Hi Charlie - I'm not able to reproduce your issue. I tried this with a random PDB and, although the symmetry operation wasn't appropriate for that particular structure, I got normal-looking cartoon representations.
One thing to consider might be that, if there are abnormalities in the numbering of your PDB residues (e.g. you have 2 residues with the same chain + residue number) this will break the cartoon representation, as PyMOL can no longer tell which N and C atoms should be bonded. To illustrate, try entering the following commands on the PyMOL command line: fab AAAAA, ala zoom as cartoon alter resi 3, resi=2 rebuild Is this something like what you see? If so, I would check the input (or output) file for sequence issues. Hope that helps. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Jun 26, 2015, at 11:33 AM, Carter, Charlie <[email protected]<mailto:[email protected]>> wrote: I'm trying to generate an oligomer using pdbset with the script attached below. The rotated molecules appear to be oriented properly, but they cannot be viewed correctly in PYMOL because the cartoon option fails to connect many of the residues. What am I doing wrong? Thanks, Charlie pdbset XYZIN $1.pdb XYZOUT temp.pdb <<EOF-pdbset CHAIN A SYMGEN Y-0.5,-X+0.5,Z OUTPUT PDB END EOF-pdbset ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================
