From: James S. <jms...@gm...> - 2012-12-27 18:53:20
|
Dear PyMol users! I'd like to build simple 2D lattice model consisted of the Carbon atoms connected by the single bonds. Could you provide me with some script which can build such lattices of the desired dimensions ? Thanks for help James |
From: James S. <jms...@gm...> - 2012-12-28 13:42:33
|
Hi Tsjerk! This is the example of such lattice which I've built using Chimera! http://imageshack.us/photo/my-images/543/lattice.png/ this is simple model of the Carbon-contained lattice without hydrogens. So I'd like to build such lattices from different atoms as nodes defining only atom type as well as number of nodes. Also I'd like to simulate this model using PBC so it seems that big dimensions of such lattice doesn't matter, doesn’t it ? ( It will be simpler to build smaller symmetric model ) James |
From: Mike M. <mar...@ho...> - 2012-12-28 14:27:49
|
What does Chimera do? I finally wrote my own c++ tool that let's a TcL script specify a molecule's layout in terms of relevance like bond length and angle. I decided it was worth the effort since I didn't want to look around much for existing stuff and would eventually add my own stuff for analysis. The real decision was to learn python or just use TcL. I guess if I was looking for a tool to generate from a script I'd probably prefer python. Thanks. ---------------------------------------- > Date: Fri, 28 Dec 2012 05:42:27 -0800 > From: jms...@gm... > To: pym...@li... > Subject: Re: [PyMOL] Building of the Carbon lattice > > Hi Tsjerk! > > This is the example of such lattice which I've built using Chimera! > http://imageshack.us/photo/my-images/543/lattice.png/ > > this is simple model of the Carbon-contained lattice without hydrogens. > So I'd like to build such lattices from different atoms as nodes > defining only atom type as well as number of nodes. > > Also I'd like to simulate this model using PBC so it seems that big > dimensions of such lattice doesn't matter, doesn’t it ? ( It will be > simpler to build smaller symmetric model ) > > James > > ------------------------------------------------------------------------------ > Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and > much more. Get web development skills now with LearnDevNow - > 350+ hours of step-by-step video tutorials by Microsoft MVPs and experts. > SALE $99.99 this month only -- learn more at: > http://p.sf.net/sfu/learnmore_122812 > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |
From: Mike M. <mar...@ho...> - 2013-01-02 16:01:58
|
I'm trying to load a self-generated xplor file and pymol keeps segfaulting. I wanted to debug the problem but can't get my debug statements to execute. The only thing that greps for "xplor" is a few pymol modules and plugin called edmplugin. If I rebuild the plugin and relink pymol nothing seems to change. Is this the right code? I also wanted to add a loader for other formats of density or vector fields and maybe do some rendering ( I have an old viewer I wrote with glut and thought I may be able to salvage parts of that for use here). Thanks. |
From: Mike M. <mar...@ho...> - 2013-01-02 21:09:39
|
never mind, it looks like the name case changes and opening in GDB gave me a bt, fwiw, presumably I can figure this out now... PyMOL>cmd.load_raw(content, 'xplor', 'map',quiet=0) ObjectMapLoadXPLOR: Loading... Program received signal SIGSEGV, Segmentation fault. transform33f3f (m1=0xffc00000ffc00044, m2=0x7fffffffa070, m3=0x7fffffffa080) at Vector.c:677 677 m3[0] = m1[0] * m2r0 + m1[1] * m2r1 + m1[2] * m2r2; (gdb) bt #0 transform33f3f (m1=0xffc00000ffc00044, m2=0x7fffffffa070, m3=0x7fffffffa080) at Vector.c:677 #1 0x00007ffff5761fdd in ObjectMapXPLORStrToMap (I=0x1dbf320, XPLORStr=<optimized out>, state=<optimized out>, quiet=0) at ObjectMap.c:3204 #2 0x00007ffff576b838 in ObjectMapReadXPLORStr (quiet=0, state=-1, XPLORStr=0x7fffeb685034 "\n 4 !NTITLE\n line 2 desc\n line 3 desc\n line 4 desc\n line 5 desc\n 080 0 080 160 0 160 080 0 080 \n 0.85336E+02 0.85336E+02 0.75650E+02 0.90000E+02 0.90000E"..., I=0x1dbf320, G=0xeb1300) at ObjectMap.c:4474 #3 ObjectMapLoadXPLOR (G=0xeb1300, obj=0x0, fname=<optimized out>, state=-1, is_file=0, quiet=0) at ObjectMap.c:5541 #4 0x00007ffff582c712 in ExecutiveLoad (G=0xeb1300, origObj=0x0, content=0x7fffeb685034 "\n 4 !NTITLE\n line 2 