pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Emily,

PyMOL's morphing performs two steps: (1) RigiMOL, and (2) refinement of non-backbone atoms by sculpting. The second part can be skipped with "refinement=0".

Unfortunately, there is no RigiMOL publication or method documentation.

The sculpting refinement tries to avoid clashes and maintain the local sidechain geometry, based on start and end conformation as references. You are right that sculpting doesn't consider the Ramachandran plot or a real energy force field. But it does consider clashes (it has a VDW term). Check "Build > Sculpting > ...", the bottom part of that submenu lists some of the available terms. The corresponding numerical values can be found here:
https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/layer2/Sculpt.h

The "morph" command refinement uses all sculpting terms. You could customize that, e.g. exclude VDW repulsion, like this:

PyMOL> morph mout, sele1, sele2, refinement=0
PyMOL> from epymol.rigimol import refine
PyMOL> refine(5, "mout", sculpt_field_mask=(0xFFF & ~0x60))

You can also "fix" atoms, e.g. all non-polymer atoms, like free ions, which tend to bounce around as a result of the refinement:

PyMOL> morph mout, sele1, sele2, refinement=0
PyMOL> from epymol.rigimol import refine
PyMOL> flag fix, (not polymer), set
PyMOL> refine(5, "mout")

Hope that helps.

Cheers,
  Thomas

On 30 May 2016, at 12:43, Emilia C. Arturo (Emily) <ec...@DR...> wrote:

> Hello.
> 
> I would like to know more about the type of interpolation that is done when morph is called, and what calculations are done at each refinement cycle. Is there a literature reference or previous forum discussion to which you can point me?
> 
> From my sifting through the internet, I settled on the likelihood that refinement is done using the "molecular sculpting" algorithm that has been employed since at least this discussion took place in 2002: http://www.mail-archive.com/pym...@li.../msg00359.html
> In other words, refinement is not done on the basis of energy differences, Ramachandran plot, interatomic clashes, or other problems with geometry that could arise at each interpolation step. 
> 
> Is that correct? If so, is there a way to customize the refinement that's done?
> 
> I am using MacPyMOL version 1.7.6.2.
> 
> Regards,
> 
> Emily.

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Filip,

Incentive PyMOL includes numpy and scipy. However, the 1.8.0.0 release on Windows was missing some dlls, that's why "import numpy" fails. The 1.8.0.7 update fixes that.

Cheers,
  Thomas

On 30 May 2016, at 06:44, Filip Leonarski <leo...@un...> wrote:

> Hi,
> 
>    I have a question - is it possible to have numpy and scipy available in pymol 1.8 incentive version. I have some plugins that worked perfectly well with pymol 1.7, however after upgrade to 1.8 they fail on "import numpy" step.
> 
> Thanks,
> Filip
> 
> -- 
> Filip Leonarski, PhD
> IBMC/CNRS
> 15 rue René Descartes
> 67084 Strasbourg Cedex

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hello all.

I'm struggling to comprehend why the morph function, as called using
MacPyMOL version 1.7.6.2, is making iron ions either migrate out of the
active site during the interpolation, or completely absent from the
interpolation.

I call the morph function like so:  morph morphresult, pdb1, pdb2, match=#,
where in place of '#' I have tried all the arguments available to match; if
#=in, then the iron ion in one, two, or three chains of the four chains in
each of pdb1 and pdb2, migrates out of the active site(s) and into some
nonsensical space; if #=like or any other argument, the iron ions do not
appear in the interpolation. Both pdb1 and pdb2 have four chains, and in
each of the chains is an iron ion labeled identically as 'FE'.

Has anyone a recommendation for how to address this?

Emily.

-- 
"Study as if you were going to live forever; live as if you were going to
die tomorrow." - Maria Mitchell

"Success is going from failure to failure without losing your enthusiasm."
- Anon.

“We are the people we have been waiting for.”
- A tag line from MIT's Vehicle Design Summit website (http://vds.mit.edu)

Hello.

I would like to know more about the type of interpolation that is done when
morph is called, and what calculations are done at each refinement cycle.
Is there a literature reference or previous forum discussion to which you
can point me?

