pymol-users Mailing List for PyMOL Molecular Graphics System

Hello:

I am trying to use pymol to view the pes for an RNA-Protein complex.

But, I want to use two different dx maps: one for RNA and one for the
protein.

Here is what I did:

1) I read into pymol the pdb file for the entire RNA-protein complex.  It
looks good.

2) I then read in a protein.dx map hoping that it would overlap with the
protein segment.  It didn't work.

Can someone please help me with this?

The reason for the two pes maps is that the RNA and protein have different
characteristics, and I want to manipulate them separately.

Thanks for all your help in advance.

Kind regards,

Angelo

Hi--

Can the roving mesh be used without changing the model appearance?   
I'd prefer to just show the entire structure as lines only, but it  
looks like the roving_detail setting controls both model and mesh.

thanks,
Nat

Thanks Warren!

That worked really well.

All the best,

--Buz


On Dec 18, 2008, at 10:08 PM, DeLano Scientific wrote:

> Buz,
>
> alter elem Na, elem='K'
>
> iterate elem K, print vdw
>
> show spheres, elem K
>
> alter elem K, vdw=1.4
>
> rebuild
>
> iterate elem K, print vdw
>
> color yellow, elem K
>
> Cheers,
> Warren
>
>
> --
> DeLano Scientific LLC
> Subscriber Support Services
> mailto:su...@de...
>
>
>
>> -----Original Message-----
>> From: Buz Barstow [mailto:bu...@ma...]
>> Sent: Thursday, December 18, 2008 2:30 PM
>> To: pym...@li...
>> Subject: [PyMOL] Mutating an Ion in Pymol and Displaying van
>> der waals Radii
>>
>> Dear All,
>>
>> I'd like to mutate an ion in pymol from a potassium to a
>> sodium. Is there an easy way to do this from the command line
>> without having to edit the pdb file of the structure?
>>
>> Also, when one displays an atom (for instance a K atom) using
>> the spheres representation, is the radius of the sphere equal
>> to the Pauling radius of the atom (under the assumption that
>> it is ionized)?
>> For K, it looks like it is.
>>
>> Thanks! and all the best,
>>
>> --Buz
>>
>>
>>
>> --------------------------------------------------------------
>> ----------------
>> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las
>> Vegas, Nevada.
>> The future of the web can't happen without you.  Join us at
>> MIX09 to help pave the way to the Next Web now. Learn more
>> and register at
>> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009
>> .visitmix.com/
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

Malcolm,

I believe the method you want is:

print cmd.get_scene_list()

Hopefully that method is present in the PyMOL build you are running!

Cheers,
Warren

> -----Original Message-----
> From: Malcolm E Davis [mailto:mal...@bm...]
> Sent: Friday, December 19, 2008 3:46 PM
> To: pym...@li...
> Subject: [PyMOL] cmd.scene('*')
> 
> In a Python script I am working on I would like to get a list of the
> scenes that are defined.  Unfortunately, cmd.scene('*') just prints
the
> list to stdout, but doesn't return anything.  That is, if I have a
> script test.py that looks like
> 
> > from pymol import cmd
> > x = cmd.scene('*')
> > print x
> 
> 
> And I type "run test.py" in PyMol I get the following output
> 
> > PyMOL>run test.py
> >  scene: stored scenes:
> >   F1  F2
> > x='None'
> 
> 
> Is there a different mechanism to get a list of defined scenes?  Or an
> argument, I've missed?
> 
>  I have the following work around
> 
> > from pymol import cmd
> > import sys
> > from StringIO import StringIO
> >
> > tmp = StringIO()
> > (tmp,sys.stdout) = (sys.stdout,tmp)
> > cmd.scene('*')
> > (tmp,sys.stdout) = (sys.stdout,tmp)
> > list = tmp.getvalue().split("\n")[1].split()
> > print list
> 
> which generates what I want
> 
> > PyMOL>run test.py
> > ['F1', 'F2']
> 
> but that seems less than elegant.
> 
> Malcolm
> 
>
------------------------------------------------------------------------
--
> ----
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 
> 

In a Python script I am working on I would like to get a list of the 
scenes that are defined.  Unfortunately, cmd.scene('*') just prints the 
list to stdout, but doesn't return anything.  That is, if I have a 
script test.py that looks like

> from pymol import cmd
> x = cmd.scene('*')
> print x


And I type "run test.py" in PyMol I get the following output

> PyMOL>run test.py
>  scene: stored scenes:
>   F1  F2
> x='None'


Is there a different mechanism to get a list of defined scenes?  Or an 
argument, I've missed?

