Hi Per
If you're still having problems, you can try to install and run pymol under the X virtual frame buffer (xvfb). Cheers, Esben Best Regards Esben Peter Friis Science Manager Novozymes A/S Krogshoejvej 36 2880 Bagsvaerd Denmark Phone: +45 44461334 Mobile: +45 30771334 E-mail: [email protected] ----------------------------------- Don't print today - contribute to a better environment tomorrow ----------------------------------- Novozymes A/S (reg. no.:10007127). Registered address: Krogshoejvej 36 DK-2880 Bagsvaerd, Denmark This e-mail (including any attachments) is for the intended addressee(s) only and may contain confidential and/or proprietary information protected by law. You are hereby notified that any unauthorized reading, disclosure, copying or distribution of this e-mail or use of information herein is strictly prohibited. If you are not an intended recipient you should delete this e-mail immediately. Thank you. -----Original Message----- From: Jason Vertrees [mailto:[email protected]] Sent: 26. november 2012 17:48 To: Per Larsson Cc: [email protected] Subject: Re: [PyMOL] Pymol in command mode - no output 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 <[email protected]> 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 ([email protected]) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: > http://www.mail-archive.com/[email protected] -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) [email protected] (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 ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected] ------------------------------------------------------------------------------ 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 ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
