Hi Bernhard, this issue came up before and we think PyMOL is doing it right. See this post (workaround included): http://sourceforge.net/p/pymol/mailman/message/32385858/
Cheers, Thomas On 09 Sep 2014, at 13:50, Bernhard Lechtenberg <blechtenb...@sanfordburnham.org> wrote: > Hi all, > > I have problems showing a EM structure in PyMol. When I open the PDB file > 3J6J in PyMol, the structure is shown very small in a diameter of about 1Ang. > This makes some representations like Cartoon or sticks unusable and > comparison with other structures impossible. I checked the file and it seems > like the unit cell is set to P1 with 1Ang dimensions in all directions: > > CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 > > ORIGX1 1.000000 0.000000 0.000000 0.00000 > > ORIGX2 0.000000 1.000000 0.000000 0.00000 > > ORIGX3 0.000000 0.000000 1.000000 0.00000 > > SCALE1 0.010081 0.000000 0.000000 0.00000 > > SCALE2 0.000000 0.010081 0.000000 0.00000 > > SCALE3 0.000000 0.000000 0.012601 0.00000 > > I think that's were the problem lies. When I manually edited the PDB file and > replaced the 1.000 values in the CRYST1 record with the values decided by the > numbers in the SCALE records, the structure is shown correctly.So I think > PyMOL is not reading the SCALE record correctly. The same file is shown > correctly in other software like Coot or CCP4MG, so I think it is a Pymol > related problem. > > I am using Pymol 1.7.2.1 on MacOSX but had the same problem on a Windows > computer. > > Bernhard > > > Bernhard C. Lechtenberg, PhD > Postdoctoral Fellow > Riedl Lab > Sanford-Burnham Medical Research Institute > 10901 North Torrey Pines Road > La Jolla, CA 92037, USA > Phone: 858.646.3100 x 4216 > Email: blechtenb...@sanfordburnham.org -- Thomas Holder PyMOL Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce. Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk _______________________________________________ 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
