[Cventura18]

Fixed an issue where systems with membranes wouldn't be prepared with probes. Also fixed an issue were the topology of some probes were not correct and prevented other probes from being used

[anupam-banerjee]

Thanks for this, Carlos. The probe assignment rewrite is a good fix.

A few observations from reading the diff.

no_gui.py, water at psfgen. The rewrite replaced both of the old selectors with one, so $sel is still the OH2-only selection when writepdb is called, where main widens to whole residues first. If I am reading it right, psfgen would receive oxygens without their hydrogens and guesscoord would have to place them, which TIP3 cannot support since it has no internal coordinates in probe2.top. Widening the first selector looks sufficient, as the renumbering keys on resid and all atoms of a water share one.

                set sel [atomselect top "segid $segidWT and (same residue as index $indicesWater)"]

no_gui.py, renumbering key. dict exists $seen $resid assumes resids are unique within a segment, and the resid field wraps past 9999. [$sel get residue] would sidestep that, and is identical wherever resids are already unique.

                set resids [$sel get residue]

Pre-existing, if you would like to pick them up. maxLz reads the min corner of the lipid bounding box in both files, where the max corner looks intended given how minLz is built just above it. As written the core-slab exclusion of water and probes would be inert. Could you confirm the intent before anyone changes it?

-                maxLz = "expr [lindex [lindex $minmaxL 0] 2] - 10"
+                maxLz = "expr [lindex [lindex $minmaxL 1] 2] - 10"

gui.py also still carries if {$neutral}{, the same parse error fixed here in no_gui.py.

-                    if {$neutral}{
+                    if {$neutral} {

Happy to test in VMD once you have had a look.

[Cventura18]

Thanks Anupam. I think the suggestions you mentioned make a lot of sense. The intent is to the max corner.