Re: [PyMOL] RMS
Carlos, The complication is that align outputs RMS values for only those atomic pairs remaining following sequence matching following by a refined structure alignment (which omits atoms above a cutoff), whereas rms outputs the value for all atoms matched by identifier (without any optimization). To run align without optimization, issue: align selection1, selection2, cycles=0 where selection1 and selection2 are replaced with your atom selections, but remember that unmatched residues will not be included in the output RMS value. Cheers, Warren > -Original Message- > From: Carlos Ríos Vera [mailto:crosv...@gmail.com] > Sent: Monday, August 24, 2009 1:44 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] RMS > > Hello people, > > I'm trying to use pymol from a custom python scrypt. What I have done > is to align two structures, but I need get the RMS value from that > align but I have no idea how to do it. > > I tried to use the RMS command but the value differs from the value > that I get from the align. > > Any Idea how to get that value? > > cheers > > ps: Sorry if my English is not so good > > -- > http://crosvera.blogspot.com > > Carlos Ríos V. > Estudiante de Ing. (E) en Computación e Informática. > Universidad del Bío-Bío > VIII Región, Chile > > Linux user number 425502 > > -- > > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30- > Day > trial. Simplify your report design, integration and deployment - and focus > on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > ___ > 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 > > > -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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
Re: [PyMOL] Zalman 3D Monitor
Joachim, I think this is more an issue of driver support rather than hardware. However, the latest drivers do not necessarily support older cards. Please see nVidia's site for details: http://www.nvidia.com/Download/index.aspx?lang=en-us and click on the "supported hardware" tab after searching. Cheers, Warren > -Original Message- > From: Joachim Reichelt [mailto:joachim.reich...@helmholtz-hzi.de] > Sent: Monday, August 24, 2009 6:08 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Zalman 3D Monitor > > Hello, > > does anyone know, which Quadro card supports the Zalman mode. > The readme states: > Stereo options 7, 8, and 9 are only supported on G8xGL and > higher GPUs. > Mode 7 is for the Zalman > -- > Joachim > > -- > > Let Crystal Reports handle the reporting - Free Crystal > Reports 2008 30-Day trial. Simplify your report design, > integration and deployment - and focus on what you do best, > core application coding. Discover what's new with Crystal > Reports now. http://p.sf.net/sfu/bobj-july > ___ > 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 > > > > > -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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
Re: [PyMOL] Calling scripted functions within alter_state
Stuart, Hmm...whoops, my mistake. Cmd.extend doesn't actually add a function to the cmd module -- only to the command keyword dictionary. So, instead, set it explicitly in your .py file: from pymol import cmd def my_fn(...): cmd.my_fn = my_fn # then later on, in the menu, etc.: cmd.alter_state(..., "cmd.my_fn(...)") Cheers, Warren From: Stuart Ballard [mailto:srball...@wisc.edu] Sent: Monday, August 24, 2009 4:06 PM To: Warren DeLano Cc: pymol-users Subject: Re: [PyMOL] Calling scripted functions within alter_state Hello Warren, When adding in the "cmd." I get these error messages: Traceback (most recent call last): File "", line 1, in AttributeError: 'module' object has no attribute 'sym_partner' Traceback (most recent call last): File "", line 1, in AttributeError: 'module' object has no attribute 'cell_shift_helper' Versus the error I get with the "cmd." not included: Traceback (most recent call last): File "", line 1, in NameError: name 'sym_partner' is not defined Traceback (most recent call last): File "", line 1, in NameError: name 'cell_shift_helper' is not defined I'm pretty stumped at this point. Does it seem like the pymol.cmd namespace isn't acquiring the new functions as it ought to be? Stuart 2009/8/24 Warren DeLano Hello Stuart, By default, alter_state expressions are evaluated in the "pymol" namespace of the current PyMOL instance, not the "cmd" (pymol.cmd) namespace. The reason why it works with 'run' is that run also executes in "pymol" by default, and thus, includes any functions you define. Try: cmd.alter_state(1, copy, "x,y,z = cmd.sym_partner([x,y,z], stored.tmpOp)") instead, after using cmd.extend in your startup or GUI script. Cheers, Warren From: Stuart Ballard [mailto:srball...