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GenerateMD example: tag is missing
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Anna

Joined: 18 Jun 2013
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Link to postPosted: Fri Jul 12, 2013 3:41 pmPost subject: GenerateMD example: tag is missing Reply with quote

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

László
ChemAxon personnel
Joined: 14 Jan 2011
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Link to postPosted: Tue Jul 16, 2013 11:53 amPost subject: Reply with quote

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

László
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Link to postPosted: Fri Jul 19, 2013 2:06 pmPost subject: Reply with quote

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

Anna

Joined: 18 Jun 2013
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Link to postPosted: Fri Jul 19, 2013 2:58 pmPost subject: Reply with quote

Dear Laszlo,

 

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

 

Thanks,

Anna

László
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Link to postPosted: Fri Jul 19, 2013 7:29 pmPost subject: Reply with quote

Dear Anna,

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

 

Laszlo

Anna

Joined: 18 Jun 2013
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Link to postPosted: Sat Jul 20, 2013 3:37 pmPost subject: Reply with quote

Thanks.

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