Hi Jacky,
Do you encounter the same error with other PDB files? If not, can you check
the file? If you don't find anything obviously wrong, can you post this PDB
file somewhere where we can access it? If you do get the same error with
other files, but you didn't have it before, you may have corrupted your
pymol installation or dependencies.
Hope it helps,
Tsjerk
On Mon, Jan 6, 2014 at 9:03 AM, Biao Ma <jackyma1...@gmail.com> wrote:
> Hi,
>
> Recently, when I use pymol to load one pdb file, I got the following
> error and the Pymol is closed.
> I install pymol from soure code, and it worked no problem .
>
> Who can give me some advice ?
> thanks a lot.
>
> Jacky
>
> # the error strart here
>
> HEADER PRION PROTEIN 31-MAR-97 1AG2
> TITLE PRION PROTEIN DOMAIN PRP(121-231) FROM MOUSE, NMR, 2
> TITLE 2 MINIMIZED AVERAGE STRUCTURE
> COMPND MOL_ID: 1;
> COMPND 2 MOLECULE: MAJOR PRION PROTEIN;
> COMPND 3 CHAIN: A
> COMPND 4 FRAGMENT: DOMAIN 121 - 231;
> COMPND 5 SYNONYM: PRP(121-231);
> COMPND 6 ENGINEERED: YES
> ObjectMolecule: Read secondary structure assignments.
> ObjectMolecule: Read crystal symmetry information.
> Symmetry: Found 1 symmetry operators.
>
> CmdLoad: "/media/home/mabiao/1ag2.pdb" loaded as "1ag2".
>
> LLVM ERROR: Cannot select: 0x33caca0: i32 = fneg 0x3445650 [ID=398]
>
> 0x3445650: i32 = extract_vector_elt 0x332f030, 0x347a7f0 [ID=394]
>
> 0x332f030: v4i32 = X86ISD::PSHUFD 0x33d6170, 0x3339740 [ID=390]
>
> 0x33d6170: v4i32 = X86ISD::PSHUFD 0x3453b30, 0x33d3840 [ID=387]
>
> 0x3453b30: v4i32 = scalar_to_vector 0x3453630 [ID=385]
>
> 0x3453630: i32,ch = load 0x34772c0, 0x3453730,
> 0x333a350<LD4[%405]> [ORD=964] [ID=384]
>
> 0x3453730: i64 = add 0x3453830, 0x343e3e0 [ORD=962] [ID=379]
>
> 0x3453830: i64,ch = load 0x34772c0, 0x33d5d70,
> 0x333a350<LD8[%282]> [ORD=961] [ID=373]
>
> 0x33d5d70: i64,ch = CopyFromReg 0x2dbaf10, 0x332a610
> [ORD=754] [ID=113]
>
> 0x332a610: i64 = Register %vreg26 [ORD=754] [ID=1]
>
> 0x333a350: i64 = undef [ORD=773] [ID=18]
>
> 0x343e3e0: i64 = Constant<48> [ORD=853] [ID=34]
>
> 0x333a350: i64 = undef [ORD=773] [ID=18]
>
> 0x33d3840: i8 = Constant<0> [ID=82]
>
> 0x3339740: i8 = Constant<3> [ID=111]
>
> 0x347a7f0: i64 = Constant<0> [ID=81]
>
> In function: fs34_variant0_partial
>
> PyMOL: abrupt program termination.
>
> # the error end here.
>
>
> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics
> Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
> _______________________________________________
> 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
>
--
Tsjerk A. Wassenaar, Ph.D.
------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
_______________________________________________
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
