Bug 431120 – sci-chemistry/pymol-1.5.0.3-r1 please stabilize

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Justin Lecher (RETIRED) 2012-08-12 17:45:50 UTC]

Please mark stable, runtime test only: download http://pdb.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=3ZUA and open in pymol

[Comment 1 Agostino Sarubbo 2012-08-12 19:11:53 UTC]

ago@amd64box ~ $ LC_ALL="C" pymol downloads/3ZUA.pdb
 Detected OpenGL version 2.0 or greater.  Shaders available.
 Detected GLSL version 1.20.
HEADER    HYDROLASE                               18-JUL-11   3ZUA
TITLE     INITIAL RECOGNITION STEPS OF THE TYPE I SECRETION SYSTEM
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: ALPHA-HEMOLYSIN TRANSLOCATION ATP-BINDING PROTEIN HLYB;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: CLD;
COMPND   5 EC: 3.4.22.2;
COMPND   6 ENGINEERED: YES
 ObjectMolecule: Read secondary structure assignments.
 ObjectMolecule: Read crystal symmetry information.
 Symmetry: Found 1 symmetry operators.
 ObjectMolReadPDBStr: read MODEL 1
 ObjectMolReadPDBStr: read MODEL 2
 ObjectMolReadPDBStr: read MODEL 3
 ObjectMolReadPDBStr: read MODEL 4
 ObjectMolReadPDBStr: read MODEL 5
 ObjectMolReadPDBStr: read MODEL 6
 ObjectMolReadPDBStr: read MODEL 7
 ObjectMolReadPDBStr: read MODEL 8
 ObjectMolReadPDBStr: read MODEL 9
 ObjectMolReadPDBStr: read MODEL 10
 CmdLoad: "downloads/3ZUA.pdb" loaded as "3ZUA".
python2.7: nv50_pc.h:351: nv_alloc_instruction: Assertion `pc->num_instructions < 2048' failed.
/usr/bin/pymol: line 2:  2521 Aborted                 python2.7 -O ${PYMOL_PATH}/__init__.py -q $*



How about it?

[Comment 2 Justin Lecher (RETIRED) 2012-08-12 19:14:28 UTC]

never seen, but a quick google suggest it to be a mesa bug.

[Comment 3 Justin Lecher (RETIRED) 2012-08-12 19:16:49 UTC]

could you please try to do

cat >> ~/.pymolrc <<- EOF
set use_shaders, 0
set sphere_mode, 0
EOF

and try again?

[Comment 4 Agostino Sarubbo 2012-08-12 19:23:16 UTC]

(In reply to comment #3)
> could you please try to do
> 
> cat >> ~/.pymolrc <<- EOF
> set use_shaders, 0
> set sphere_mode, 0
> EOF
> 
> and try again?

works, can be stabilized?

[Comment 5 Justin Lecher (RETIRED) 2012-08-12 20:39:51 UTC]

give me night to sleep about aka. I will dig for the severity.

[Comment 6 Justin Lecher (RETIRED) 2012-08-14 06:47:49 UTC]

PLease go ahead. I will add a post inst notice.

[Comment 7 Justin Lecher (RETIRED) 2012-08-14 06:47:53 UTC]

PLease go ahead. I will add a post inst notice.

[Comment 8 Agostino Sarubbo 2012-08-14 12:54:37 UTC]

amd64 stable

[Comment 9 Anthony Basile 2012-08-14 20:19:02 UTC]

Stable ppc

[Comment 10 Paweł Hajdan, Jr. (RETIRED) 2012-09-23 07:50:59 UTC]

x86 stable, closing