[PyMOL] Pymol cannot load pdb file
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 HEADERPRION PROTEIN 31-MAR-97 1AG2 TITLE PRION PROTEIN DOMAIN PRP(121-231) FROM MOUSE, NMR, 2 TITLE2 MINIMIZED AVERAGE STRUCTURE COMPNDMOL_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 [ORD=964] [ID=384] 0x3453730: i64 = add 0x3453830, 0x343e3e0 [ORD=962] [ID=379] 0x3453830: i64,ch = load 0x34772c0, 0x33d5d70, 0x333a350 [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
Re: [PyMOL] Pymol cannot load pdb file
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 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 > > HEADERPRION PROTEIN 31-MAR-97 1AG2 > TITLE PRION PROTEIN DOMAIN PRP(121-231) FROM MOUSE, NMR, 2 > TITLE2 MINIMIZED AVERAGE STRUCTURE > COMPNDMOL_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 [ORD=964] [ID=384] > >0x3453730: i64 = add 0x3453830, 0x343e3e0 [ORD=962] [ID=379] > > 0x3453830: i64,ch = load 0x34772c0, 0x33d5d70, > 0x333a350 [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
Re: [PyMOL] Pymol cannot load pdb file
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 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 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 >> >> HEADERPRION PROTEIN 31-MAR-97 1AG2 >> TITLE PRION PROTEIN DOMAIN PRP(121-231) FROM MOUSE, NMR, 2 >> TITLE2 MINIMIZED AVERAGE STRUCTURE >> COMPNDMOL_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 [ORD=964] [ID=384] >> >>0x3453730: i64 = add 0x3453830, 0x343e3e0 [ORD=962] [ID=379] >> >> 0x3453830: i64,ch = load 0x34772c0, 0x33d5d70, >> 0x333a350 [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
[PyMOL] show atoms as circle
Dear all,I want to draw CA atoms of a peptide as circles, but not spheres. How can I do that? Thanks Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- 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
Re: [PyMOL] show atoms as circle
Hi Yeping, PyMOL> show spheres, name CA PyMOL> set sphere_mode, 3 an eventually (example numbers): PyMOL> set sphere_point_max_size, 100 PyMOL> set sphere_scale, 0.5 Hope that helps. Cheers, Thomas On 06 Jan 2014, at 09:34, sunyeping wrote: > Dear all, > > I want to draw CA atoms of a peptide as circles, but not spheres. How can I > do that? > Thanks > > Yeping Sun > > Institute of Microbiology, Chinese Academy of Sciences -- 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
