[PyMOL] FW: colouring states of a md trajectory
Hi Tsjerk, Many thanks for pointing this out. Thanks to the spectrum_states script authors as well. It worked perfectly! Kind regards, Sid. From: Tsjerk Wassenaar [mailto:tsje...@gmail.com] Sent: 02 June 2013 20:34 To: Sridharan, Sudharsan Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] colouring states of a md trajectory Hi Sid, Have a look at this: http://pymolwiki.org/index.php/Spectrum_states Hope it helps, Tsjerk On Sun, Jun 2, 2013 at 8:06 PM, Sridharan, Sudharsan sridhar...@medimmune.commailto:sridhar...@medimmune.com wrote: Hi all, Sorry this may be a naive question and probably has a simple answer but I haven't been able to figure it out! I'd like to colour all the states of a md trajectory shown as ribbons with state 1 coloured the darkest, say black, gradually going to the lightest shade for the last state. How do I do this please. If I have two chains, how can I colour similarly but using two different colours for the two chains. (I was able to colour all the states using rainbow colours) Many thanks. Kind regards, Sid. Sudharsan Sridharan, Ph.D. Scientist I Protein Sciences, Department of Antibody Discovery and Protein Engineering MedImmune* Ltd., Aaron Klug Building, Granta Park, Cambridge, CB21 6GH, UK. Direct telephone: + 44(0)1223 898195 Facsimile: + 44(0)1223 471472 Email: sridhar...@medimmune.commailto:sridhar...@medimmune.com Web: www.medimmune.comhttp://www.medimmune.com MedImmune * Milstein Building, Granta Park, Cambridge, CB21 6GH, UK (formerly Cambridge Antibody Technology Limited) Registered Office: Milstein Building, Granta Park, Cambridge, CB21 6GH, UK Registered in England and Wales number 2451177. Confidentiality Note: This information and any attachments is confidential and only for use by the individual or entity to whom it has been sent. Any unauthorised dissemination, distribution or copying of this message is strictly prohibited. If you are not the intended recipient please inform the sender immediately by reply e-mail and delete this message from your system. Thank you for your co-operation. We may monitor or record emails to or from MedImmune. E-mails may contain viruses or other harmful software that may damage your system. Whilst we have tried to eliminate such viruses and other harmful software we cannot accept liability for any damage caused to your system by any that remain. It is your responsibility to protect your system and you are advised to carry out your own checks on e-mails from us. To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.netmailto: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 -- Tsjerk A. Wassenaar, Ph.D. To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page:
Re: [PyMOL] PyMOL APBS plugin on Ubuntu 12.10 - error after 'run APBS'
Hej Tobias.
Some time ago, a year+?, I played around fixing some small things in APBS,
to make it easier to work. (Most fixing small path things)
Orginal version:
http://pymolwiki.org/index.php/APBS
Small modified version:
http://pymolwiki.org/index.php/Apbsplugin
The modified version, is packed into the Pymol-script-repo
http://pymolwiki.org/index.php/Git
I made this installation script some time ago,
http://www.pymolwiki.org/index.php/User:Tlinnet/Linux_Install#Install_script
which download the Pymol-script-repo, and sets the path right.
at the moment I can't test it? since:
svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
svn: E210002: Unable to connect to a repository at URL 'svn://
svn.code.sf.net/p/pymol/code/trunk/pymol'
svn: E210002: Network connection closed unexpectedly
But maybe you can see from the script, what you have to do.
Best
Troels Emtekær Linnet
2013/5/31 Tobias Beck tobiasb...@gmail.com:
Dear all,
I am trying to run the ABPS plugin with PyMOL Version 1.6.0.0 on Ubuntu
12.10. I have compiled pymol from source
(http://www.pymolwiki.org/index.php/Linux_Install).
When running the plugin, I can set the grid, but after clicking on Run
APBS,
I get the following error:
Unexpected error: (type 'exceptions.ImportError', ImportError('No module
named pdb2pqr.pdb2pqr',), traceback object at 0x7fd130771200)
type 'exceptions.UnboundLocalError' Exception in Tk callback
Function: function lambda at 0x7fd13078e398 (type: type
'function')
Args: ()
Traceback (innermost last):
File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line
1747, in __call__
return apply(self.func, args)
File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
line
153, in lambda
command=lambda self=self, name=name: self._doCommand(name))
File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
line
132, in _doCommand
return command(name)
File /home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py, line 1036,
in
execute
good = self.generatePqrFile()
File /home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py, line 1007,
in
generatePqrFile
good = self._generatePdb2pqrPqrFile()
File /home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py, line 1615,
in
_generatePdb2pqrPqrFile
if retval != 0:
type 'exceptions.UnboundLocalError': local variable 'retval' referenced
before assignment
The first line suggests that the pdb2pqr module cannot be loaded. However,
the grid seems to be set okay. Has anybody encountered this error before
and
knows how to solve it?
I have also tried the pymol version that can be installed with apt-get,
but
same error.
Thanks for any advice!
Best wishes, Tobias.