@wisc.edu] Sent: Monday, August 24, 2009 3:38 PM To: pymol-users Subject: [PyMOL] Calling scripted functions within alter_state Hello Warren, all, I've been working on a plugin for PyMOLX11Hybrid, in which I have a few lines of code such as: cmd.alter_state(1, copy, "x,y,z = sym_partner([x,y,z], stored.tmpOp)") AND cmd.alter_state(1, object, "x,y,z = cell_shift_helper([x,y,z],stored.shift)") Both those functions (sym_partner and cell_shift_helper) are extended through cmd.extend() function, along with several others which work perfectly well. The issue arises only when I attempt to use these functions through a menu added to PyMOL GUI, which does not involve issuing the run /(filepath)/(script).py command in PyMOL, but rather initializes necessary commands on startup. I've confirmed that the cmd.extend() calls are made properly, but I can only fix the problem by issuing the run command independent of my initialization scripts. Because this script is planned to be incorporated into a build of PyMOL which will be run from a variety of file paths, I'd like to know how I can solve this problem without simply jury rigging a run command. Is there a way to properly make commands available within an alter_state command without using the run command? Thanks, Stuart Ballard Dept. of Biochemistry UW-Madison -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ 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
Re: [PyMOL] Calling scripted functions within alter_state
Hello Warren, When adding in the "cmd." I get these error messages: Traceback (most recent call last): File "", line 1, in AttributeError: 'module' object has no attribute 'sym_partner' Traceback (most recent call last): File "", line 1, in AttributeError: 'module' object has no attribute 'cell_shift_helper' Versus the error I get with the "cmd." not included: Traceback (most recent call last): File "", line 1, in NameError: name 'sym_partner' is not defined Traceback (most recent call last): File "", line 1, in NameError: name 'cell_shift_helper' is not defined I'm pretty stumped at this point. Does it seem like the pymol.cmd namespace isn't acquiring the new functions as it ought to be? Stuart 2009/8/24 Warren DeLano > Hello Stuart, > > > > By default, alter_state expressions are evaluated in the “pymol” namespace > of the current PyMOL instance, not the “cmd” (pymol.cmd) namespace. The > reason why it works with ‘run’ is that run also executes in “pymol” by > default, and thus, includes any functions you define. > > > > Try: > > > > cmd.alter_state(1, copy, "x,y,z = cmd.sym_partner([x,y,z], stored.tmpOp)") > > instead, after using cmd.extend in your startup or GUI script. > > > > Cheers, > > Warren > > > > > -- > > *From:* Stuart Ballard [mailto:srball...@wisc.edu] > *Sent:* Monday, August 24, 2009 3:38 PM > *To:* pymol-users > *Subject:* [PyMOL] Calling scripted functions within alter_state > > > > Hello Warren, all, > > > I've been working on a plugin for PyMOLX11Hybrid, in which I have a few > lines of code such as: > > cmd.alter_state(1, copy, "x,y,z = sym_partner([x,y,z], > stored.tmpOp)") > > AND > > cmd.alter_state(1, object, "x,y,z = > cell_shift_helper([x,y,z],stored.shift)") > > Both those functions (sym_partner and cell_shift_helper) are extended > through cmd.extend() function, along with several others which work > perfectly well. The issue arises only when I attempt to use these functions > through a menu added to PyMOL GUI, which does not involve issuing the run > /(filepath)/(script).py command in PyMOL, but rather initializes necessary > commands on startup. I've confirmed that the cmd.extend() calls are made > properly, but I can only fix the problem by issuing the run command > independent of my initialization scripts. > > Because this script is planned to be incorporated into a build of PyMOL > which will be run from a variety of file paths, I'd like to know how I can > solve this problem without simply jury rigging a run command. Is there a way > to properly make commands available within an alter_state command without > using the run command? > > > Thanks, > Stuart Ballard > Dept. of Biochemistry > UW-Madison > -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ 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
