Anyway, to answer your questions fwiw.
I did get the molecule alginments to work but I had to sort the atoms in the two files. This was just a test as my compaint with gdis is that I could not turn off the alignement and it ignored my attempts to load the files offset from each other... This seems to be Ubuntau 11.10, running on a Dell Laptop apparently E6510 The hardware I have apparently is this, the "ldd" output for the pymol lib is shown below too. marchywka@marchywka-Latitude-E6510:~/d/jdft/jdftx$ lshw WARNING: you should run this program as super-user. marchywka-latitude-e6510 description: Computer width: 64 bits capabilities: vsyscall64 vsyscall32 *-core description: Motherboard physical id: 0 *-memory description: System memory physical id: 0 size: 3887MiB *-cpu product: Intel(R) Core(TM) i5 CPU M 520 @ 2.40GHz vendor: Intel Corp. physical id: 1 bus info: cpu@0 size: 1199MHz capacity: 1199MHz width: 64 bits capabilities: fpu fpu_exception wp vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx rdtscp x86-64 constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm sse4_1 sse4_2 popcnt aes lahf_lm ida arat tpr_shadow vnmi flexpriority ept vpid cpufreq *-pci:0 description: Host bridge product: Core Processor DRAM Controller vendor: Intel Corporation physical id: 100 bus info: pci@0000:00:00.0 version: 02 width: 32 bits clock: 33MHz *-pci:0 description: PCI bridge product: Core Processor PCI Express x16 Root Port vendor: Intel Corporation physical id: 1 bus info: pci@0000:00:01.0 version: 02 width: 32 bits clock: 33MHz capabilities: pci normal_decode bus_master cap_list configuration: driver=pcieport resources: irq:40 ioport:7000(size=4096) memory:d0000000-e30fffff *-display description: VGA compatible controller product: GT218 [NVS 3100M] vendor: nVidia Corporation physical id: 0 bus info: pci@0000:01:00.0 version: a2 width: 64 bits clock: 33MHz capabilities: vga_controller bus_master cap_list rom configuration: driver=nouveau latency=0 resources: irq:16 memory:e2000000-e2ffffff memory:d0000000-dfffffff memory:e0000000-e1ffffff ioport:7000(size=128) memory:e3000000-e307ffff *-multimedia description: Audio device product: High Definition Audio Controller vendor: nVidia Corporation physical id: 0.1 bus info: pci@0000:01:00.1 version: a1 width: 32 bits clock: 33MHz capabilities: bus_master cap_list configuration: driver=HDA Intel latency=0 resources: irq:16 memory:e3080000-e3083fff *-network description: Ethernet interface product: 82577LM Gigabit Network Connection vendor: Intel Corporation physical id: 19 bus info: pci@0000:00:19.0 logical name: eth0 version: 05 serial: 00:26:b9:d4:f8:6e capacity: 1Gbit/s width: 32 bits clock: 33MHz capabilities: bus_master cap_list ethernet physical tp 10bt 10bt-fd 100bt 100bt-fd 1000bt-fd autonegotiation configuration: autonegotiation=on broadcast=yes driver=e1000e driverversion=1.3.10-k2 firmware=0.12-1 latency=0 multicast=yes port=twisted pair resources: irq:42 memory:e9600000-e961ffff memory:e9680000-e9680fff ioport:8040(size=32) *-usb:0 description: USB Controller product: 5 Series/3400 Series Chipset USB2 Enhanced Host Controller vendor: Intel Corporation physical id: 1a bus info: pci@0000:00:1a.0 version: 05 width: 32 bits clock: 33MHz capabilities: ehci bus_master cap_list configuration: driver=ehci_hcd latency=0 resources: irq:16 memory:e9670000-e96703ff *-multimedia description: Audio device product: 5 Series/3400 Series Chipset High Definition Audio vendor: Intel Corporation physical id: 1b bus info: pci@0000:00:1b.0 version: 05 width: 64 bits clock: 33MHz capabilities: bus_master cap_list