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Re: [PyMOL] PyMOL APBS plugin on Ubuntu 12.10 - error after 'run APBS'
Hi Troels,
Many thanks for your email!
I found a work around for my problem this morning: I copied the pdb2pqr
directory from my Mac and now the plugin works. I guess for the Ubuntu
pymol package, the pdb2pqr is not installed by default?
svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
svn: E210002: Unable to connect to a repository at URL 'svn://
svn.code.sf.net/p/pymol/code/trunk/pymol'
svn: E210002: Network connection closed unexpectedly
Yes, I have also tried to use svn this morning, but got same error.
Thanks again!
Best wishes, Tobias.
On Mon, Jun 3, 2013 at 11:28 AM, Troels Emtekær Linnet tlin...@gmail.comwrote:
Hej Tobias.
Some time ago, a year+?, I played around fixing some small things in APBS,
to make it easier to work. (Most fixing small path things)
Orginal version:
http://pymolwiki.org/index.php/APBS
Small modified version:
http://pymolwiki.org/index.php/Apbsplugin
The modified version, is packed into the Pymol-script-repo
http://pymolwiki.org/index.php/Git
I made this installation script some time ago,
http://www.pymolwiki.org/index.php/User:Tlinnet/Linux_Install#Install_script
which download the Pymol-script-repo, and sets the path right.
at the moment I can't test it? since:
svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
svn: E210002: Unable to connect to a repository at URL 'svn://
svn.code.sf.net/p/pymol/code/trunk/pymol'
svn: E210002: Network connection closed unexpectedly
But maybe you can see from the script, what you have to do.
Best
Troels Emtekær Linnet
2013/5/31 Tobias Beck tobiasb...@gmail.com:
Dear all,
I am trying to run the ABPS plugin with PyMOL Version 1.6.0.0 on Ubuntu
12.10. I have compiled pymol from source
(http://www.pymolwiki.org/index.php/Linux_Install).
When running the plugin, I can set the grid, but after clicking on Run
APBS,
I get the following error:
Unexpected error: (type 'exceptions.ImportError', ImportError('No
module
named pdb2pqr.pdb2pqr',), traceback object at 0x7fd130771200)
type 'exceptions.UnboundLocalError' Exception in Tk callback
Function: function lambda at 0x7fd13078e398 (type: type
'function')
Args: ()
Traceback (innermost last):
File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py,
line
1747, in __call__
return apply(self.func, args)
File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
line
153, in lambda
command=lambda self=self, name=name: self._doCommand(name))
File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
line
132, in _doCommand
return command(name)
File /home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py, line
1036, in
execute
good = self.generatePqrFile()
File /home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py, line
1007, in
generatePqrFile
good = self._generatePdb2pqrPqrFile()
File /home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py, line
1615, in
_generatePdb2pqrPqrFile
if retval != 0:
type 'exceptions.UnboundLocalError': local variable 'retval' referenced
before assignment
The first line suggests that the pdb2pqr module cannot be loaded.
However,
the grid seems to be set okay. Has anybody encountered this error before
and
knows how to solve it?
I have also tried the pymol version that can be installed with apt-get,
but
same error.
Thanks for any advice!
Best wishes, Tobias.
--
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Download for free and get started troubleshooting in minutes.
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[PyMOL] settings
I'm trying to understand settings. I see that there are at least these levels of settings: - global - object - state - unique atom/bond Are there more? I'm unclear on when one overrides another. It looks to me that the general getSetting methods have the option of up to three levels of settings, but there are four here. Thus, for example: If I have unique settings for a bond and then apply the sort of script that Sid recently was interested in, that might change stick_color, would that unique bond setting be overridden? If a state's color is set using Spectrum_states.py, does that override already-set scene colors? Or is it incorporated into defined scenes then? -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2___ 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] scenes and states
Questions: Can two objects be in two different states -- object1 in state 3 and object2 in state 10, for instance, at the same time? If so, how is that set up? How is that then incorporated into a scene? Do CGO, measurements, mesh, and volume objects have states as well? Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2___ 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] scenes and states
Hi Bob, The answer is yes to all. fetch 1ubq, state=3 fetch 6lzm, state=10 cmd.load_cgo([7.0,0,0,0,2],name=sphere,state=2) The representations (e.g. surface) do have states in the sense that the each state gives a different surface. But whether the surface is shown or not is controlled globally. It is not possible to have the surface representation only in one state, such that looping over the states, the surface would suddenly pop up for one. Hope it helps, Tsjerk On Mon, Jun 3, 2013 at 2:38 PM, Robert Hanson hans...@stolaf.edu wrote: Questions: Can two objects be in two different states -- object1 in state 3 and object2 in state 10, for instance, at the same time? If so, how is that set up? How is that then incorporated into a scene? Do CGO, measurements, mesh, and volume objects have states as well? Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 ___ 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 -- Tsjerk A. Wassenaar, Ph.D. -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2___ 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] settings
