Hello,
I use PDB read node from MOE.
I need to specify the path for the PDB file.
To automate this, I would like to control the PDB file with a flow variable. ie, instead of selecting a set of files, I would like to specify this set in a flow variable then PDB read node reads this set automatically.
In flow variable tab, I cannot choose a valid flow variable.
Thanks,
Iâm not sure about the MOE PDB Read node, but there are several nodes for reading PDB files in the Vernalis community contribution:
If you want to download from RCSB PDB starting from a list of PDB Structure IDs, then there are these two (a source node and a manipulator, if your IDs are in a table column):
https://kni.me/n/JgeezXz08XDs2LE4
https://kni.me/n/QcKIYttzPhj--4rc
Alternatively, if your PDB files are stored on your filesystem, then the following two nodes will do the job. Again, there is a manipulator node, which accepts an incoming table with a column containing paths to the files:
https://kni.me/n/5ZwlFg52o2J_RFux
And a source node, which allows you to add one or more files from the node dialog, or via a flow variable:
https://kni.me/n/mLwLL3kbsSsLXbL7
Steve
4 Likes
Hi Steve,
The Load Local PDB Files can do the job that I need. It did not work when I put this node between âTable Row to variable loop startâ node and an âEnd Loopâ node.
Is it possible to get rid of this loop and feed all the column that contains the paths for the PDB files in one go.
Thanks,
3 Likes
The PDB Loader node should be able to replace the whole loop.
Could you tell me the error message for the Load Local PDB Files node, as it should work, however?
Thanks
Steve
2 Likes
I have to choose only one row from the list in the column of URL as you can see in the picture.
I would like to feed the node with all the files in one go.
Add a Groupby node immediately after your List Files node, no grouping columns, and concatenate with ; as deliminator, or just use the âPDB Loadwrâ straight after list files
Steve
2 Likes
Hi @s.roughley and @Vernalis ,
I tried your method as the workflow shows
I get this error.
ERROR Load Local PDB Files 3:98 Execute failed: Unable to download file after 5 tries
I see the correct list of paths in the flow variable that I specify in the âLoad Local PDB Filesâ nodes.
I tried the different encoding but I get the same error:
ERROR Load Local PDB Files 3:98 Execute failed: Unable to download file after 5 tries
I put below a portion of my workflow. My goal is to call a number of files from a specific folder. Only the files that contain a specific string in their titles should be selected. To achieve that, I used String Manipulation to add a star * to the keyword that I am serching in files titles (ie: red* instead of red), then I convert this string to a variable, then I send it to GroupBy node and Table column to variable node then I obtain the error in the last node (Load local PDB files).
Is there any solution?
I am stuck.
Thanks,
I would strongly suggest using List Files followed directly by the PDB Loader node
You can see how to do thisin the second part of the example workflow at:
Steve
1 Like
Thanks @Vernalis @s.roughley Steve,
Are you aware of any node or script that can convert the PDB to mol in Knime?
I would lieke to use the RDkit despritors for these proteins.
I tried Molecule Type Cast node but failed to convert PDB.
Thanks,
Does the MolConvertor node from the free Marvin nodes do it?
https://www.knime.com/free-marvin-chemistry-extensions
RDKit can take PDB as an input now, but it is not enabled in KNIME yet to my knowledge - @greglandrum - maybe that should be a feature request?
Steve
1 Like
@s.roughley,
MolConvertor from Marvin did not work but the one from MOE did. 
Thanks,
2 Likes
Makes sense to me.
Thereâs an old feature request open for this already that has somehow been forgotten:
3 Likes
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