configuration: driver=HDA Intel latency=0 resources: irq:41 memory:e9660000-e9663fff *-pci:1 description: PCI bridge product: 5 Series/3400 Series Chipset PCI Express Root Port 1 vendor: Intel Corporation physical id: 1c bus info: pci@0000:00:1c.0 version: 05 width: 32 bits clock: 33MHz capabilities: pci normal_decode bus_master cap_list configuration: driver=pcieport resources: irq:16 ioport:6000(size=4096) memory:e8200000-e95fffff ioport:e9b00000(size=2097152) *-pci:2 description: PCI bridge product: 5 Series/3400 Series Chipset PCI Express Root Port 2 vendor: Intel Corporation physical id: 1c.1 bus info: pci@0000:00:1c.1 version: 05 width: 32 bits clock: 33MHz capabilities: pci normal_decode bus_master cap_list configuration: driver=pcieport resources: irq:17 ioport:5000(size=4096) memory:e6e00000-e81fffff ioport:e9900000(size=2097152) *-network description: Wireless interface product: BCM43224 802.11a/b/g/n vendor: Broadcom Corporation physical id: 0 bus info: pci@0000:03:00.0 logical name: wlan0 version: 01 serial: 78:e4:00:83:fa:b9 width: 64 bits clock: 33MHz capabilities: bus_master cap_list ethernet physical wireless configuration: broadcast=yes driver=brcmsmac driverversion=3.0.0-12-generic firmware=N/A ip=192.168.15.246 latency=0 multicast=yes wireless=IEEE 802.11abgn resources: irq:17 memory:e6e00000-e6e03fff *-pci:3 description: PCI bridge product: 5 Series/3400 Series Chipset PCI Express Root Port 3 vendor: Intel Corporation physical id: 1c.2 bus info: pci@0000:00:1c.2 version: 05 width: 32 bits clock: 33MHz capabilities: pci normal_decode bus_master cap_list configuration: driver=pcieport resources: irq:18 ioport:2000(size=8192) memory:e3100000-e59fffff ioport:ec000000(size=67108864) *-pcmcia description: CardBus bridge product: Ricoh Co Ltd vendor: Ricoh Co Ltd physical id: 0 bus info: pci@0000:04:00.0 version: 02 width: 64 bits clock: 33MHz capabilities: pcmcia bus_master cap_list configuration: driver=yenta_cardbus latency=176 maxlatency=5 mingnt=128 resources: iomemory:ec0000000-ebfffffff irq:18 memory:e5940000-e5940fff ioport:2000(size=256) ioport:2400(size=256) memory:ec000000-efffffff memory:e3400000-e37fffff *-generic description: SD Host controller product: MMC/SD Host Controller vendor: Ricoh Co Ltd physical id: 0.1 bus info: pci@0000:04:00.1 version: 03 width: 32 bits clock: 33MHz capabilities: bus_master cap_list configuration: driver=sdhci-pci latency=0 resources: irq:19 memory:e5930000-e59300ff *-firewire description: FireWire (IEEE 1394) product: FireWire Host Controller vendor: Ricoh Co Ltd physical id: 0.4 bus info: pci@0000:04:00.4 version: 03 width: 32 bits clock: 33MHz capabilities: ohci bus_master cap_list configuration: driver=firewire_ohci latency=0 resources: irq:44 memory:e5900000-e59007ff *-pci:4 description: PCI bridge product: 5 Series/3400 Series Chipset PCI Express Root Port 4 vendor: Intel Corporation physical id: 1c.3 bus info: pci@0000:00:1c.3 version: 05 width: 32 bits clock: 33MHz capabilities: pci normal_decode bus_master cap_list configuration: driver=pcieport resources: irq:19 ioport:4000(size=4096) memory:e5a00000-e6dfffff ioport:e9700000(size=2097152) *-usb:1 description: USB Controller product: 5 Series/3400 Series Chipset USB2 Enhanced Host Controller vendor: Intel Corporation physical id: 1d bus info: pci@0000:00:1d.0 version: 05 width: 32 bits clock: 33MHz capabilities: ehci bus_master cap_list configuration: driver=ehci_hcd latency=0 resources: irq:17 memory:e9650000-e96503ff *-pci:5 description: PCI bridge product: 82801 Mobile PCI Bridge vendor: Intel Corporation physical id: 1e bus info: pci@0000:00:1e.0 