ChemAxon 89bfcec588
24-07-2009 03:19:36
I use your Marvin Bean to convert sdf files to jpg files. We used to
do it with Chemdraw, but I have not figured out how to make it
automatic using Chemdraw. A couple of small problems I have
encountered: (1) When exporting in jpg, the background is not clean
when using antialias, and the structure does not look good without
it; (2) Chemical groups like COOH are not placed at the correct
position. (The bond was supposed to be connected to the C letter,
but in most cases it was pointing to the middle of the group); (3) I
need it to export to eps file, but it does not have this function,
while using other software to convert the jpg file to eps file does
not produce good result. But I guess these are just my problems. I
would not recommend you working hard on them unless there are demands
from other users as well.
ChemAxon 0a9e2a55e1
24-07-2009 17:59:20
Hi,
My colleague who is working on image export is on sick leave now. He will answer You when he is back.
Best Regards,
Peter
ChemAxon 7c2d26e5cf
27-07-2009 12:52:55
(1) When exporting in jpg, the background is not clean when using antialias, and the structure does not look good without it;
I guess when you talk about clean background, you think on transparency. Current Marvin does not support transparent background in JPEG export. Antialiasing is a property of line drawing. In default, antialiasing is switched on. If you switch it off, the drawn lines will be less smooth.
I recommend to use PNG format, Marvin's PNG export support transparent background:
molconvert png:transbg 1.mrv -o 1.sdf
(2) Chemical groups like COOH are not placed at the correct
position. (The bond was supposed to be connected to the C letter,
but in most cases it was pointing to the middle of the group)
Can you show a concrete example when bond was not connect properly to the COOH group?
(3) I need it to export to eps file, but it does not have this function, while using other software to convert the jpg file to eps file does not produce good result.
I don't think that converting JPEG to EPS is a good idea. JPEG is a raster image, meanwhile EPS is a vector graphics format. The quality of the EPS will be poor if you would like to scale the converted raster image.
If you need EPS, I recommend to convert SVG or PDF into EPS. Marvin supports both formats.
User fef2a60ce0
21-05-2011 08:12:53
Can you email me a way of converting .sdf to .jpeg or .png using molconvert ? I have installed Marvin beans and tried to run the command line
molconvert png:transbg 1.mrv -o 1.sdf
it says molconvert is not recognised as a internal or external command, operable program or batch file
Thamks
Sam
ChemAxon 7c2d26e5cf
23-05-2011 09:20:01
I have to say that the given statement is a bit strange.
It converts an MRV file into PNG image format meanwhile the output file is an SD file (1.sdf). The extenstion can be misleading later. If somebody receives this file, he expects an SD file but in fact it is an image.
I assume that you have tried launching the molconvert tool on a Windows machine. Can you confirm it?
The error message says that the molconvert batch file is neither in the PATH nor in the current directory.
You can choose among three options:
- Enter to the folder there the batch file is located and invoke the statement from there (the bin folder of the Marvin Beans or the installed JChem package: C:\Program Files\ChemAxon\MarvinBeans\bin or C:\Program Files\ChemAxon\JChem\bin
- Refer to the batch file with its absolute path in the statement
C:\Program Files\ChemAxon\Marvin Beans\bin\molconvert
- Insert the folder of the batch file into your system PATH to be able to refer any executable from the folder without full path. If the referred folder is in the PATH, you can use the original statement.
User fef2a60ce0
24-05-2011 23:55:27