Hi Warren, run pdb2pqr with the "--whitespace" argument to make sure the columns are separated with whitespace.
If you still want to adjust the coordinates, you can use the "alter_state" command in PyMOL. alter_state 1, all, (x,y,z)=(x+100,y+100,z+100) http://www.pymolwiki.org/index.php/Alter_State Cheers, Thomas Warren Gallin wrote, On 08/30/12 06:54: > Hi, > > I am having trouble running APBS on a structure, and it appears to be > because some of the coordinates are -100 or more negative. This > leads to APBS reading numbers from adjacent columns as concatenated > strings because there is no space between the columns. > > This is happening either if I use the plugin or run PDB2PQR and APBS > as stand-alone applications. > > If I can adjust the co-ordinates such that the relative positions of > the atoms do not change but the coordinates stay greater than -100 I > think that the problem would be solved. > > Has anyone ever encountered this problem, and is there a simple > solution in PyMol to adjust the coordinates and then save a simple > PDB file with the corrected values? > > Thanks, > > Warren Gallin -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ 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