desc\n line 3 desc\n line 4 desc\n line 5 desc\n 080 0 080 160 0 160 080 0 080 \n 0.85336E+02 0.85336E+02 0.75650E+02 0.90000E+02 0.90000E"..., content_length=<optimized out>, content_format=26, object_name=0x7fffffffb210 "map", state=-1, zoom=-1, discrete=0, finish=1, multiplex=-1, quiet=0, plugin=0x0) at Executive.c:3724 #5 0x00007ffff586a572 in CmdLoad (self=0x7ffff6177dc8, args=<optimized out>) at Cmd.c:7866 #6 0x00000000004b66b9 in PyEval_EvalFrameEx () #7 0x00000000004bcdbd in PyEval_EvalCodeEx () ---Type <return> to continue, or q <return> to quit--- #8 0x00000000004b6c34 in PyEval_EvalFrameEx () #9 0x00000000004bcdbd in PyEval_EvalCodeEx () #10 0x00000000004bd892 in PyEval_EvalCode () #11 0x00000000004dcd82 in ?? () #12 0x00000000004dd7a5 in PyRun_StringFlags () #13 0x00000000004bafc6 in PyEval_EvalFrameEx () #14 0x00000000004bcdbd in PyEval_EvalCodeEx () #15 0x00000000004b6c34 in PyEval_EvalFrameEx () #16 0x00000000004bcdbd in PyEval_EvalCodeEx () #17 0x00000000004b6c34 in PyEval_EvalFrameEx () #18 0x00000000004bcdbd in PyEval_EvalCodeEx () #19 0x000000000044914f in ?? () #20 0x000000000042423c in ?? () #21 0x000000000042704d in PyObject_CallFunction () #22 0x00007ffff56f7414 in PFlushFast (G=0xeb1300) at P.c:2665 #23 0x00007ffff586b616 in CmdFlushNow (self=0x7ffff6177dc8, args=<optimized out>) at Cmd.c:2931 #24 0x00000000004b66b9 in PyEval_EvalFrameEx () #25 0x00000000004bcdbd in PyEval_EvalCodeEx () #26 0x00000000004b6c34 in PyEval_EvalFrameEx () #27 0x00000000004bcdbd in PyEval_EvalCodeEx () #28 0x00000000004b6c34 in PyEval_EvalFrameEx () #29 0x00000000004bcdbd in PyEval_EvalCodeEx () ---Type <return> to continue, or q <return> to quit--- #30 0x000000000044914f in ?? () #31 0x000000000042423c in ?? () #32 0x00000000004242e7 in ?? () #33 0x0000000000427248 in PyObject_CallMethod () #34 0x00007ffff586fd96 in MainDrawLocked () at main.c:811 #35 0x00007ffff586ff53 in MainDraw () at main.c:1081 #36 0x00007ffff47a0220 in ?? () from /usr/lib/libglut.so.3 #37 0x00007ffff47a3939 in fgEnumWindows () from /usr/lib/libglut.so.3 #38 0x00007ffff47a065a in glutMainLoopEvent () from /usr/lib/libglut.so.3 #39 0x00007ffff47a0f65 in glutMainLoop () from /usr/lib/libglut.so.3 #40 0x00007ffff5871504 in launch (options=0xeaf520, own_the_options=<optimized out>) at main.c:1955 #41 was_main () at main.c:2006 #42 0x00007ffff5853dd4 in CmdRunPyMOL (self=0x7ffff6177df0, args=<optimized out>) at Cmd.c:4771 #43 0x00000000004b66b9 in PyEval_EvalFrameEx () 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: Wed, 2 Jan 2013 11:01:52 -0500 > Subject: [PyMOL] which code actually executes to load axplor file? Debugstatements not executing. > > > > I'm trying to load a self-generated xplor file and pymol keeps segfaulting. I wanted to debug the > problem but can't get my debug statements to execute. The only thing that greps for "xplor" > is a few pymol modules and plugin called edmplugin. If I rebuild the plugin and relink pymol > nothing seems to change. Is this the right code? I also wanted to add a loader for other > formats of density or vector fields and maybe do some rendering ( I have an old viewer I wrote > with glut and thought I may be able to salvage parts of that for use here). > > Thanks. > > ------------------------------------------------------------------------------ > Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery > and much more. Keep your Java skills current with LearnJavaNow - > 200+ hours of step-by-step video tutorials by Java experts. > SALE $49.99 this month only -- learn more at: > http://p.sf.net/sfu/learnmore_122612 > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |
From: Thomas H. <tho...@sc...> - 2013-01-03 11:32:16
|
Hi Mike, I guess you are on Linux with Open-Source PyMOL, right? Can you send me the xplor file that causes PyMOL to segfault? From your backtrace it looks like the problem is related to crystal symmetry information. If you want to load some format which is not yet supported by PyMOL, the easiest solution is to convert it to some already supported format on the fly and feed that to PyMOL, if possible. Cheers, Thomas Mike Marchywka wrote, On 01/02/13 17:01: > I'm trying to load a self-generated xplor file and pymol keeps segfaulting. I wanted to debug the > problem but can't get my debug statements to execute. The only thing that greps for "xplor" > is a few pymol modules and plugin called edmplugin. If I rebuild the plugin and relink pymol > nothing seems to change. Is this the right code? I also wanted to add a loader for other > formats of density or vector fields and maybe do some rendering (I have an old viewer I wrote > with glut and thought I may be able to salvage parts of that for use here). > > Thanks. -- Thomas Holder PyMOL Developer Schrödinger Contractor |
