Hi Wolfram, Yes, mmCIF has been suggested to PDB2PQR developers, see: https://github.com/Electrostatics/apbs-pdb2pqr/issues/471
Cheers, Thomas > On Dec 7, 2017, at 8:06 PM, wtempel <wtem...@gmail.com> wrote: > > Thomas, > how did you know? I removed the --whitespace switch, and get a meaningful > model displayed in PyMOL. Has the mmcif format been suggested to the PDB2PQR > developers? > Many thanks. > Wolfram > > On Thu, Dec 7, 2017 at 3:01 AM, Thomas Holder <thomas.hol...@schrodinger.com> > wrote: > 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