>From my sifting through the internet, I settled on the likelihood that
refinement is done using the "molecular sculpting" algorithm that has been
employed since at least this discussion took place in 2002:
http://www.mail-archive.com/pym...@li.../msg00359.html
In other words, refinement is not done on the basis of energy differences,
Ramachandran plot, interatomic clashes, or other problems with geometry
that could arise at each interpolation step.

Is that correct? If so, is there a way to customize the refinement that's
done?

I am using MacPyMOL version 1.7.6.2.

Regards,

Emily.


-- 
"Study as if you were going to live forever; live as if you were going to
die tomorrow." - Maria Mitchell

"Success is going from failure to failure without losing your enthusiasm."
- Anon.

“We are the people we have been waiting for.”
- A tag line from MIT's Vehicle Design Summit website (http://vds.mit.edu)

Hello.

I would like to know more about the type of interpolation that is done when
morph is called, and what calculations are done at each refinement cycle.
Is there a reference or previous forum discussion to which you can point me?

I am using MacPyMOL version 1.7.6.2.

Regards,

Emily.

-- 
"Study as if you were going to live forever; live as if you were going to
die tomorrow." - Maria Mitchell

"Success is going from failure to failure without losing your enthusiasm."
- Anon.

“We are the people we have been waiting for.”
- A tag line from MIT's Vehicle Design Summit website (http://vds.mit.edu)

Hi,

    I'm trying to access electron density maps from PyMol. Everything is
fine, when the map is orthorombic. I take map extremities with get_extend
and compare them with shape of array accessed via get_volume_field .
However when map is non-orthorombic I need to shuffle between
fractional/real coordinates. And here is the problem:

I have a map calculated exactly for the unit cell. However map_extend
provides values around 1% smaller. Why can it be?

Thanks,
Filip


-- 
Filip Leonarski, PhD
IBMC/CNRS
15 rue René Descartes
67084 Strasbourg Cedex

Hi,

   I have a question - is it possible to have numpy and scipy available in
pymol 1.8 incentive version. I have some plugins that worked perfectly well
with pymol 1.7, however after upgrade to 1.8 they fail on "import numpy"
step.

Thanks,
Filip

-- 
Filip Leonarski, PhD
IBMC/CNRS
15 rue René Descartes
67084 Strasbourg Cedex

Greetings,

PyMOL 1.8.2.1 fixes a bug in the mutagenesis wizard and adds the "pick32bit" setting to work around graphics cards which don't support 32bit color depth for picking. Builds are available as usual from http://pymol.org/download

If you have encountered picking errors where the wrong atoms are selected or reported when clicking on them, please drop me an email with your graphics card and driver information. Thanks.

Cheers,
- The PyMOL Team at Schrödinger

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Thanks to Christoph and Jeroen!

This was the perfect resource to make it work.

Cheers,

Chris

--
Christopher L. Colbert, Ph.D.
Assistant Professor
Department of Chemistry and Biochemistry
North Dakota State University
P.O. Box 6050 Dept. 2710
Fargo, ND 58108-6050
PH: (701) 231-7946
FAX: (701) 231-8324

From: Christoph Parthier <cpa...@go...<mailto:cpa...@go...>>
Date: Friday, May 27, 2016 6:59 AM
To: "pym...@li...<mailto:pym...@li...>" <pym...@li...<mailto:pym...@li...>>
Cc: Christopher Colbert <chr...@nd...<mailto:chr...@nd...>>
Subject: Re: [PyMOL] Stereo Set up with PyMOL v1.7.4.4 EDU

Dear Chris,

We have  a similar setup using an older Quadro card employing a dual screen output (one DP/DVI-port for each projector). The two "screens" are in "clone mode" (NVIDIA control panel), as described e.h. here:

http://nvidia.custhelp.com/app/answers/detail/a_id/3012/~/how-to-configure-passive-or-dual-pipe-stereo-with-quadro-cards-in-windows-7.

The projectors are aligned using a projector-built-in test pattern.