From: Mike M. <mar...@ho...> - 2013-01-03 12:42:43
|
Thanks but it looks like I am ok now ( aside from orignally posting this on the wrong list LOL). My python build still hangs and has problems with the list area on right but the configure/make build process works fine and I could find the problem. Generally error checking is the last thing ayone wants to do and the positions sensitive fields are a big problem to find from a segfault. I think this is the 5..0.2 open source version. In any case, I wanted to allow for input of some custom file formats and maybe integrate with some of my old code and it now looks like I can do that. Would be happy to contribute at some point if I get something that works LOL. Thanks. ---------------------------------------- > Date: Thu, 3 Jan 2013 12:32:01 +0100 > From: tho...@sc... > To: pym...@li... > Subject: Re: [PyMOL] which code actually executes to load axplor file? Debugstatements not executing. > > Hi Mike, > > I guess you are on Linux with Open-Source PyMOL, right? Can you send me > the xplor file that causes PyMOL to segfault? From your backtrace it > looks like the problem is related to crystal symmetry information. > > If you want to load some format which is not yet supported by PyMOL, the > easiest solution is to convert it to some already supported format on > the fly and feed that to PyMOL, if possible. > > Cheers, > Thomas > > Mike Marchywka wrote, On 01/02/13 17:01: > > I'm trying to load a self-generated xplor file and pymol keeps segfaulting. I wanted to debug the > > problem but can't get my debug statements to execute. The only thing that greps for "xplor" > > is a few pymol modules and plugin called edmplugin. If I rebuild the plugin and relink pymol > > nothing seems to change. Is this the right code? I also wanted to add a loader for other > > formats of density or vector fields and maybe do some rendering (I have an old viewer I wrote > > with glut and thought I may be able to salvage parts of that for use here). > > > > Thanks. > > -- > Thomas Holder > PyMOL Developer > Schrödinger Contractor > > ------------------------------------------------------------------------------ > Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, > MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current > with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft > MVPs and experts. ON SALE this month only -- learn more at: > http://p.sf.net/sfu/learnmore_122712 > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |
From: James S. <jms...@gm...> - 2013-01-04 08:15:04
|
Hi Mike, Chimera can build such lattices by means of it's build structure module. On other hand I want to build such 2D lattices http://imageshack.us/photo/my-images/543/lattice.png/ made from SP3 carbons as the nodes via some automatic script to obtain lattices with desired dimensions. James 2013/1/3, James Starlight <jms...@gm...>: > Hi Mike, > > > Chimera can build such lattices by means of it's build structure > module. On other hand I want to build such 2D lattices > http://imageshack.us/photo/my-images/543/lattice.png/ > made from SP3 carbons via some automatic script. > > > > James > > 2012/12/28, Mike Marchywka <mar...@ho...>: >> >> >> >> What does Chimera do? I finally wrote my own c++ tool that let's a TcL >> script >> specify a molecule's layout in terms of relevance like bond length and >> angle. >> I decided it was worth the effort since I didn't want to look around much >> for existing >> stuff and would eventually add my own stuff for analysis. The real >> decision >> was >> to learn python or just use TcL. I guess if I was looking for a tool to >> generate >> from a script I'd probably prefer python. Thanks. >> >> >> >> >> ---------------------------------------- >>> Date: Fri, 28 Dec 2012 05:42:27 -0800 >>> From: jms...@gm... >>> To: pym...