version: a5 width: 32 bits clock: 33MHz capabilities: pci subtractive_decode bus_master cap_list *-isa description: ISA bridge product: Mobile 5 Series Chipset LPC Interface Controller vendor: Intel Corporation physical id: 1f bus info: pci@0000:00:1f.0 version: 05 width: 32 bits clock: 33MHz capabilities: isa bus_master cap_list configuration: latency=0 *-storage description: RAID bus controller product: Mobile 82801 SATA RAID Controller vendor: Intel Corporation physical id: 1f.2 bus info: pci@0000:00:1f.2 version: 05 width: 32 bits clock: 66MHz capabilities: storage bus_master cap_list configuration: driver=ahci latency=0 resources: irq:43 ioport:8090(size=8) ioport:8080(size=4) ioport:8070(size=8) ioport:8060(size=4) ioport:8020(size=32) memory:e9640000-e96407ff *-serial UNCLAIMED description: SMBus product: 5 Series/3400 Series Chipset SMBus Controller vendor: Intel Corporation physical id: 1f.3 bus info: pci@0000:00:1f.3 version: 05 width: 64 bits clock: 33MHz configuration: latency=0 resources: memory:e9630000-e96300ff ioport:8000(size=32) *-generic description: Signal processing controller product: 5 Series/3400 Series Chipset Thermal Subsystem vendor: Intel Corporation physical id: 1f.6 bus info: pci@0000:00:1f.6 version: 05 width: 64 bits clock: 33MHz capabilities: bus_master cap_list configuration: driver=intel ips latency=0 resources: irq:18 memory:e9620000-e9620fff *-pci:1 description: Host bridge product: Core Processor QuickPath Architecture Generic Non-core Registers vendor: Intel Corporation physical id: 101 bus info: pci@0000:3f:00.0 version: 02 width: 32 bits clock: 33MHz *-pci:2 description: Host bridge product: Core Processor QuickPath Architecture System Address Decoder vendor: Intel Corporation physical id: 102 bus info: pci@0000:3f:00.1 version: 02 width: 32 bits clock: 33MHz *-pci:3 description: Host bridge product: Core Processor QPI Link 0 vendor: Intel Corporation physical id: 103 bus info: pci@0000:3f:02.0 version: 02 width: 32 bits clock: 33MHz *-pci:4 description: Host bridge product: Core Processor QPI Physical 0 vendor: Intel Corporation physical id: 104 bus info: pci@0000:3f:02.1 version: 02 width: 32 bits clock: 33MHz *-pci:5 description: Host bridge product: Core Processor Reserved vendor: Intel Corporation physical id: 105 bus info: pci@0000:3f:02.2 version: 02 width: 32 bits clock: 33MHz *-pci:6 description: Host bridge product: Core Processor Reserved vendor: Intel Corporation physical id: 106 bus info: pci@0000:3f:02.3 version: 02 width: 32 bits clock: 33MHz WARNING: output may be incomplete or inaccurate, you should run this program as super-user. marchywka@marchywka-Latitude-E6510:~/d/jdft/jdftx$ marchywka@marchywka-Latitude-E6510:~/d/jdft/jdftx$ ldd ../../pymol/pymol/built/libpymol.so linux-vdso.so.1 => (0x00007fffd9bf0000) libGLEW.so.1.6 => /usr/lib/x86_64-linux-gnu/libGLEW.so.1.6 (0x00007f4890fcd000) libGL.so.1 => /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1 (0x00007f4890d71000) libGLU.so.1 => /usr/lib/x86_64-linux-gnu/libGLU.so.1 (0x00007f4890b03000) libfreetype.so.6 => /usr/lib/x86_64-linux-gnu/libfreetype.so.6 (0x00007f489086b000) libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f4890653000) libpng12.so.0 => /lib/x86_64-linux-gnu/libpng12.so.0 (0x00007f489042b000) libglut.so.3 => /usr/lib/libglut.so.3 (0x00007f48901e5000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f488ffe1000) libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f488fdca000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f488fa2b000) libglapi.so.0 => /usr/lib/x86_64-linux-gnu/libglapi.so.0 (0x00007f488f807000) libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6 (0x00007f488f4ce000) libXext.so.6 => /usr/lib/x86_64-linux-gnu/libXext.so.6 (0x00007f488f2bb000) libXdamage.so.1 => /usr/lib/x86_64-linux-gnu/libXdamage.so.1 (0x00007f488f0b8000) libXfixes.so.3 => /usr/lib/x86_64-linux-gnu/libXfixes.so.3 (0x00007f488eeb1000) libXxf86vm.so.1 => /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1 (0x00007f488ecab000) libdrm.so.2 => /usr/lib/x86_64-linux-gnu/libdrm.so.2 (0x00007f488eaa0000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f488e882000) /lib64/ld-linux-x86-64.so.2 (0x00007f4891be5000) libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f488e57b000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f488e2f7000) libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1 (0x00007f488e0da000) librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f488ded2000) libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6 (0x00007f488dcce000) libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6 (0x00007f488dac8000) marchywka@marchywka-Latitude-E6510:~/d/jdft/jdftx$ ---------------------------------------- > From: jason.vertr...@schrodinger.com > Date: Fri, 5 Oct 2012 09:36:29 -0500 > Subject: Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to > view a "test" pdb. > To: marchy...@hotmail.com > CC: li...@cowsandmilk.net; pymol-users@lists.sourceforge.net > > Hi Mike, > > >> I suggest downloading the latest code, v1.5.0.4, from the open-source > >> project page, if you want to build by hand. > >> > > see comments in my last post, I think that is what I did. Although > > autoreconf may not have helped anything. > > I see the confusion now. We'll update SourceForge on our next release > so that it says the latest is v1.5.0.5, not v1.5.0.1. To get the > latest code, please do this: > > svn co https://pymol.svn.sourceforge.net/svnroot/pymol/root/pymol/trunk/pymol > pymol > > > >> To build, you need Python 2.7 or later and the process is very simple: > >> > >> sudo python setup.py install > >> sudo python setup2.py install > >> > > that was what created the first version I ran, it seemed fine until > > I tried to display a test pdb then it hung in 100 cpu on one core. > > What kind of computer is this? What video card do you have? > > > > I don't really recall what the first version said, I think it was > > hypothetical > > as in "may need license" etc. The version from "./configure" had a whole > > bunch of problems- simple syntax errors like missing comma to no > > link to the ccealignmodule but once I kluged around the CGO problems > > I think I was on my own :) > > The "make; make install" setup was deprecated a long time ago which is > why this didn't work. We use Python distutils to build, as you've > found out. > > > > Anyway it seems fine now, although attempting to use "fit" on my > > 2 molecules gave a non-intuitive result I think the one was so mangled that > > it had problems aligning them. > > Glad it's working. Fit is a mathematically optimal superposition of > vector sets. Are your atom pairings correct? If you want to specify > them manually, check out Wizard > Pair Fitting. If you send me the > molecules I'm happy to take a look for you, too. > > > Cheers, > > -- Jason > > > > >> > >> > >> On Thu, Oct 4, 2012 at 9:18 PM, Mike Marchywka <marchy...@hotmail.com> > >> wrote: > >> > > >> > > >> > > >> > ---------------------------------------- > >> >> CC: pymol-users@lists.sourceforge.net > >> >> From: li...@cowsandmilk.net > >> >> Subject: Re: [PyMOL] I just built pymol, comes up but hangs on any > >> >> attempt to view a "test" pdb. > >> >> Date: Thu, 4 Oct 2012 22:03:59 -0400 > >> >> To: marchy...