MDAnalysis HOLE problem

[Rulong. Ma]

Dear  MDAnalysis  developers ,  

I am a new user of MDAnalysis. First of all, thank you for developing this software.  

I had a problem when I analysis pore dimensions with HOLE (https://userguide.mdanalysis.org/stable/examples/analysis/polymers_and_membranes/hole.html#Using-HOLE-with-a-trajectoryp-loop)   

Your example (using HOLE with a PDB file) works well on my computer. (in this example, Note that we pass HOLE a PDB file directly, without creating a MDAnalysis.Universe.) However, there is a problem when I worked on my PDB file. I used command (u = MDAnalysis.analysis(“my_pdf_file.pdb”)) to load my PDB file. But it is not work on your script.  

h = hole.HOLE(u, executable='~/hole2/exe/hole', 

              logfile='hole1.out', 

              sphpdb='hole1.sph', 

              raseed=31415) 

  

the attachment has the script and outputs, could you help to solve this problem. Thank you in advance.  

[Lily Wang]

Hi Rulong,

Welcome to MDAnalysis! Please let me know if there is a better way to address you than Rulong.

(in this example, Note that we pass HOLE a PDB file directly, without creating a MDAnalysis.Universe.) 

I think the issue with your script may lie here. What happens if you try the below?

h = hole.HOLE(“my_pdb_file.pdb", executable='~/hole2/exe/hole', 

              logfile='hole1.out', 

              sphpdb='hole1.sph', 

              raseed=31415) 

If you want to use the analysis with a Universe, you may want to try using the HoleAnalysis class instead.

Cheers,

Lily

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<hole_problem.pdf>

[Rulong. Ma]

Hi Lily,

Thank you for your help.

after run your script,  these are still  some issues, here is the output.

[Lily Wang]

Hi Rulong,

It seems to suggest that you don’t have anything in your profiles dictionary. This dictionary is created when you call collect() and it reads the hole output from hole.out . Maybe that didn’t execute correctly? What is in hole.out ?

By the way, if your version is > 0.20.1, you should also have access to the updated HOLE analysis class. This is likely easier to troubleshoot. The user guide has an example of how to use the updated HOLE analysis in the development version here.

Cheers,

Lily

To view this discussion on the web visit https://groups.google.com/d/msgid/mdnalysis-discussion/842a2bf0-ebc1-48c5-ba9e-193211327a37n%40googlegroups.com.
<hole_problem.png>

[Rulong. Ma]

hi

[Rulong. Ma]

HI Lily,

Thank you for you reply,
the example in your updated HOLE analysis class works well in my computer  ( https://userguide.mdanalysis.org/dev/examples/analysis/polymers_and_membranes/hole.html ). However, it does not work my PDB file. In the your example, you used  PDB_HOLE (from MDAnalysis.tests.datafiles import PDB_HOLE). Here, I have a question: do you make any changes in original pdb file (to create PDB_HOLE)  for HOLE software?   (could you give me a genernal example that works on my PDB file?)

the attachment are the script and outputs. thanks.

[Rulong. Ma]

[Oliver Beckstein]

Hi Rulong,

Your output indicates an error in HOLE finding atoms for “DOP” residues. I don’t know if this stops HOLE or not but if you run HOLE on its own (as opposed to HoleAnalysis) you might need to clean up your PDB file and only include protein. At least that’s something to try. You could also try ignore_residues, something like hole(PDB, ignore_residues=[“DOP”], ...) 

With HoleAnalysis you can exert better control with the select=“protein” kwarg.

Oliver

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<hole_issue.pdf>

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[Rulong. Ma]

HI Oliver

The issue was solved.  the "DOP" should be the lipids.

Thank you so much,