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
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