 64 bit Windows 7 SP1 (I've changed the theme settings if you're wondering why it looks Mac OS X-like). Intel Core i5-3230M CPU @ 2.6 GHz, if needed. My PC's brand is Lenovo, if relevant. 

User e3f03c303b

21-04-2015 10:19:33

Is that today afternoon/tomorrow in Budapest time (UTC+1)? 

ChemAxon f052bdfe3c

21-04-2015 10:33:06

Yes. And thank you for the example.


Unfortunately with this settings the bug still exists. I am sorry. If you set the margin to 10.0, the cut off will not appear. 


Best regards,


Efi

User e3f03c303b

21-04-2015 10:41:42

Is there any way to set the default text font in the GUI so that whenever one tries to insert text (e.g., labels under skeletal structures) into a drawing in MarvinSketch it'll be the font-size and family that was set to default automatically? 

ChemAxon f052bdfe3c

22-04-2015 08:02:05

Unfortunately there is no way to set this currently. We are understand that this is an important issue and will work on it in the Q3/Q4 this year.


Best regards,


Efi

ChemAxon f052bdfe3c

22-04-2015 08:10:50

Sorry that I was not clear. If everything goes according to the current plans, we will work on this issue between August and December this year.


Regards,


Efi

User e3f03c303b

22-04-2015 13:41:49

Hi,


I've noticed another issue with MarvinSketch, isoleucine (3 letter code: Xle)'s symbol in the Advanced Templates toolbar is larger and otherwise differently-formatted (without the blue square brackets) than the symbols of the other amino acids in the toolbar. Attached is a screenshot I've taken showing what I mean. 

ChemAxon 5693b0ec15

23-04-2015 14:49:33

Dear Fusion 809,


 


thank you very much for your comment.


Could you summarize briefly how the amino acids were added to the Advanced Tool panel please?


Best regards,


Nikolett Mihala

User e3f03c303b

23-04-2015 15:18:31

Not sure, I honestly thought this was just how the "Advanced Templates" (View->Toolbars->Advanced Templates was how I enabled it) toolbar appeared by default. I added this toolbar probably over a year ago, so I must confess if there was some sort of configuration that was needed to be done I probably have completely forgotten it. Attached is the template library entry for the amino acid isoleucine which is represented abnormally in the toolbar. 

ChemAxon 5693b0ec15

27-04-2015 09:14:34

It's OK, thank you. 


The bug report was created in our issue tracking system and you will be informed in due course.


Thank you again.



Best regards,


Nikolett Mihala