In the NVIDIA 3D settings you have to activate 'Stereo' using the 'NVidia Clone Mode Stereo' (or similarly named). In PyMol you use the 'Quad-buffered Stereo' option. The NVIDIA driver will do the rest to provide the individual left/right images. It works for full screen and also for windowed PyMol (OpenGL windows with activated stereo only). The rest of the desktop remains "cloned".

Hope this helps,
Christoph



On 05/26/2016 08:34 PM, Christopher Colbert wrote:
Hi All,

We "upgraded" our 3D viewing room with a computer that has a Quadro K2000 video card running Windows 7.  The computer displays through two NEC projectors with polarizing filters that display agains a special screen.  Stereo is viewed through polarized glasses just like in the movie theater.   We had the stereo working a couple years ago, but it stopped with the upgrade.  Here is my question:

Are there any special Quadro settings I need to set to have the video card play nice with PyMOL?
Which stereo_mode do I set for this type of setup?  I ran through all the options (1 - 12), but none caused the appropriate stereo effect
Am I restricted to full screen mode or can I run stereo in windowed mode?  We only tried Windowed mode.
Does the stereo_mode change if I am using full screen mode versus window mode?

Any help or resources you can point me to would be greatly appreciated.  (Proper procedure for aligning the projectors would be greatly appreciated.  They are fairly well aligned centrally, but become blurry from misalignment at the edges.)

Your help is greatly appreciated.

Cheers,

Chris



--
Christopher L. Colbert, Ph.D.
Associate Professor
Department of Chemistry and Biochemistry
North Dakota State University
P.O. Box 6050 Dept. 2710
Fargo, ND 58108-6050
PH: (701) 231-7946
FAX: (701) 231-8324



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Dear Chris,

We have  a similar setup using an older Quadro card employing a dual 
screen output (one DP/DVI-port for each projector). The two "screens" 
are in "clone mode" (NVIDIA control panel), as described e.h. here:

http://nvidia.custhelp.com/app/answers/detail/a_id/3012/~/how-to-configure-passive-or-dual-pipe-stereo-with-quadro-cards-in-windows-7.

The projectors are aligned using a projector-built-in test pattern.

In the NVIDIA 3D settings you have to activate 'Stereo' using the 
'NVidia Clone Mode Stereo' (or similarly named). In PyMol you use the 
'Quad-buffered Stereo' option. The NVIDIA driver will do the rest to 
provide the individual left/right images. It works for full screen and 
also for windowed PyMol (OpenGL windows with activated stereo only). The 
rest of the desktop remains "cloned".

Hope this helps,
Christoph



On 05/26/2016 08:34 PM, Christopher Colbert wrote:
> Hi All,
>
> We "upgraded" our 3D viewing room with a computer that has a Quadro 
> K2000 video card running Windows 7.  The computer displays through two 
> NEC projectors with polarizing filters that display agains a special 
> screen.  Stereo is viewed through polarized glasses just like in the 
> movie theater.   We had the stereo working a couple years ago, but it 
> stopped with the upgrade.  Here is my question:
>
> Are there any special Quadro settings I need to set to have the video 
> card play nice with PyMOL?
> Which stereo_mode do I set for this type of setup?  I ran through all 
> the options (1 – 12), but none caused the appropriate stereo effect
> Am I restricted to full screen mode or can I run stereo in windowed 
> mode?  We only tried Windowed mode.
> Does the stereo_mode change if I am using full screen mode versus 
> window mode?
>
> Any help or resources you can point me to would be greatly 
> appreciated.  (Proper procedure for aligning the projectors would be 
> greatly appreciated.  They are fairly well aligned centrally, but 
> become blurry from misalignment at the edges.)
>
> Your help is greatly appreciated.
>
> Cheers,
>
> Chris
>
>
>
> --
> Christopher L. Colbert, Ph.D.
> Associate Professor
> Department of Chemistry and Biochemistry
> North Dakota State University
> P.O. Box 6050 Dept. 2710
> Fargo, ND 58108-6050
> PH: (701) 231-7946
> FAX: (701) 231-8324
>
>
> ------------------------------------------------------------------------------
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Hi All,