@li... >>> Subject: Re: [PyMOL] Building of the Carbon lattice >>> >>> Hi Tsjerk! >>> >>> This is the example of such lattice which I've built using Chimera! >>> http://imageshack.us/photo/my-images/543/lattice.png/ >>> >>> this is simple model of the Carbon-contained lattice without hydrogens. >>> So I'd like to build such lattices from different atoms as nodes >>> defining only atom type as well as number of nodes. >>> >>> Also I'd like to simulate this model using PBC so it seems that big >>> dimensions of such lattice doesn't matter, doesn’t it ? ( It will be >>> simpler to build smaller symmetric model ) >>> >>> James >>> >>> ------------------------------------------------------------------------------ >>> Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and >>> much more. Get web development skills now with LearnDevNow - >>> 350+ hours of step-by-step video tutorials by Microsoft MVPs and >>> experts. >>> SALE $99.99 this month only -- learn more at: >>> http://p.sf.net/sfu/learnmore_122812 >>> _______________________________________________ >>> PyMOL-users mailing list (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >> > |
From: Thomas H. <sp...@us...> - 2013-01-04 10:36:24
Attachments:
buildlattice.py
|
Hi James, just calculate the coordinates and write them out in PDB format, quite simple task. Try the attached script. Cheers, Thomas James Starlight wrote, On 01/04/13 09:14: > Hi Mike, > > Chimera can build such lattices by means of it's build structure > module. On other hand I want to build such 2D lattices > http://imageshack.us/photo/my-images/543/lattice.png/ > made from SP3 carbons as the nodes via some automatic script to > obtain lattices with desired dimensions. > > James -- Thomas Holder PyMOL Developer Schrödinger Contractor |
From: Mike M. <mar...@ho...> - 2013-01-04 14:44:17
|
Where do you get the x_shift and y_shift values? I ended up writing a program to take bond lengths and directions relative to select coord systems to generate periodic or almost periodic things. Right now polyenes but extensible. Is there some program that does this easily? This allows me to write a simple TcL script and reorient the whole molecule by changing one parameter . I don't currently have a way to include library items, like say a methyl group, and I was debating about doing this in python but I wanted to have easy access to lapack etc for later extensions. Thanks. ---------------------------------------- Date: Fri, 4 Jan 2013 11:13:39 +0100 From: sp...@us... To: jms...@gm... CC: pym...@li... Subject: Re: [PyMOL] Building of the Carbon lattice Hi James, just calculate the coordinates and write them out in PDB format, quite simple task. Try the attached script. Cheers, Thomas James Starlight wrote, On 01/04/13 09:14: > Hi Mike, > > Chimera can build such lattices by means of it's build structure > module. On other hand I want to build such 2D lattices > http://imageshack.us/photo/my-images/543/lattice.png/ > made from SP3 carbons as the nodes via some automatic script to > obtain lattices with desired dimensions. > > James -- Thomas Holder PyMOL Developer Schrödinger Contractor ------------------------------------------------------------------------------ Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and much more. Get web development skills now with LearnDevNow - 350+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122812 _______________________________________________ PyMOL-users mailing list (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |
From: Thomas H. <sp...@us...> - 2013-01-04 14:52:27
|
Hi Mike, I simply measured x_shift and y_shift from a cyclohexane fragment. Use the graphical Builder or the "fragment" command to load stuff from the fragment library. PyMOL> fragment cyclohexane Cheers, Thomas Mike Marchywka wrote, On 01/04/13 15:44: > Where do you get the x_shift and y_shift values? I ended up writing a program to > take bond lengths and directions relative to select coord systems to generate periodic or > almost periodic things. Right now polyenes but extensible. Is there some program that > does this easily? This allows me to write a simple TcL script and reorient the whole > molecule by changing one parameter . I don't currently have a way to include library > items, like say a methyl group, and I was debating about doing this in python > but I wanted to have easy access to lapack etc for later extensions. > Thanks. -- Thomas Holder PyMOL Developer Schrödinger Contractor |
