----------------------------------------
> 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?
>
Dell Laitittude, but this is probably due to other issues.
>
> > 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.
>
I never use python and I probably never would have gotten .1 to work if
I had to deal with that :) I'm not sure of the rationale here but while
you were phasing out a number of things I thought that "make" was
just lagging, intended for developers.
>
> > 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.
>
Thanks, I have no idea. Naive overlap was a bit confusing but I'm
dealing with simple things right now. I have 2 beta-carotene xtz files
created from scripts, one from the mmcif files on pdb.org and another
derived from jdftx after 300 position iterations using very
simple C and H models. In any case, I think part of the problem
is just using .53 for atomic/angstrom conversions but it looks like
"fit" results were bizarre: the 2 ends of the molecule were in about the same
place
but the chains extended in opposite directions from there ( it wasn't
immediately
obvious if I created some wierd linking errors based on this behaviour LOL).
>
> 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
------------------------------------------------------------------------------
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Deploy New Relic app performance management and know exactly
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Try New Relic at no cost today and get our sweet Data Nerd shirt too!
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