We "upgraded" our 3D viewing room with a computer that has a Quadro K2000 video card running Windows 7.  The computer displays through two NEC projectors with polarizing filters that display agains a special screen.  Stereo is viewed through polarized glasses just like in the movie theater.   We had the stereo working a couple years ago, but it stopped with the upgrade.  Here is my question:

Are there any special Quadro settings I need to set to have the video card play nice with PyMOL?
Which stereo_mode do I set for this type of setup?  I ran through all the options (1 - 12), but none caused the appropriate stereo effect
Am I restricted to full screen mode or can I run stereo in windowed mode?  We only tried Windowed mode.
Does the stereo_mode change if I am using full screen mode versus window mode?

Any help or resources you can point me to would be greatly appreciated.  (Proper procedure for aligning the projectors would be greatly appreciated.  They are fairly well aligned centrally, but become blurry from misalignment at the edges.)

Your help is greatly appreciated.

Cheers,

Chris



--
Christopher L. Colbert, Ph.D.
Associate Professor
Department of Chemistry and Biochemistry
North Dakota State University
P.O. Box 6050 Dept. 2710
Fargo, ND 58108-6050
PH: (701) 231-7946
FAX: (701) 231-8324

... of course 8-o

:p

T.
On May 25, 2016 18:32, "Thomas Holder" <tho...@sc...>
wrote:

> or simply:
>
> alter bound_combined, chain = chr(ord(chain) - 1)
>
> Cheers,
>   Thomas
>
> On 25 May 2016, at 11:06, Tsjerk Wassenaar <ts...@gm...> wrote:
>
> > Hi James,
> >
> > This should do:
> >
> > for i in range(65:78): cmd.alter("bound_combined and chain
> %s"%chr(i+1),'chain="%s"'%chr(i))
> >
> > Cheers,
> >
> > Tsjerk
> >
> >
> > On Wed, May 25, 2016 at 5:00 PM, James Starlight <jms...@gm...>
> wrote:
> > More precisely I would like to know how to script in pymol the
> > following alteration fo the chains for the multi-chain pdb
> >
> >
> > PyMOL>alter (bound_combined and chain B), chain="A"
> >  Alter: modified 5157 atoms.
> > PyMOL>alter (bound_combined and chain C), chain="B"
> >  Alter: modified 2285 atoms.
> > PyMOL>alter (bound_combined and chain D), chain="C"
> >  Alter: modified 2778 atoms.
> > PyMOL>alter (bound_combined and chain E), chain="D"
> >  Alter: modified 1560 atoms.
> > PyMOL>alter (bound_combined and chain F), chain="E"
> >  Alter: modified 1114 atoms.
> > PyMOL>alter (bound_combined and chain G), chain="F"
> >  Alter: modified 950 atoms.
> > PyMOL>alter (bound_combined and chain H), chain="G"
> >  Alter: modified 895 atoms.
> > PyMOL>alter (bound_combined and chain I), chain="H"
> >  Alter: modified 843 atoms.
> > PyMOL>alter (bound_combined and chain J), chain="I"
> >  Alter: modified 806 atoms.
> > PyMOL>alter (bound_combined and chain K), chain="J"
> >  Alter: modified 574 atoms.
> > PyMOL>alter (bound_combined and chain L), chain="K"
> >  Alter: modified 501 atoms.
> > PyMOL>alter (bound_combined and chain M), chain="L"
> >  Alter: modified 511 atoms.
> > PyMOL>alter (bound_combined and chain N), chain="M"
> >  Alter: modified 433 atoms.
> >
> >
> > So each step we rename chain i to the i-1 name within given model :)
> >
> > Thanks!
> >
> > J.
> >
> > 2016-05-23 19:11 GMT+02:00 James Starlight <jms...@gm...>:
> > > Dear Pymol users!
> > >
> > > After some post-processing of MD simulation I have extracted from the
> > > traejctory several snapshots as individual pdbs which I need to
> > > 1-  to re-assign information regarding chain letters (which was lost
> > > after some operations on pdbs)  for all of those structures assuming
> > > that within each of these pdbs residues are ordered correctly e.g from
> > > (1-104 which
> > > should be chain A) than from 1-100 (it should be chain B), than 1-70
> > > (in should be chain C) etc.
> > >
> > > 2- superimpose and combine all of the pdbs within one model in
> nmr-like format.
> > >
> > > Thanks for help!
> > >
> > > James
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

or simply:

alter bound_combined, chain = chr(ord(chain) - 1)

