protein-RNA results are AWOL since APBS 1.0.0

[keith923]

The README.html file has not been updated since 1.0.0. The test is also not being run from the new-fangled Python-based testing script.

I do not know if this is in error, or if something changed. If the latter turns out to be the case, perhaps we can move the example to a "historical" directory, under examples?

[sobolevnrm]

Hi Keith --

This is an important example so I'd like to include it. There should be
two scripts: a test script and another script that runs a series of
calculations at different ionic strengths to calculate the number of ions
linked to binding. Are both scripts there? Do they work?

Thanks,

Nathan

On Tue, Jul 15, 2014 at 4:55 PM, Keith T. Star [email protected]
wrote:

The README.html
https://github.com/Electrostatics/apbs-pdb2pqr/blob/7c0f57e0699e40bf92b2182deaf7889a35ea8ec7/apbs/examples/protein-rna/README.html
file has not been updated since 1.0.0. The test is also not being run from
the new-fangled Python-based testing script.

I do not know if this is in error, or if something changed. If the latter
turns out to be the case, perhaps we can move the example to a "historical"
directory, under examples?

—
Reply to this email directly or view it on GitHub
#149.

[keith923]

There are two bash scripts and a Python script, as well as a Makefile.in and a Makefile.am. I'll have to dig into it a bit to get it working, since the bash scripts want to be called from make. Everything does appear to be there though, so I don't currently see any reason why it can't be made to work.

@lizutah, I'm going to add this issue to the milestone for the current release.

[keith923]

Also @sobolevnrm, this link in the README.html file is dead. Can you verify that this one that I discovered is a proper replacement?

[keith923]

@sobolevnrm one more thing. It's always "one more thing", right?

In Makefile.am, as well as on the above webpage, I noticed that the set of ion concentrations skips 0.200, which appears to be a mistake. Is it in fact a mistake, and I should add that in, or shall I leave it as is?

[sobolevnrm]

Yes,
http://www.poissonboltzmann.org/apbs/examples/binding-energies/ionic-strength-dependence-of-peptide-rna-interactions
is the correct link.

On Thu, Jul 17, 2014 at 12:41 PM, Keith T. Star [email protected]
wrote:

Also @sobolevnrm https://github.com/sobolevnrm, this link
http://apbs.wustl.edu/MediaWiki/index.php/Ionic_strength_dependence_of_peptide-RNA_interactions
in the README.html file is dead. Can you verify that this one
http://www.poissonboltzmann.org/apbs/examples/binding-energies/ionic-strength-dependence-of-peptide-rna-interactions
that I discovered is a proper replacement?

—
Reply to this email directly or view it on GitHub
#149 (comment)
.

[sobolevnrm]

Skipping that concentration is likely a mistake and it would be great if
you can fix it.

On Thu, Jul 17, 2014 at 12:57 PM, Keith T. Star [email protected]
wrote:

@sobolevnrm https://github.com/sobolevnrm one more thing. It's always
"one more thing", right?

In Makefile.am, as well as on the above webpage, I noticed that the set of
ion concentrations skips 0.200, which appears to be a mistake. Is it in
fact a mistake, and I should add that in, or shall I leave it as is?

—
Reply to this email directly or view it on GitHub
#149 (comment)
.

[keith923]

Excellent -- yes, I'll fix it while I'm in there making the scripts work without the automake stuff. Sometimes it's good to be a little bit OCD. 😉

[keith923]

I'm putting this off in favor of releasing sooner, per @lizutah's suggestion.

[pzli3]

When running the template file, the error non-float (IONSTR) while parsing ION conc keyword came up. After going through both Makefile.in and Makefile.am (which can no longer be compiled to make the template because of a switch from automake to cmake) Kyle noticed the ion string is not being replaced by the values in line 389 of the Makefile.in. You can get the apbs to run the template by making a copy and replacing "IONSTR" with the values (or at least 0.025) worked.

edit: not sure how accurate numbers are

[keith923]

Peter's above comment comes from the work he did for the tutorial.

[kozlac]

If people follow Peter's tutorial, the downloads fail for the python script and shell script can't with the error that the server can't find the file. (e.g https://raw.githubusercontent.com/PEMIfolder/github.io-PEMIfolder/gh-pages/Tut_scripts_PR/apbs_unix_dx.py). All the scripts are displayed and they can be cut and pasted. However the instructions would have to be changed.

[kozlac]

Got the example to run. The issues are:

1. The scripts and bash download links are/were down in the tutorial webpage. This is in issue Server Can't Find Download Files in the Protein-RNA Tutorial Page #348.
2. The template.in file is missing write statements to print dx file that dxmath will use later.(Also, in the tutorial it ask to rename template.in to template.txt why don't we have it like this to begin with?).
3. Like pzli3 mentioned above the makefiles can't be run anymore.
4. I had to manually add dxmath to my path. I am guessing this may be done at building time? Otherwise, it may be useful to comment you have to do it or show how to do it in the tutorial.

Do we want to create cmake files for this? Or how do you want to proceed @lizutah , @keith923 ?

[keith923]

This still needs to be integrated into the automated unit tests.

[keith923]

I've incorporated these tests into the test suite. I think that we still need a README.md file in the directory to mirror what's in the other example directories.

[kozlac]

I can do the readme's unless you really, really, really want to do it.:)

[keith923]

That would be perfect! Thanks @kozlac!

[kozlac]

Table is there. Will be updated as per issue #407. Closing issue.