Hi Wenfu Getting a putty representation out of a series of MD snapshots should be equivalent to producing a putty representation from an NMR ensembles: Multiple models in one pdb files, and you want the putty width to represent the structural variation between the models.
This site https://kpwu.wordpress.com/2007/03/19/sausage-view-of-a-nmr-ensemble-structure/ offers a script average3d.py, available from http://mccammon.ucsd.edu/~cmura/PyMOL/ that solves the problem of setting the b-factor field for NMR ensembles. I think this should also work for MD ensembles Annemarie > On Mon, Apr 13, 2015 at 10:34 AM, <m...@mskcc.org> wrote: > >> Hi pymol users, >> >> I have a pdb file, which is from the result of a molecular dynamics >> simulation. I want to present the structure with cartoon putty in pymol. >> But I can only make it cartoon putty in Macpymol 0.99 version. When I use >> pymol1.7 or 1.3 version, the error is like this: Extrude-Warning: invalid >> putty settings (division by zero) >> I attach part of the pdb file and hope to get your suggestions. >> >> Thanks, >> Wenfu >> >> ===================================================================== >> >> Please note that this e-mail and any files transmitted from >> Memorial Sloan-Kettering Cancer Center may be privileged, confidential, >> and protected from disclosure under applicable law. If the reader of >> this message is not the intended recipient, or an employee or agent >> responsible for delivering this message to the intended recipient, >> you are hereby notified that any reading, dissemination, distribution, >> copying, or other use of this communication or any of its attachments >> is strictly prohibited. If you have received this communication in >> error, please notify the sender immediately by replying to this message >> and deleting this message, any attachments, and all copies and backups >> from your computer. >> >> ------------------------------------------------------------------------------ BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF _______________________________________________ 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
