GenerateMD example: tag is missing

User fc80487671

12-07-2013 14:41:55


Hi,


I am new to JChem and started looking
at the examples for GenerateMD
(http://www.chemaxon.com/jchem/doc/user/GenerateMD.html). When I run (on Fedora 18)
generatemd c molecules/nci1000.sdf -o
nci1000.sdf -S -k PF -c config/pharma-frag.xml
(example 3), only one
new tag (<PF>) is generated in the output file, the <PMAP>
tag is missing.


Similarly, when executing
'generatemd_example' (in JChem/Examples/bin from JChem for end users
and Java developers, version 6.0.2), the output file nci1000-PF.sdf
does not contain <PMAP> tags, and the displayed structures are
not coloured.


Do I have to change something in the
configuration file?


Thanks,
Anna

ChemAxon 5fc3e8d7d0

16-07-2013 10:53:42

Dear Anna,


Thank you for reporting this issue, we could reproduce it. We will try to solve it as soon as possible.


Best regards,
Laszlo

ChemAxon 5fc3e8d7d0

19-07-2013 13:06:15

Dear Anna,


 


I have fixed this issue. The fix will be available in the 6.1 or in the 6.2 version.

If you want to find only pharmacophore points (and display these using MarvinView), please visit the following link:
http://www.chemaxon.com/jchem/doc/user/PMapper.html (Example 4.)

Or use the following commands:
pmapper -c config/pharma-frag.xml -o nci1000.sdf -S molecules/nci1000.sdf
mview -t PMAP -p config/PF.colors nci1000.sdf

examples/bin/pmapper_example




 


Best regards,
Laszlo

User fc80487671

19-07-2013 13:58:21


Dear Laszlo,


 


Thanks explaining an alternative
option. Could you point out where I could find a summary of the
command line tools?


 


Thanks,


Anna

ChemAxon 5fc3e8d7d0

19-07-2013 18:29:34

Dear Anna,


List of available JChem command line tools can be found below:
http://www.chemaxon.com/jchem/doc/admin/prepscripts.html


 


Laszlo

User fc80487671

20-07-2013 14:37:44

Thanks.