 I have the following work around

> from pymol import cmd
> import sys
> from StringIO import StringIO
>
> tmp = StringIO()
> (tmp,sys.stdout) = (sys.stdout,tmp)
> cmd.scene('*')
> (tmp,sys.stdout) = (sys.stdout,tmp)
> list = tmp.getvalue().split("\n")[1].split()
> print list

which generates what I want

> PyMOL>run test.py
> ['F1', 'F2']

but that seems less than elegant.

Malcolm

Hi Mark,

I remember that Kristian Rother's rTools could do hydrophobicity coloring:
http://www.rubor.de/pymol_extensions.html
it is some years ago, so maybe it needs some updateing..

Best,
Andreas

DeLano Scientific wrote:
> Mark,
>
> PyMOL does not have such abilities at present.  
>
> Can such concepts even be defined in a precise, objective, and unambiguous
> fashion?  
>
> Cheers,
> Warren
>
> --
> DeLano Scientific LLC
> Subscriber Support Services
> mailto:su...@de...
>
>   
>> -----Original Message-----
>> From: Mark Collins [mailto:mn...@co...] 
>> Sent: Thursday, December 18, 2008 7:38 AM
>> To: pym...@li...
>> Subject: [PyMOL] surface properties
>>
>> Hi All
>> I have searched thru the archive and couldn't find an answer, 
>> to this.  I would like to make pymol surface(s) colored by 
>> (1) hydrophobicity and (2) concavity/convexity.
>> These are easily produced in grasp, so one possibility maybe 
>> to import some type of grasp file.
>> Thanks in advance for suggestions, websites, or tutorials, etc.
>> Mark
>>
>> --------------------------------------------------------------
>> ----------------
>> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las 
>> Vegas, Nevada.
>> The future of the web can't happen without you.  Join us at 
>> MIX09 to help pave the way to the Next Web now. Learn more 
>> and register at 
>> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009
>> .visitmix.com/
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>     
>
>
> ------------------------------------------------------------------------------
> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
> The future of the web can't happen without you.  Join us at MIX09 to help
> pave the way to the Next Web now. Learn more and register at
> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>   

-- 
Andreas Henschel
Bioinformatics Group
TU Dresden
Tatzberg 47-51
01307 Dresden, Germany

Phone: +49 351 463 40063
EMail: ah...@bi...

Hi Annalisa,

Is the original coordinate file an NMR structure? It looks to me like
there are several copies of each atom, which is consistent with the pdb
file resulting from an NMR refinement. These will usually have several
different models of the peptide, all consistent with the NMR data. 

You will need to extract just one set of coordinates and look at those.
Which set of coordinates to use depends on the software used to generate
the pdb, but look for the first or the 'best' model, the pdb header
should tell you which is best. 

Hope this helps at bit

Andrew Purkiss-Trew

On Thu, 2008-12-18 at 15:40 +0100, annalisa bordogna wrote:
> Hi all,
> I have a little problem with the visualization of a peptide
> conformation: as you can see from the picture I enclose, the structure
> appears as if every atom is bound to every neighbour atom. What (and
> how) can I set in PyMOL, to visualize a correct structure?
> 
> Thank you very much for your help.
> Best regards,
> Annalisa
> 
> -------------------------------------------------------
> Annalisa Bordogna
> Ph.D. Student
> Università degli Studi di Milano - Bicocca
> Milano, IT
> ------------------------------------------------------------------------------
> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
> The future of the web can't happen without you.  Join us at MIX09 to help
> pave the way to the Next Web now. Learn more and register at
> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/
> _______________________________________________ PyMOL-users mailing list PyM...@li... https://lists.sourceforge.net/lists/listinfo/pymol-users

Hi Andrew,

thank you for your answer: now I have a clue!
I knew that the structure is a NMR model, but what I didn't understand was
that some atoms were repeated (with different coordinates). Now I have
pruned my structure file and I can see a much more acceptable structure.

