Cannot open PDB file in MarvinSpace

Dear all,

I wanted to trying to upload protein structure file in .pdb format but i m getting an error message...

"cannot load file" after clicking details i m getting following messages:

at java.awt.EventDispatchThread.pumpEvents(Unknown Source)

at java.awt.EventDispatchThread.run(Unknown Source)

java.lang.RuntimeException: Internal error  in PDBImport, caused by null

Current record: processATOM

at chemaxon.marvin.io.formats.pdb.PDBReader.processRecord(PDBReader.java:672)

at chemaxon.marvin.io.formats.pdb.PDBReader.readPass(PDBReader.java:635)

at chemaxon.marvin.io.formats.pdb.PDBReader.read(PDBReader.java:565)

at chemaxon.marvin.space.MSpaceEventHandler.readPDB(MSpaceEventHandler.java:367)

at chemaxon.marvin.space.MSpaceEventHandler.readMoleculeFile(MSpaceEventHandler.java:473)

at chemaxon.marvin.space.gui.JMSpaceMenuBar$32.run(JMSpaceMenuBar.java:1104)

at java.awt.event.InvocationEvent.dispatch(Unknown Source)

at java.awt.EventQueue.dispatchEvent(Unknown Source)

at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)

at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)

at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)

at java.awt.EventDispatchThread.pumpEvents(Unknown Source)

at java.awt.EventDispatchThread.pumpEvents(Unknown Source)

at java.awt.EventDispatchThread.run(Unknown Source)

java.lang.RuntimeException: Internal error  in PDBImport, caused by null

Current record: processATOM

at chemaxon.marvin.io.formats.pdb.PDBReader.processRecord(PDBReader.java:672)

at chemaxon.marvin.io.formats.pdb.PDBReader.readPass(PDBReader.java:635)

at chemaxon.marvin.io.formats.pdb.PDBReader.read(PDBReader.java:565)

at chemaxon.marvin.space.MSpaceEventHandler.readPDB(MSpaceEventHandler.java:367)

at chemaxon.marvin.space.MSpaceEventHandler.readMoleculeFile(MSpaceEventHandler.java:473)

at chemaxon.marvin.space.gui.JMSpaceMenuBar$32.run(JMSpaceMenuBar.java:1104)

at java.awt.event.InvocationEvent.dispatch(Unknown Source)

at java.awt.EventQueue.dispatchEvent(Unknown Source)

at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)

at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)

at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)

at java.awt.EventDispatchThread.pumpEvents(Unknown Source)

at java.awt.EventDispatchThread.pumpEvents(Unknown Source)

at java.awt.EventDispatchThread.run(Unknown Source)

Hi, 

is your PDB file a standard one form the RCSB PDB repository? If yes, what is the 4 letter code of it?

If not, which 3rd party tool did you use to generate it? Can you share it with us or it contains a proprietary structure?

Regards

Miklos

Dear Miklos,

The pdb file is not having standard RCSB  code... we have generated it using some software... its protein structure called PfHsp90... the 3D structure is already published so there nthing as such proprietary in it...  I dont remember the tool which was used to generate it.... but i have the file.. 

Can you suggest me why marvin space is not accepting it?

Dear All,

As per the information i'm sharing a pdb file which I'm unable to open in marvin space.. 

Can you tell me how to do this?

Waiting for your reply

Regards,

Ankit

Dear Ankit,

Thanks for sharing the PDB file with us, it is a great help to trace back the problem. We will investigate and also try to find a workaround. I'll talk to you later.

Regards,

Miklos

Any luck with the file? Can you open it with your version?

I'm waiting for your reply

Regards,

Ankit

Hi Ankit,

i just wanted to inform you, Miklós is on holiday this week, and he is the one who deals with MarvinSpace issues. When he gets back, he will answer for your question as soon as possible.

Thank you for your patience.

Regards,
Istvan

Hi Ankit, 

Your file was not read due to a bug in our pdb import module. This bug has been traced back and fixed. It's release is scheduled in version 5.9.1.

Please accept our apologies for the inconvenience this bug caused.

Regards,

Miklos

so i cant work on it now? when will your new verison be release? please tell me that.... or if u can share some thing so that i can fix it in present version... i m really counting on it right now....

let me know if you can help?

You can workaround the problem by editing the PDB file. If this suits you then I try to figure out the minumum changes needed.

Yeah please if can either make changes in the pdb file i have shared with you and send the the altered file with minimum few changes.... it will be a good help which can work on this 5.9 version?

I'm not a software developer so kinda difficult for me to look into specifics of file format and changes required. Hope you understand the problem.

Please suggest some solution

waiting for your reply

Regards,

Ankit

Hi Ankit,

Version 5.9.1 has been released, it should solve the PDB import issues. Can you try and check it?

Thanks, Miklos