#210 executing pymol script from shell

[santiago miranda]

Hi, I'm new to pymol and I'm having a hard time with a script. This is what I wrote:

  #!/bin/bash
    pwd
    echo '
fetch 1OYT
    remove resn HOH 
    ' > scriptt.pml
    pymol scriptt.pml

But pymol returns:

/home/santi/trials-smina/web-example
 PyMOL(TM) 2.3.1 - Incentive Product
 Copyright (C) Schrodinger, LLC

 This Executable Build integrates and extends Open-Source PyMOL.
Segmentation fault (core dumped)

Any idea what's going on and how to fix it?

[santiago miranda]

-Computer specs-
Processor : AMD A12-9720P RADEON R7, 12 COMPUTE CORES 4C+8G
Memory : 7603MB (3084MB used)
Machine Type : Notebook
Operating System : Ubuntu 18.04.2 LTS
Date/Time : Fri 05 Apr 2019 19:41:04 BST
-Display-
Resolution : 1366x768 pixels
OpenGL Renderer : (Unknown)
X11 Vendor : The X.Org Foundation
-Audio Devices-
Audio Adapter : HDA-Intel - HDA ATI HDMI
Audio Adapter : HDA-Intel - HD-Audio Generic
EPSON_WF_2750_Series@EPSON85C2A6.local
HP_Deskjet_3050A_J611_series_2_Evelyn_s_MacBook_Air
-SCSI Disks-
ATA WDC WD10SPZX-24Z
HL-DT-ST DVDRAM GUE0N
UFD 2.0 Silicon-Power8G

[Thomas Holder]

Does it work headless?

pymol -c scriptt.pml

This looks suspicious: "OpenGL Renderer : (Unknown)"

[santiago miranda]

Hi Thomas, Thank you. uhmm yes but I can't open any .pdb file the only workaround was to install an older version of PyMOL and open the files with an older version (1.8)

[Thomas Holder]

What does PyMOL 1.8 report as "OpenGL graphics engine" and what OpenGL version does it detect?