Thank you very much,
Annalisa


2008/12/19 Andrew Purkiss-Trew <a.p...@ma...>

> Hi Annalisa,
>
> Is the original coordinate file an NMR structure? It looks to me like
> there are several copies of each atom, which is consistent with the pdb
> file resulting from an NMR refinement. These will usually have several
> different models of the peptide, all consistent with the NMR data.
>
> You will need to extract just one set of coordinates and look at those.
> Which set of coordinates to use depends on the software used to generate
> the pdb, but look for the first or the 'best' model, the pdb header
> should tell you which is best.
>
> Hope this helps at bit
>
> Andrew Purkiss-Trew
>
> On Thu, 2008-12-18 at 15:40 +0100, annalisa bordogna wrote:
> > Hi all,
> > I have a little problem with the visualization of a peptide
> > conformation: as you can see from the picture I enclose, the structure
> > appears as if every atom is bound to every neighbour atom. What (and
> > how) can I set in PyMOL, to visualize a correct structure?
> >
> > Thank you very much for your help.
> > Best regards,
> > Annalisa
> >
> > -------------------------------------------------------
> > Annalisa Bordogna
> > Ph.D. Student
> > Università degli Studi di Milano - Bicocca
> > Milano, IT
> >
> ------------------------------------------------------------------------------
> > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas,
> Nevada.
> > The future of the web can't happen without you.  Join us at MIX09 to help
> > pave the way to the Next Web now. Learn more and register at
> >
> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/
> > _______________________________________________ PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>

> 1. Use the grid_mode option (only available in the compiled from
> source pymols)

FYI: grid_mode and many other enhancements will be present in the
soon-to-be-available PyMOL 1.2 BETA builds.  The annual PyMOL release
cycle for "official" PyMOL builds has settled down as follows:

- Summer:  The major annual release is cut in June/July, followed by any
necessary patch/updates during the summer so that we enter the academic
cycle with a robust build intended for widespread adoption.

- Fall:  We hunker down and tackle the toughest development challenges
for the year, issuing few releases since the code at its most unstable
and incompatible condition.  

- Winter:  Starting in January, we begin issuing a series of routine
beta builds with all the new stuff, so that the bold and the daring can
try things out and begin reporting any issues.

- Spring:  We freeze the feature set then stabilize and test everything
as much as possible in anticipation of the robust major release at the
start of summer.

Of course, the open-source "trunk" is available to developers at any
time of the year :).

Cheers,
Warren

> -----Original Message-----
> From: Buz Barstow [mailto:bu...@ma...]
> Sent: Thursday, December 18, 2008 3:27 PM
> To: pym...@li...
> Subject: Re: [PyMOL] Ray Tracing A Protein Gallery
> 
> Dear All,
> 
> Thanks for all your suggestions on ray tracing the protein gallery.
> 
> In the end, I used several of the techniques suggested, and everything
> worked out really well!
> 
> To summarize:
> 
> 1. Use the grid_mode option (only available in the compiled from
> source pymols)
> 2. Make a fake .pdb that has the corners and centers of a 3D box to
> use for alignment
> 3. Use the set_view command to apply the same viewing matrix
> 4. Use the zoom command with a center and a distance specified.
> 
> Also, the cealign package is really helpful for aligning and
> translating very dissimilar molecules.
> 
> Thanks! and all the best,
> 
> --Buz
> 
> 
> 
> 
> On Dec 16, 2008, at 4:05 PM, DeLano Scientific wrote:
> 
> > Hi Buz,
> >
> > You can use "center" as a selection name for input with zoom, along
> > with a
> > distance value.
> >
> > zoom center, distance
> >
> > e.g.
> >
> > # first, get the object you want in the center of the screen
> >
> > orient
> >
> > # then zoom the viewer by a fixed amount about the center point
> >
> > zoom center, 10
> >
> > # you may also wish to move the clipping planes in/out to avoid
> > cutting into
> > any of the molecular representations:
> >
> > clip atoms, 4, selection=all
> >
> > # also, depending upon the application, you might want to disable
> > perspective
> >
> > set orthoscopic
> >
> > # get rid of background pixels
> >
> > unset opaque_background
> >
> > # render
> >
> > ray
> >
> > # and save
> >
> > save struct001.png
> >
> > Cheers,
> > Warren
> >
> >
> > --
> > DeLano Scientific LLC
> > Subscriber Support Services
> > mailto:su...@de...
> >
> >
> >
> >> -----Original Message-----
> >> From: Buz Barstow [mailto:bu...@ma...]
> >> Sent: Monday, December 15, 2008 11:42 AM
> >> To: pym...@li...
> >> Subject: [PyMOL] Ray Tracing A Protein Gallery
> >>
> >> Dear All,
> >>
> >> I'm making a gallery of protein molecules for my PhD thesis.
> >> I'd like to find an automatic way to ensure that all of the
> >> ray traced images have the same scale. Is there an easy way
> >> to do this?
> >>
> >> Thanks! and all the best,
> >>
> >> --Buz
> >>
> >> --------------------------------------------------------------
> >> ----------------
> >> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las
> >> Vegas, Nevada.
> >> The future of the web can't happen without you.  Join us at
> >> MIX09 to help pave the way to the Next Web now. Learn more
> >> and register at
> >> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009
> > .visitmix.com/
> >> _______________________________________________
> >> PyMOL-users mailing list
> >> PyM...@li...
> >> https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> >
> >
------------------------------------------------------------------------
> ------
> > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas,
> > Nevada.
> > The future of the web can't happen without you.  Join us at MIX09 to
> > help
> > pave the way to the Next Web now. Learn more and register at
> >
>
http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.
co
> m/
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 
>
------------------------------------------------------------------------
--
> ----
> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas,
> Nevada.
> The future of the web can't happen without you.  Join us at MIX09 to
help
> pave the way to the Next Web now. Learn more and register at
>
http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.
co
> m/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 

