Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a "test" pdb.

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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 <mar...@ho...> wrote:
>> >
>> >
>> >
>> > ----------------------------------------
>> >> CC: pym...@li...
>> >> From: li...@co...
>> >> 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: mar...@ho...
>> >>
>> >> 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 <mar...@ho...> 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: mar...@ho...
>> >> >> To: pym...@li...
>> >> >> 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 (PyM...@li...)
>> >> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> >> >> Archives: http://www.mail-archive.com/pym...@li...
>> >> >
>> >> > ------------------------------------------------------------------------------
>> >> > 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 (PyM...@li...)
>> >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> >> > Archives: http://www.mail-archive.com/pym...@li...
>> >
>> > ------------------------------------------------------------------------------
>> > 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 (PyM...@li...)
>> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> > Archives: http://www.mail-archive.com/pym...@li...
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrödinger, Inc.
>>
>> (e) Jas...@sc...
>> (o) +1 (603) 374-7120
>

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120

Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a "test" pdb.

PyMOL is an OpenGL based molecular visualization system

Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a "test" pdb.