Hi Wolfram, Do you run pdb2pqr with the --whitespace option? If yes, remove that and see if PyMOL is happy with the output.
Some versions of PyMOL's APBS Tools plugin have the --whitespace option by default (first page, "pdb2pqr command line options") but it seems that this flag creates about as many problems as it solves. The correct solution would be to retire the PQR format and replace it with mmCIF, which is not a fixed column format. Cheers, Thomas > On Dec 7, 2017, at 1:14 AM, wtempel <wtem...@gmail.com> wrote: > > Hello, > loading a pqr (PDB2PQR version 2.1.1) file into pymol 1.7 … 1.9 garbles the > model in some systematic way, whereas PDB2PQR version 1.8 output appears to > be displayed correctly. After superficial inspection I concluded that in > 2.1.1 output, columns from (and including) the atom number appear to be > shifted to the right by one position. Indeed, when I apply > sed 's/^ATOM /ATOM/', the so modified 2.1.1 output appears to be displayed > correctly in PyMOL. My question to those familiar with pqr models and the > pymol source: is the sed hack safe as in that it would not distort any > subsequently calculated APBS surfaces? > Best regards. > Wolfram Tempel -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