Hi Ben,

Current versions of MacPyMOL make use of the 2.3 version of the
operating-system-provided Python interpreter.  Future versions may behave
differently.

Officially speaking, if you need to integrate external
native-code-containing Python modules, then DeLano Scientific's sole
recommended approach is to compile the Open-Source PyMOL source code for X11
instead of using MacPyMOL/PyMOLX11Hybrid.  Unfortunately, the Python C ABI
is just too fragile for anything else to be practical...

Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:su...@de...

> -----Original Message-----
> From: Ben Eisenbraun [mailto:be...@cr...] 
> Sent: Wednesday, December 17, 2008 9:53 AM
> To: pym...@li...
> Subject: [PyMOL] adding python modules for MacPyMOL
> 
> 
> Is it possible to add additional python modules to a MacPyMOL 
> installation?
> 
> I am trying to install the PyNMR plugin:
> 
> http://maple.rsvs.ulaval.ca/mediawiki/index.php/PyNMR
> 
> And it requires the Numeric python module.  I have an 
> external python installation  built with the module, but it 
> seems that MacPyMOL uses a bundled python interpreter.
> 
> I tried setting the PYTHONPATH to the modules directory of my 
> python build, but I get errors like this:
> 
> /programs/i386-mac/python/2.5.2/lib/python2.5/site-packages/Nu
meric/Numeric.py:91: RuntimeWarning: Python C API version > mismatch for
module multiarray: This Python has API version 
> 1012, module multiarray has version 1013.
> 
> I poked around in the PyMOLX11Hybrid.app directories, but 
> didn't see an obvious place I could add a module installation.
> 
> Thanks.
> 
> -ben
> 
> --
> Ben Eisenbraun
> Structural Biology Grid                           Harvard 
> Medical School
> http://sbgrid.org                                 
> http://hms.harvard.edu
> 
> --------------------------------------------------------------
> ----------------
> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las 
> Vegas, Nevada.
> The future of the web can't happen without you.  Join us at 
> MIX09 to help pave the way to the Next Web now. Learn more 
> and register at 
> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009
.visitmix.com/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Mark,

PyMOL does not have such abilities at present.  

Can such concepts even be defined in a precise, objective, and unambiguous
fashion?  

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:su...@de...