@hotmail.com > >> >> > >> >> You don't need a license for the open source version. > >> >> > >> >> If you provided details on what OS/distribution you are building on, > >> >> people may try to replicate and understand why the python version hung. > >> >> In my experience, using setup.py generally worked out of the box. > >> > > >> > Well, I thought there may be a dev list or something for the most of > >> > this stuff but in any case I'm on Ubuntu > >> > but that probably was not a big factor for some of the issues I ran into > >> > I just wanted to display > >> > 2 molecules side by side and could not get jmol or gdis to work right > >> > away and someone suggested > >> > this. ( fwiw, I have my own molecule viewer that IIRC I wrote to learn > >> > glut on cygwin but > >> > I imagine that would be an even bigger chore to port LOL). > >> > > >> > If I can reconstruct, I apparently started with pymol-v1.5.0.1.tar and I > >> > think at some point I ran > >> > autoreconf -l thinking I could go the "configure" route but then did > >> > python setup.py build and > >> > install in separeate steps., This seemed to work but attempts to display > >> > the test pdb > >> > files never displayed anything, I could not get any more menu's and one > >> > core was running > >> > at 100 percent until I killed it. > >> > > >> > Going the confugre route, I think the first problem was with a bunch of > >> > undefined CGO things. > >> > but you can see the changes below. The EXT thing was spurious probably > >> > as there was a missing -lGLEW > >> > and I had to relink. This is obviously a raw dump of things that I tried > >> > along with stuff that ultimately > >> > worked but fwiw. > >> > > >> > > >> > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ find -mtime -2 -name > >> > "*.h" > >> > ./layer0/os_gl.h > >> > ./contrib/uiuc/plugins/include/molfile_plugin.h > >> > ./generated/include/ShaderText.h > >> > ./config.h > >> > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ find -mtime -2 -name > >> > "*.c" > >> > ./layer0/ShaderText.c > >> > ./layer0/ShaderMgr.c > >> > ./layer3/Executive.c > >> > ./generated/src/ShaderText.c > >> > ./layer2/ObjectVolume.c > >> > ./layer1/CGO.c > >> > ./layer1/Scene.c > >> > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ > >> > > >> > > >> > > >> > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ grep -n -A 2 mjm > >> > `find -mtime -2 -name "*.c" ` > >> > ./layer0/ShaderMgr.c:97: FeedbackAdd(G, " mjm forcing glew ok Shaders > >> > available.\n"); > >> > ./layer0/ShaderMgr.c:98:// this should work but turn off for now mjm > >> > ./layer0/ShaderMgr.c-99-// if (GLEW_VERSION_2_0) > >> > ./layer0/ShaderMgr.c-100- if (1) > >> > -- > >> > ./layer3/Executive.c:76:// mjm > >> > ./layer3/Executive.c-77-#include"modules/cealign/src/ce_types.h" > >> > ./layer3/Executive.c-78-/* Externals for CEAlign */ > >> > -- > >> > ./layer1/Scene.c:2910://mjm > >> > ./layer1/Scene.c-2911- 1.0F, 1.0F, 0.1F, 1.f > >> > ./layer1/Scene.c-2912- }; > >> > -- > >> > ./layer1/Scene.c:10000: //mjm > >> > ./layer1/Scene.c-10001-//glBlitFramebufferEXT (0, 0, I->offscreen_width > >> > / 2, I->offscreen_height, > >> > ./layer1/Scene.c-10002- glBlitFramebuffer (0, 0, I->offscreen_width / 2, > >> > I->offscreen_height, > >> > -- > >> > ./layer1/Scene.c:10007://mjm > >> > ./layer1/Scene.c-10008- glBlitFramebuffer (I->offscreen_width / 2, 0, > >> > I->offscreen_width, I->offscreen_height, > >> > ./layer1/Scene.c-10009- //glBlitFramebufferEXT (I->offscreen_width / 2, > >> > 