Hi Robert, you got the levels right. The cmd.get method actually doesn't support querying atom level settings, even though you can set them with cmd.set. Atom settings are not state specific, unless you have a discrete object. Scenes do not store settings, so using spectrum_states overrides scene colors. Hope that helps. Cheers, Thomas On Jun 3, 2013, at 8:34 AM, Robert Hanson hans...@stolaf.edu wrote: I'm trying to understand settings. I see that there are at least these levels of settings: - global - object - state - unique atom/bond Are there more? I'm unclear on when one overrides another. It looks to me that the general getSetting methods have the option of up to three levels of settings, but there are four here. Thus, for example: If I have unique settings for a bond and then apply the sort of script that Sid recently was interested in, that might change stick_color, would that unique bond setting be overridden? If a state's color is set using Spectrum_states.py, does that override already-set scene colors? Or is it incorporated into defined scenes then? -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 ___ 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] scenes and states
[[sorry -- not used to a list that requires reply-all to go back to the list]] What you describe there is a way to load a specific file into a specific state, I think. I meant, once you have a set of multi-state objects, can I select to compare two different states, one from one and one from the other? 1cdr2/10 1sq35/30 and then could I make a scene that does that? -- without viewing all states Bob On Mon, Jun 3, 2013 at 9:07 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bob, The answer is yes to all. fetch 1ubq, state=3 fetch 6lzm, state=10 cmd.load_cgo([7.0,0,0,0,2],name=sphere,state=2) The representations (e.g. surface) do have states in the sense that the each state gives a different surface. But whether the surface is shown or not is controlled globally. It is not possible to have the surface representation only in one state, such that looping over the states, the surface would suddenly pop up for one. Hope it helps, Tsjerk On Mon, Jun 3, 2013 at 2:38 PM, Robert Hanson hans...@stolaf.edu wrote: Questions: Can two objects be in two different states -- object1 in state 3 and object2 in state 10, for instance, at the same time? If so, how is that set up? How is that then incorporated into a scene? Do CGO, measurements, mesh, and volume objects have states as well? Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 ___ 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 -- Tsjerk A. Wassenaar, Ph.D. -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2___ 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] scenes and states
Hi Bob, it's the object-level state setting: fetch 1nmr 1d7q, async=0 set state, 3, 1nmr set state, 10, 1d7q And since scenes do not store settings, this cannot be stored with a scene. Cheers, Thomas On Jun 3, 2013, at 10:41 AM, Robert Hanson hans...@stolaf.edu wrote: [[sorry -- not used to a list that requires reply-all to go back to the list]] What you describe there is a way to load a specific file into a specific state, I think. I meant, once you have a set of multi-state objects, can I select to compare two different states, one from one and one from the other? 1cdr2/10 1sq35/30 and then could I make a scene that does that? -- without viewing all states Bob On Mon, Jun 3, 2013 at 9:07 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bob, The answer is yes to all. fetch 1ubq, state=3 fetch 6lzm, state=10 cmd.load_cgo([7.0,0,0,0,2],name=sphere,state=2) The representations (e.g. surface) do have states in the sense that the each state gives a different surface. But whether the surface is shown or not is controlled globally. It is not possible to have the surface representation only in one state, such that looping over the states, the surface would suddenly pop up for one. Hope it helps, Tsjerk On Mon, Jun 3, 2013 at 2:38 PM, Robert Hanson hans...@stolaf.edu wrote: Questions: Can two objects be in two different states -- object1 in state 3 and object2 in state 10, for instance, at the same time? If so, how is that set up? How is that then incorporated into a scene? Do CGO, measurements, mesh, and volume objects have states as well? Bob -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 ___ 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] settings
Thanks, Thomas On Mon, Jun 3, 2013 at 9:36 AM, Thomas Holder thomas.hol...@schrodinger.com wrote: Hi Robert, you got the levels right. The cmd.get method actually doesn't support querying atom level settings, even though you can set them with cmd.set. I see. That's helpful. Atom settings are not state specific, unless you have a discrete object. I see, because then every atom in a multi-model file has is own record, and thus its own unique ID. Sure. For now, Jmol is loading all PSE files as though discrete=1. The Jmol equivalent of discrete=0 would be (in Jmol) *load TRAJECTORY xxx.pse*, but I don't have that right now able to load some models as trajectories and some not, as would generally be needed in PSE file loading. So that will have to wait. Scenes do not store settings, so using spectrum_states overrides scene colors. But a scene does store settings in the sense that there are, at least for colors, for example, _!c_scene_xxx_sticks settings. How does that fit in, then? I'll look into that. Hope that helps. definitely! Cheers, Thomas On Jun 3, 2013, at 8:34 AM, Robert Hanson hans...@stolaf.edu wrote: I'm trying to understand settings. I see that there are at least these levels of settings: - global - object - state - unique atom/bond Are there more? I'm unclear on when one overrides another. It looks to me that the general getSetting methods have the option of up to three levels of settings, but there are four here. Thus, for example: If I have unique settings for a bond and then apply the sort of script that Sid recently was interested in, that might change stick_color, would that unique bond setting be overridden? If a state's color is set using Spectrum_states.py, does that override already-set scene colors? Or is it incorporated into defined scenes then? -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2___ 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