Re: [PyMOL] Calling scripted functions within alter_state
Hello Stuart, By default, alter_state expressions are evaluated in the "pymol" namespace of the current PyMOL instance, not the "cmd" (pymol.cmd) namespace. The reason why it works with 'run' is that run also executes in "pymol" by default, and thus, includes any functions you define. Try: cmd.alter_state(1, copy, "x,y,z = cmd.sym_partner([x,y,z], stored.tmpOp)") instead, after using cmd.extend in your startup or GUI script. Cheers, Warren From: Stuart Ballard [mailto:srball...@wisc.edu] Sent: Monday, August 24, 2009 3:38 PM To: pymol-users Subject: [PyMOL] Calling scripted functions within alter_state Hello Warren, all, I've been working on a plugin for PyMOLX11Hybrid, in which I have a few lines of code such as: cmd.alter_state(1, copy, "x,y,z = sym_partner([x,y,z], stored.tmpOp)") AND cmd.alter_state(1, object, "x,y,z = cell_shift_helper([x,y,z],stored.shift)") Both those functions (sym_partner and cell_shift_helper) are extended through cmd.extend() function, along with several others which work perfectly well. The issue arises only when I attempt to use these functions through a menu added to PyMOL GUI, which does not involve issuing the run /(filepath)/(script).py command in PyMOL, but rather initializes necessary commands on startup. I've confirmed that the cmd.extend() calls are made properly, but I can only fix the problem by issuing the run command independent of my initialization scripts. Because this script is planned to be incorporated into a build of PyMOL which will be run from a variety of file paths, I'd like to know how I can solve this problem without simply jury rigging a run command. Is there a way to properly make commands available within an alter_state command without using the run command? Thanks, Stuart Ballard Dept. of Biochemistry UW-Madison -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ 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
[PyMOL] Calling scripted functions within alter_state
Hello Warren, all, I've been working on a plugin for PyMOLX11Hybrid, in which I have a few lines of code such as: cmd.alter_state(1, copy, "x,y,z = sym_partner([x,y,z], stored.tmpOp)") AND cmd.alter_state(1, object, "x,y,z = cell_shift_helper([x,y,z],stored.shift)") Both those functions (sym_partner and cell_shift_helper) are extended through cmd.extend() function, along with several others which work perfectly well. The issue arises only when I attempt to use these functions through a menu added to PyMOL GUI, which does not involve issuing the run /(filepath)/(script).py command in PyMOL, but rather initializes necessary commands on startup. I've confirmed that the cmd.extend() calls are made properly, but I can only fix the problem by issuing the run command independent of my initialization scripts. Because this script is planned to be incorporated into a build of PyMOL which will be run from a variety of file paths, I'd like to know how I can solve this problem without simply jury rigging a run command. Is there a way to properly make commands available within an alter_state command without using the run command? Thanks, Stuart Ballard Dept. of Biochemistry UW-Madison -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ 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
[PyMOL] RMS
Hello people, I'm trying to use pymol from a custom python scrypt. What I have done is to align two structures, but I need get the RMS value from that align but I have no idea how to do it. I tried to use the RMS command but the value differs from the value that I get from the align. Any Idea how to get that value? cheers ps: Sorry if my English is not so good -- http://crosvera.blogspot.com Carlos Ríos V. Estudiante de Ing. (E) en Computación e Informática. Universidad del Bío-Bío VIII Región, Chile Linux user number 425502 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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
[PyMOL] Zalman 3D Monitor
Hello, does anyone know, which Quadro card supports the Zalman mode. The readme states: Stereo options 7, 8, and 9 are only supported on G8xGL and higher GPUs. Mode 7 is for the Zalman -- Joachim -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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