From: Mike M. <mar...@ho...> - 2013-01-04 14:55:01
|
well, my point was just that they seem to be orientation sensitive although I didn't look at entire script in any detail and that if you wanted to re-orient the fragment you would have to recalculate these. Nothing difficult but just easier if there was a script that said something like "put this thing here with this orientation wrt some prior fragment " ( no absolute directions at this point. ) ---------------------------------------- > Date: Fri, 4 Jan 2013 15:52:13 +0100 > From: sp...@us... > To: mar...@ho... > CC: pym...@li... > Subject: Re: [PyMOL] Building of the Carbon lattice > > Hi Mike, > > I simply measured x_shift and y_shift from a cyclohexane fragment. Use > the graphical Builder or the "fragment" command to load stuff from the > fragment library. > > PyMOL> fragment cyclohexane > > Cheers, > Thomas > > Mike Marchywka wrote, On 01/04/13 15:44: > > Where do you get the x_shift and y_shift values? I ended up writing a program to > > take bond lengths and directions relative to select coord systems to generate periodic or > > almost periodic things. Right now polyenes but extensible. Is there some program that > > does this easily? This allows me to write a simple TcL script and reorient the whole > > molecule by changing one parameter . I don't currently have a way to include library > > items, like say a methyl group, and I was debating about doing this in python > > but I wanted to have easy access to lapack etc for later extensions. > > Thanks. > > -- > Thomas Holder > PyMOL Developer > Schrödinger Contractor |
From: Martin H. <ma...@bl...> - 2013-01-07 11:58:21
|
Hi PyMOL users I wonder, what is a most meaningful way of programmatically determining that a line of text in an arbitrary file contains atomic coordinates? The context of this question is that I plan to write a program that reads two files containing coordinates and has to perform operations on pairs of coordinates r1 and r2, where ri is the coordinate value from file i. Example format 1 (MOPAC): C( <LABEL TEXT> ) 1.0 +0 1.0 +0 1.0 +0 Example format 2 (PDB): ATOM 1 N ALA A 1 32.517 42.012 20.144 1.00 0.00 PROT N (some whitespace omitted). In example 1, the coordinates are "1.0", "1.0" and "1.0", the "+0" are program specific labels to identify the coordinate as fixed or relaxed. Can this really only be done by hardcoding the positions of the coordinates? Can this be unittested? I mean, if it indeed is only possible to read the coordinate by collecting, say [python] s="ATOM 1 N ALA A 1 32.517 42.012 20.144 1.00 0.00 PROT N" def get_x(s): x=s[32:38] return x [/python] what would a unittest for get_x look like? Would it even make sense to write such a test? Looking forward to discussions. Martin |
From: Jason V. <jas...@sc...> - 2013-01-11 06:59:40
|
Hi Martin, > I wonder, what is a most meaningful way of programmatically determining > that a line of text in an arbitrary file contains atomic coordinates? > The context of this question is that I plan to write a program that > reads two files containing coordinates and has to perform operations on > pairs of coordinates r1 and r2, where ri is the coordinate value from > file i. > > [snip] You ask about reading and testing coordinate data from files in various formats. There are two things I can think of to consider. First, each file format will have a different definition and therefore properties for extracting data. Some, like the PDB will be column-based, so you'll need to focus on getting your columns exactly right. Others might be binary (MTZ) or dictionaries (CIF) in which higher-order parsing might be necessary. Thus, for each format, you'd need a specific test which will be defined by that format. Second, and this happens all the time, many application writers will produce files that are nearly properly formatted--read incorrectly formatted--and will break a strict parser. If you're working on a large set of files, I suggest you write a "scrubber" that you can apply across your files to ensure they're properly formatted before use. If you're lucky, your format will come with a nicely defined BNF grammar. Good luck. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) Jas...@sc... (o) +1 (603) 374-7120 |