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dimchris / mdanalysis

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Can't write single frames at all while using xtc files, creates infinite loop #114

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. u = MDA.Universe("prot.pdb", "traj.xtc") 
2. u.trajectory[x] 
3. u.atoms.write("output.pdb") (OR u.selectAtoms('all').write("output.pdb")

What is the expected output? What do you see instead?
A single frame in a pdb. Just like the issue 99.

What version of the product are you using? On what operating system?
MDAnalysis0.7.5.1, Ubuntu 12.04

Please provide any additional information below.
Just like issue 99 this creates an infinite loop which writes the same frame 
over and over again to the same file. I've tried doing the same thing several 
different ways (W = MDA.Writer and using the PDBWriter instead of 
PrimitivePDBWriter etc.), almost all (I couldn't get the PDBWriter to work 
properly to write a single frame) gave the same error. Issue 99 seems to be 
resolved but as far as I can see it only addresses the issue where x = -1 (the 
last frame) whereas the issue raises (at least for me) for any value of x. I'm 
assuming it has to do with the fact that I'm dealing with xtc files.

Original issue reported on code.google.com by asinansa...@gmail.com on 8 Jun 2012 at 5:23

GoogleCodeExporter commented 9 years ago 
Hi,

This problem was fully addressed in Issue 105. This is fixed and will be 
working in the upcoming 0.7.6 release (end of June). It is fully working in the 
current DevelopmentBranch.

Thanks for reporting.

Oliver

Original comment by orbeckst on 8 Jun 2012 at 6:24