0, I->offscreen_width, I->offscreen_height, > >> > -- > >> > ./layer1/Scene.c:10016: //mjm > >> > ./layer1/Scene.c-10017- //glBlitFramebufferEXT (0, 0, > >> > I->offscreen_width, I->offscreen_height, > >> > ./layer1/Scene.c-10018- glBlitFramebuffer (0, 0, I->offscreen_width, > >> > I->offscreen_height, > >> > -- > >> > ./layer1/Scene.c:10024: //mjm > >> > ./layer1/Scene.c-10025-// glBlitFramebufferEXT (0, 0, > >> > I->offscreen_width, I->offscreen_height, > >> > ./layer1/Scene.c-10026- glBlitFramebuffer (0, 0, I->offscreen_width, > >> > I->offscreen_height, > >> > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ > >> > > >> > > >> > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ grep -n -A 2 mjm > >> > `find -mtime -2 -name "*.h" ` > >> > ./layer0/os_gl.h:6:// mjm > >> > ./layer0/os_gl.h-7-//#if defined(_PYMOL_IOS) || defined(ANDROID) > >> > ./layer0/os_gl.h-8-#if 1 > >> > ./layer0/os_gl.h:9:// mjm > >> > ./layer0/os_gl.h-10-// #define _PYMOL_PURE_OPENGL_ES > >> > ./layer0/os_gl.h-11-#define _PYMOL_CGO_DRAWARRAYS > >> > -- > >> > ./contrib/uiuc/plugins/include/molfile_plugin.h:249:// mjm - these are > >> > in the games lass LOL > >> > ./contrib/uiuc/plugins/include/molfile_plugin.h-250-int have_esp; > >> > ./contrib/uiuc/plugins/include/molfile_plugin.h-251-int have_npa; > >> > -- > >> > ./contrib/uiuc/plugins/include/molfile_plugin.h:312:// mjm > >> > ./contrib/uiuc/plugins/include/molfile_plugin.h-313-int multiplicity; > >> > ./contrib/uiuc/plugins/include/molfile_plugin.h-314-int * esp_charges; > >> > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ > >> > > >> > > >> > > >> > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ cat relink > >> > gcc --verbose -shared -fPIC -DPIC -Wl,--no-as-needed -Wl,--whole-archive > >> > contrib/uiuc/plugins/molfile_plugin/src/.libs/libmolfile_plugin0.a > >> > modules/cealign/src/ccealignmodule.o ov/src/.libs/libov.a > >> > layer0/.libs/liblayer0.a layer1/.libs/liblayer1.a > >> > layer2/.libs/liblayer2.a layer3/.libs/liblayer3.a > >> > layer4/.libs/liblayer4.a layer5/.libs/liblayer5.a -Wl,--no-whole-archive > >> > -L/usr/lib/x86_64-linux-gnu -Wl,--whole-archive -lGLEW -lGL -lGLU > >> > /usr/lib/x86_64-linux-gnu/libfreetype.so -lz -lpng -lglut > >> > -Wl,--no-whole-archive -ldl -O2 -Wl,-soname -Wl,libpymol.so.0 -o > >> > .libs/libpymol.so.0.0.0 > >> > #gcc -shared -fPIC -DPIC -Wl,--whole-archive > >> > contrib/uiuc/plugins/molfile_plugin/src/.libs/libmolfile_plugin0.a > >> > ov/src/.libs/libov.a layer0/.libs/liblayer0.a layer1/.libs/liblayer1.a > >> > layer2/.libs/liblayer2.a layer3/.libs/liblayer3.a > >> > layer4/.libs/liblayer4.a layer5/.libs/liblayer5.a -Wl,--no-whole-archive > >> > -L/usr/lib/x86_64-linux-gnu -lGL -lGLU > >> > /usr/lib/x86_64-linux-gnu/libfreetype.so -lz -lpng -lglut -ldl -O2 > >> > -Wl,-soname -Wl,libpymol.so.0 -o .libs/libpymol.so.0.0.0 > >> > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ > >> > > >> > > >> > > >> > > >> > > >> >> > >> >> -David > >> >> > >> >> On Oct 4, 2012, at 9:22 PM, Mike Marchywka <marchy...@hotmail.com> > >> >> wrote: > >> >> > >> >> > > >> >> > > >> >> > > >> >> > fwiw, I never figured out why the out-of-the-box build hung using the > >> >> > python approach > >> >> > but I went through the "./cogifure, make make install route" > >> >> > and did get the test molecules to display. However, I ran into lots > >> >> > of problems with the ShaderMgr and > >> >> > ccealignmodule and then finally the link was missing -lGLEW. > >> >> > > >> >> > In any case it looks like I am all set but I thought the download > >> >> > would come closer to working right > >> >> > away. > >> >> > > >> >> > And the xyz files I wanted to display do appear to come up just great. > >> >> > > >> >> > So do I need a license for the open source version? > >> >> > Thanks. > >> >> > > >> >> > > >> >> > > >> >> > note new address > >> >> > Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. > >> >> > formerly 487 Salem Woods Drive Marietta GA 30067 404-788-1216 (C)<- > >> >> > leave message 989-348-4796 (P)<- emergency > >> >> > > >> >> > > >> >> > > >> >> > ---------------------------------------- > >> >> >> From: marchy...@hotmail.com > >> >> >> To: pymol-users@lists.sourceforge.net > >> >> >> Date: Thu, 4 Oct 2012 15:43:53 -0400 > >> >> >> Subject: [PyMOL] I just built pymol, comes up but hangs on any > >> >> >> attempt to view a "test" pdb. > >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> Is there some common reason for this? > >> >> >> CPU on one core stays at 100 percent and no more menu's come up. > >> >> >> > >> >> >> The larger window says at the bottom that the version is supposed to > >> >> >> be licensed > >> >> >> but I just pulled it down from sourceforge and not sure that this > >> >> >> version needs a key > >> >> >> to work. > >> >> >> > >> >> >> Thanks. > >> >> >> > >> >> >> > >> >> >> note new address > >> >> >> Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. > >> >> >> formerly 487 Salem Woods Drive Marietta GA 30067 404-788-1216 (C)<- > >> >> >> leave message 989-348-4796 (P)<- emergency > >> >> >> > >> >> >> > >> >> >> ------------------------------------------------------------------------------ > >> >> >> Don't let slow site performance ruin your business. Deploy New Relic > >> >> >> APM > >> >> >> Deploy New Relic app performance management and know exactly > >> >> >> what is happening inside your Ruby, Python, PHP, Java, and .NET app > >> >> >> Try New Relic at no cost today and get our sweet Data Nerd shirt too! > >> >> >> http://p.sf.net/sfu/newrelic-dev2dev > >> >> >> _______________________________________________ > >> >> >> 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 > >> >> > > >> >> > ------------------------------------------------------------------------------ > >> >> > Don't let slow site performance ruin your business. Deploy New Relic > >> >> > APM > >> >> > Deploy New Relic app performance management and know exactly > >> >> > what is happening inside your Ruby, Python, PHP, Java, and .NET app > >> >> > Try New Relic at no cost today and get our sweet Data Nerd shirt too! > >> >> > http://p.sf.net/sfu/newrelic-dev2dev > >> >> > _______________________________________________ > >> >> > 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 > >> > > >> > ------------------------------------------------------------------------------ > >> > Don't let slow site performance ruin your business. Deploy New Relic APM > >> > Deploy New Relic app performance management and know exactly > >> > what is happening inside your Ruby, Python, PHP, Java, and .NET app > >> > Try New Relic at no cost today and get our sweet Data Nerd shirt too! > >> > http://p.sf.net/sfu/newrelic-dev2dev > >> > _______________________________________________ > >> > 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 > >> > >> > >> > >> -- > >> Jason Vertrees, PhD > >> PyMOL Product Manager > >> Schrödinger, Inc. > >> > >> (e) jason.vertr...@schrodinger.com > >> (o) +1 (603) 374-7120 > > > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrödinger, Inc. > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev _______________________________________________ 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