Cheers,
  Thomas

On 25 May 2016, at 11:06, Tsjerk Wassenaar <ts...@gm...> wrote:

> Hi James,
> 
> This should do:
> 
> for i in range(65:78): cmd.alter("bound_combined and chain %s"%chr(i+1),'chain="%s"'%chr(i))
> 
> Cheers,
> 
> Tsjerk
> 
> 
> On Wed, May 25, 2016 at 5:00 PM, James Starlight <jms...@gm...> wrote:
> More precisely I would like to know how to script in pymol the
> following alteration fo the chains for the multi-chain pdb
> 
> 
> PyMOL>alter (bound_combined and chain B), chain="A"
>  Alter: modified 5157 atoms.
> PyMOL>alter (bound_combined and chain C), chain="B"
>  Alter: modified 2285 atoms.
> PyMOL>alter (bound_combined and chain D), chain="C"
>  Alter: modified 2778 atoms.
> PyMOL>alter (bound_combined and chain E), chain="D"
>  Alter: modified 1560 atoms.
> PyMOL>alter (bound_combined and chain F), chain="E"
>  Alter: modified 1114 atoms.
> PyMOL>alter (bound_combined and chain G), chain="F"
>  Alter: modified 950 atoms.
> PyMOL>alter (bound_combined and chain H), chain="G"
>  Alter: modified 895 atoms.
> PyMOL>alter (bound_combined and chain I), chain="H"
>  Alter: modified 843 atoms.
> PyMOL>alter (bound_combined and chain J), chain="I"
>  Alter: modified 806 atoms.
> PyMOL>alter (bound_combined and chain K), chain="J"
>  Alter: modified 574 atoms.
> PyMOL>alter (bound_combined and chain L), chain="K"
>  Alter: modified 501 atoms.
> PyMOL>alter (bound_combined and chain M), chain="L"
>  Alter: modified 511 atoms.
> PyMOL>alter (bound_combined and chain N), chain="M"
>  Alter: modified 433 atoms.
> 
> 
> So each step we rename chain i to the i-1 name within given model :)
> 
> Thanks!
> 
> J.
> 
> 2016-05-23 19:11 GMT+02:00 James Starlight <jms...@gm...>:
> > Dear Pymol users!
> >
> > After some post-processing of MD simulation I have extracted from the
> > traejctory several snapshots as individual pdbs which I need to
> > 1-  to re-assign information regarding chain letters (which was lost
> > after some operations on pdbs)  for all of those structures assuming
> > that within each of these pdbs residues are ordered correctly e.g from
> > (1-104 which
> > should be chain A) than from 1-100 (it should be chain B), than 1-70
> > (in should be chain C) etc.
> >
> > 2- superimpose and combine all of the pdbs within one model in nmr-like format.
> >
> > Thanks for help!
> >
> > James
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi James,

This should do:

for i in range(65:78): cmd.alter("bound_combined and chain
%s"%chr(i+1),'chain="%s"'%chr(i))

Cheers,

Tsjerk


On Wed, May 25, 2016 at 5:00 PM, James Starlight <jms...@gm...>
wrote:

> More precisely I would like to know how to script in pymol the
> following alteration fo the chains for the multi-chain pdb
>
>
> PyMOL>alter (bound_combined and chain B), chain="A"
>  Alter: modified 5157 atoms.
> PyMOL>alter (bound_combined and chain C), chain="B"
>  Alter: modified 2285 atoms.
> PyMOL>alter (bound_combined and chain D), chain="C"
>  Alter: modified 2778 atoms.
> PyMOL>alter (bound_combined and chain E), chain="D"
>  Alter: modified 1560 atoms.
> PyMOL>alter (bound_combined and chain F), chain="E"
>  Alter: modified 1114 atoms.
> PyMOL>alter (bound_combined and chain G), chain="F"
>  Alter: modified 950 atoms.
> PyMOL>alter (bound_combined and chain H), chain="G"
>  Alter: modified 895 atoms.
> PyMOL>alter (bound_combined and chain I), chain="H"
>  Alter: modified 843 atoms.
> PyMOL>alter (bound_combined and chain J), chain="I"
>  Alter: modified 806 atoms.
> PyMOL>alter (bound_combined and chain K), chain="J"
>  Alter: modified 574 atoms.
> PyMOL>alter (bound_combined and chain L), chain="K"
>  Alter: modified 501 atoms.
> PyMOL>alter (bound_combined and chain M), chain="L"
>  Alter: modified 511 atoms.
> PyMOL>alter (bound_combined and chain N), chain="M"
>  Alter: modified 433 atoms.
>
>
> So each step we rename chain i to the i-1 name within given model :)
>
> Thanks!
>
> J.
>
> 2016-05-23 19:11 GMT+02:00 James Starlight <jms...@gm...>:
> > Dear Pymol users!
> >
> > After some post-processing of MD simulation I have extracted from the
> > traejctory several snapshots as individual pdbs which I need to
> > 1-  to re-assign information regarding chain letters (which was lost
> > after some operations on pdbs)  for all of those structures assuming
> > that within each of these pdbs residues are ordered correctly e.g from
> > (1-104 which
> > should be chain A) than from 1-100 (it should be chain B), than 1-70
> > (in should be chain C) etc.
> >
> > 2- superimpose and combine all of the pdbs within one model in nmr-like
> format.
> >
> > Thanks for help!
> >
> > James
>
>
> ------------------------------------------------------------------------------
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data
> untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Tsjerk A. Wassenaar, Ph.D.

More precisely I would like to know how to script in pymol the
following alteration fo the chains for the multi-chain pdb


PyMOL>alter (bound_combined and chain B), chain="A"
 Alter: modified 5157 atoms.
PyMOL>alter (bound_combined and chain C), chain="B"
 Alter: modified 2285 atoms.
PyMOL>alter (bound_combined and chain D), chain="C"
 Alter: modified 2778 atoms.
PyMOL>alter (bound_combined and chain E), chain="D"
 Alter: modified 1560 atoms.
PyMOL>alter (bound_combined and chain F), chain="E"
 Alter: modified 1114 atoms.
PyMOL>alter (bound_combined and chain G), chain="F"
 Alter: modified 950 atoms.
PyMOL>alter (bound_combined and chain H), chain="G"
 Alter: modified 895 atoms.
PyMOL>alter (bound_combined and chain I), chain="H"
 Alter: modified 843 atoms.
PyMOL>alter (bound_combined and chain J), chain="I"
 Alter: modified 806 atoms.
PyMOL>alter (bound_combined and chain K), chain="J"
 Alter: modified 574 atoms.
PyMOL>alter (bound_combined and chain L), chain="K"
 Alter: modified 501 atoms.
PyMOL>alter (bound_combined and chain M), chain="L"
 Alter: modified 511 atoms.
PyMOL>alter (bound_combined and chain N), chain="M"
 Alter: modified 433 atoms.


So each step we rename chain i to the i-1 name within given model :)

Thanks!

J.

2016-05-23 19:11 GMT+02:00 James Starlight <jms...@gm...>:
> Dear Pymol users!
>
> After some post-processing of MD simulation I have extracted from the
> traejctory several snapshots as individual pdbs which I need to
> 1-  to re-assign information regarding chain letters (which was lost
> after some operations on pdbs)  for all of those structures assuming
> that within each of these pdbs residues are ordered correctly e.g from
> (1-104 which
> should be chain A) than from 1-100 (it should be chain B), than 1-70
> (in should be chain C) etc.
>
> 2- superimpose and combine all of the pdbs within one model in nmr-like format.
>
> Thanks for help!
>
> James

Hi Martin,

you need to compile PyMOL in order to see effects of code changes.
The installation instructions
<" rel="nofollow">http://www.pymolwiki.org/index.php/Category:Installation> on the wiki
include some information on how to compile PyMOL from source.

