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rlabduke / probe

Evaluate and visualize protein interatomic packing
http://kinemage.biochem.duke.edu/software/probe.php
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Probe 2.23 leads to slightly different results than 2.21 #11

Open tillea opened 2 years ago

tillea commented 2 years ago

Hi again as I reported in issue #9 we now again have a change in the checksum of results between version 2.21 of probe (which was the last one we have packaged) and the latest version 2.23 I intend to package for Debian. Is this change expected again? Would you be able to craft some test suite from your side we can simply run to prove expected behaviour? Kind regards Andreas.

russell-taylor commented 2 years ago

Andreas,

Thank you for updating the Debian packages and also for continuing to check to make sure the changes are desired.

In this case, I pulled some changes into the main branch so that the Richardson Lab can test them in MolProbity before we're sure that the results are better. I recommend that you maintain the previous version until that testing is complete. I'll let you know when that is.

The longer story is that we're developing a version of Probe that is embedded in the CCTBX Python library and our regression tests are turning up issues in the C code that should be improved. This one removes marking atoms in 5-membered Aromatic rings as Acceptors, which should prevent Hydrogen bonds to the rings from the side.

Thanks, Russ

tillea commented 2 years ago

Hi Russ, Am Mon, May 02, 2022 at 05:50:21PM -0700 schrieb Russell Taylor:

I recommend that you maintain the previous version until that testing is complete. I'll let you know when that is. OK, I'm just waiting for your signal. Thanks a lot, Andreas.