Hi Tsjerk,
Thanks for your comment, I found the reason of this error.
After I post the last mail, had noticed the error message at below:
$ pymol 1ag2.pdb
> OpenGL Warning: Failed to connect to host. Make sure 3D acceleration is
> enabled for this VM.
> libGL error: failed to load driver: vboxvideo
> libGL error: Try again with LIBGL_DEBUG=verbose for more details.
> PyMOL(TM) Molecular Graphics System, Version 1.6.9.0.
Because I use Linux system on VirtualBox, and I turn off the "3D
acceleration" option accidentally, thus the virtual machine been not
support accelerated 3D graphics and the pymol give me Error.
When I Enable "3D acceleration" option, the error is fixed.
Just hope this can help another person.
Jacky
On Mon, Jan 6, 2014 at 6:46 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
> 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.
>>
>>
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>
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