Cheers,
Julian

On Tue, May 24, 2016 at 7:54 PM Martin Hediger <ma...@bl...> wrote:

> Can one run PyMOL from source (in order to see effects of changes to the
> source code whenever restarting) or can one only run a compiled version of
> PyMOL?
>
> Are there instructions for running from source?
>
> Best regards
> Martin
>
>
>
>
> --
> Martin R. Hediger, PhD
> Mittlere Strasse 65
> 4056 Basel
>
>
> ------------------------------------------------------------------------------
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data
> untouched!
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> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
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> Archives: http://www.mail-archive.com/pym...@li...

Can one run PyMOL from source (in order to see effects of changes to the 
source code whenever restarting) or can one only run a compiled version 
of PyMOL?

Are there instructions for running from source?

Best regards
Martin




-- 
Martin R. Hediger, PhD
Mittlere Strasse 65
4056 Basel

Dear Pymol users!

After some post-processing of MD simulation I have extracted from the
traejctory several snapshots as individual pdbs which I need to
1-  to re-assign information regarding chain letters (which was lost
after some operations on pdbs)  for all of those structures assuming
that within each of these pdbs residues are ordered correctly e.g from
(1-104 which
should be chain A) than from 1-100 (it should be chain B), than 1-70
(in should be chain C) etc.

2- superimpose and combine all of the pdbs within one model in nmr-like format.

Thanks for help!

James

Hi Rituraj,

To get a meaningful stack trace, import a plugin's module, e.g.:

PyMOL> import pmg_tk.startup.align_all

Not all plugins will add an entry to the "Plugin" menu, some just register new commands.

Hope that helps.

Cheers,
  Thomas

On 19 May 2016, at 02:28, Rituraj Purohit <rit...@gm...> wrote:

> Hello,
> 
> I am using pymol (1.6.x) in ubuntu 14.04, I install few plugins (Autodock, tconcoord and align_all) but none of them are displaying in plugin list. I am getting  following error in pymol command screen. Please help me to rectify this error.
> 
> .
> 
> .
> 
> convert given font files to the PIL raster font format.
> 
> This version of pilfont supports X BDF and PCF fonts.
> 
> Unable to initialize plugin 'pilfont' (pmg_tk.startup.pilfont).
> 
> Unable to initialize plugin 'tconcoord' (pmg_tk.startup.tconcoord).
> 
> Unable to initialize plugin 'align_all' (pmg_tk.startup.align_all).
> 
> Regards
> 
> RP

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Andrew,

Currently there seems to be no option to disable the SpaceNavigator. I can send you a custom build. For the next major version we could consider a setting.

Cheers,
  Thomas

On 16 May 2016, at 09:18, Andrew Chadwick <and...@yo...> wrote:

> Hi All,
> 
> With apologies if I have missed something obvious - is it possible to disable 3DConnexion SpaceNavigator support in Pymol?
> 
> To be more specific, I am trying to build a system in which Pymol is being directed by a background application. Pymol with therefore have focus (be the foremost application) but I want the control input to go to the background application without Pymol acting on it.
> 
> I can disable the device while Pymol has focus (through the OS), but this means that background applications do not receive the data while Pymol is active. Is there a command in pymol to disable the SpaceNavigator?
> 
> Hope this makes sense - thanks for your time,
> 
> Andrew.
> 
> -- 
> -- 
> Andrew Chadwick
> Studio Manager & Associate Lecturer, Audio Lab
> Department of Electronics
> University of York
> Heslington, York
> YO10 5DD
> Tel. 01904 32 x4235
> 
> Times Higher Education University of the Year 2010
> 
> EMAIL DISCLAIMER: 
> http://www.york.ac.uk/docs/disclaimer/email.htm 

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Smith,

You probably hit the <insert> key. Or you clicked the down triangle in the
lower right menu.

