Hi Per, You'll probably want to use something like this:
# load the file load http://molecules.gnu-darwin.org/html/00150001_00175000/153919/153919.pdb, myMolecule # ray trace and save the image; you need to do this since you're running # PyMOL headlessly png ~/foo.png, height=768, width=1024, ray=1 As far as missing output that's most likely because you're running remotely and the stdout/stderr are being piped elsewhere. This is common on clusters. Cheers, -- Jason On Mon, Nov 26, 2012 at 10:28 AM, Per Larsson <per.lars...@sbc.su.se> wrote: > Hi Pymol-users, > > I'm running a pml-script file to render some images on a remote server, using > pymol 1.4, but I do not get any output at all. And no error message, so it is > hard to troubleshoot, unfortunately. > > To reduce the complexity of my script, I have reduced it to basically just > loading a pdb-file and saving as a png-image (two lines in the pml-script), > but even that does not work. Any suggestions? > > I envoke the whole thing using > $pymol -c script.pml > > > Thanks > /Per > > > > > ------------------------------------------------------------------------------ > Monitor your physical, virtual and cloud infrastructure from a single > web console. Get in-depth insight into apps, servers, databases, vmware, > SAP, cloud infrastructure, etc. Download 30-day Free Trial. > Pricing starts from $795 for 25 servers or applications! > http://p.sf.net/sfu/zoho_dev2dev_nov > _______________________________________________ > 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 -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov _______________________________________________ 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
