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: [email protected]
> 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: [email protected]
> CC: [email protected]; [email protected]
>
> 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 <[email protected]>
> >> wrote:
> >> >
> >> >
> >> >
> >> > ----------------------------------------
> >> >> CC: [email protected]
> >> >> From: [email protected]
> >> >> 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: [email protected]
> >> >>
> >> >> 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 <[email protected]>
> >> >> 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: [email protected]
> >> >> >> To: [email protected]
> >> >> >> 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 ([email protected])
> >> >> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> >> >> Archives:
> >> >> >> http://www.mail-archive.com/[email protected]
> >> >> >
> >> >> > ------------------------------------------------------------------------------
> >> >> > 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 ([email protected])
> >> >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> >> > Archives:
> >> >> > http://www.mail-archive.com/[email protected]
> >> >
> >> > ------------------------------------------------------------------------------
> >> > 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 ([email protected])
> >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> > Archives: http://www.mail-archive.com/[email protected]
> >>
> >>
> >>
> >> --
> >> Jason Vertrees, PhD
> >> PyMOL Product Manager
> >> Schrödinger, Inc.
> >>
> >> (e) [email protected]
> >> (o) +1 (603) 374-7120
> >
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrödinger, Inc.
>
> (e) [email protected]
> (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
_______________________________________________
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