Cheers,

Tsjerk

On Fri, May 20, 2016 at 7:56 AM, Smith Liu <smi...@16...> wrote:

> Dear All,
>
> Today as every day I do, I align 2 pdb files by pymol. After a moment, I
> find the aligned 2 molecules start to rock back and forth continuously in
> the pymol window (from about 45 degree to -45 degree). Today I never used
> the rotate or rock command.
>
> Will you please explain why this phenomenon can occur?
>
> Smith
>
>
> ------------------------------------------------------------------------------
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data
> untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Tsjerk A. Wassenaar, Ph.D.

Dear All,


Today as every day I do, I align 2 pdb files by pymol. After a moment, I find the aligned 2 molecules start to rock back and forth continuously in the pymol window (from about 45 degree to -45 degree). Today I never used the rotate or rock command.


Will you please explain why this phenomenon can occur?


Smith

Hello,

I am using pymol (1.6.x) in ubuntu 14.04, I install few plugins (Autodock,
tconcoord and align_all) but none of them are displaying in plugin list. I
am getting following error in pymol command screen. Please help me to
rectify this error.

.

*.*

*convert given font files to the PIL raster font format.*

*This version of pilfont supports X BDF and PCF fonts.*

*Unable to initialize plugin 'pilfont' (pmg_tk.startup.pilfont).*

*Unable to initialize plugin 'tconcoord' (pmg_tk.startup.tconcoord).*

*Unable to initialize plugin 'align_all' (pmg_tk.startup.align_all).*

Regards

RP

Hi Julian,
Thank you so much. I just tested it and it worked as well!


Yours sincerely
Cheng




------------------ Original ------------------
From:  "Julian Heinrich";<ju...@jo...>;
Date:  Wed, May 18, 2016 01:37 AM
To:  "ZHANG Cheng"<272...@qq...>; "pymol-users"<pym...@li...>; 

Subject:  Re: [PyMOL] How to export secondary structure information from a PDBusing PyMol?



Hi,

in case you haven't solved this yet, the following command prints the residue number and secondary structure:


iterate n. CA, print resi + ':' + ss



Cheers,
Julian


On Fri, May 13, 2016 at 10:40 PM ZHANG Cheng <272...@qq...> wrote:

Dear PyMol friends,
I would like to export the secondary structure of individual residues from a PDB. Can I ask if I can use PyMol to do that?


I would like something like this:


Residue 1: alpha-helix
Residue 2: beta-sheet
......






I think "http://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py" can also do that. However, I found that one residue is loop in Pymol but is indicated as "strand" in the website. So I wonder if Pymol can output the secondary structure of individual residues from a PDB?


Thank you.
------------------------------------------------------------------------------
 Mobile security can be enabling, not merely restricting. Employees who
 bring their own devices (BYOD) to work are irked by the imposition of MDM
 restrictions. Mobile Device Manager Plus allows you to control only the
 apps on BYO-devices by containerizing them, leaving personal data untouched!
 https://ad.doubleclick.net/ddm/clk/304595813;131938128;j_______________________________________________
 PyMOL-users mailing list (PyM...@li...)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
 Archives: http://www.mail-archive.com/pym...@li...

Hi,

in case you haven't solved this yet, the following command prints the
residue number and secondary structure:

iterate n. CA, print resi + ':' + ss

Cheers,
Julian

On Fri, May 13, 2016 at 10:40 PM ZHANG Cheng <272...@qq...> wrote:

> Dear PyMol friends,
> I would like to export the secondary structure of individual residues from
> a PDB. Can I ask if I can use PyMol to do that?
>
> I would like something like this:
>
> Residue 1: alpha-helix
> Residue 2: beta-sheet
> ......
>
>
>
> I think "http://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py" can
> also do that. However, I found that one residue is loop in Pymol but is
> indicated as "strand" in the website. So I wonder if Pymol can output the secondary
> structure of individual residues from a PDB?
>
> Thank you.
>
> ------------------------------------------------------------------------------
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data
> untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...