> -----Original Message-----
> From: Mark Collins [mailto:mn...@co...] 
> Sent: Thursday, December 18, 2008 7:38 AM
> To: pym...@li...
> Subject: [PyMOL] surface properties
> 
> Hi All
> I have searched thru the archive and couldn't find an answer, 
> to this.  I would like to make pymol surface(s) colored by 
> (1) hydrophobicity and (2) concavity/convexity.
> These are easily produced in grasp, so one possibility maybe 
> to import some type of grasp file.
> Thanks in advance for suggestions, websites, or tutorials, etc.
> Mark
> 
> --------------------------------------------------------------
> ----------------
> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las 
> Vegas, Nevada.
> The future of the web can't happen without you.  Join us at 
> MIX09 to help pave the way to the Next Web now. Learn more 
> and register at 
> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009
> .visitmix.com/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Buz,

alter elem Na, elem='K'

iterate elem K, print vdw

show spheres, elem K

alter elem K, vdw=1.4

rebuild

iterate elem K, print vdw

color yellow, elem K

Cheers,
Warren


--
DeLano Scientific LLC
Subscriber Support Services
mailto:su...@de...

 

> -----Original Message-----
> From: Buz Barstow [mailto:bu...@ma...] 
> Sent: Thursday, December 18, 2008 2:30 PM
> To: pym...@li...
> Subject: [PyMOL] Mutating an Ion in Pymol and Displaying van 
> der waals Radii
> 
> Dear All,
> 
> I'd like to mutate an ion in pymol from a potassium to a 
> sodium. Is there an easy way to do this from the command line 
> without having to edit the pdb file of the structure?
> 
> Also, when one displays an atom (for instance a K atom) using 
> the spheres representation, is the radius of the sphere equal 
> to the Pauling radius of the atom (under the assumption that 
> it is ionized)?  
> For K, it looks like it is.
> 
> Thanks! and all the best,
> 
> --Buz
> 
> 
> 
> --------------------------------------------------------------
> ----------------
> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las 
> Vegas, Nevada.
> The future of the web can't happen without you.  Join us at 
> MIX09 to help pave the way to the Next Web now. Learn more 
> and register at 
> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009
> .visitmix.com/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Annalisa,
 
If bonds are not explicitly provided in the input file, then PyMOL infers
bonding based on distance.  Are the input coordinates valid?  It looks like
the atoms may be too close together in space...
 
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:su...@de...
 


  _____  

From: annalisa bordogna [mailto:ann...@gm...] 
Sent: Thursday, December 18, 2008 6:40 AM
To: pym...@li...
Subject: [PyMOL] weird visualization of a peptide structure


Hi all,
I have a little problem with the visualization of a peptide conformation: as
you can see from the picture I enclose, the structure appears as if every
atom is bound to every neighbour atom. What (and how) can I set in PyMOL, to
visualize a correct structure?

Thank you very much for your help.
Best regards,
Annalisa

-------------------------------------------------------
Annalisa Bordogna
Ph.D. Student
Università degli Studi di Milano - Bicocca
Milano, IT

Dear All,

Thanks for all your suggestions on ray tracing the protein gallery.

In the end, I used several of the techniques suggested, and everything  
worked out really well!

To summarize:

1. Use the grid_mode option (only available in the compiled from  
source pymols)
2. Make a fake .pdb that has the corners and centers of a 3D box to  
use for alignment
3. Use the set_view command to apply the same viewing matrix
4. Use the zoom command with a center and a distance specified.

Also, the cealign package is really helpful for aligning and  
translating very dissimilar molecules.

Thanks! and all the best,

--Buz




On Dec 16, 2008, at 4:05 PM, DeLano Scientific wrote:

> Hi Buz,
>
> You can use "center" as a selection name for input with zoom, along  
> with a
> distance value.
>
> zoom center, distance
>
> e.g.
>
> # first, get the object you want in the center of the screen
>
> orient
>
> # then zoom the viewer by a fixed amount about the center point
>
> zoom center, 10
>
> # you may also wish to move the clipping planes in/out to avoid  
> cutting into
> any of the molecular representations:
>
> clip atoms, 4, selection=all
>
> # also, depending upon the application, you might want to disable
> perspective
>
> set orthoscopic
>
> # get rid of background pixels
>
> unset opaque_background
>
> # render
>
> ray
>
> # and save
>
> save struct001.png
>
> Cheers,
> Warren
>
>
> --
> DeLano Scientific LLC
> Subscriber Support Services
> mailto:su...@de...
>
>
>
>> -----Original Message-----
>> From: Buz Barstow [mailto:bu...@ma...]
>> Sent: Monday, December 15, 2008 11:42 AM
>> To: pym...@li...
>> Subject: [PyMOL] Ray Tracing A Protein Gallery
>>
>> Dear All,
>>
>> I'm making a gallery of protein molecules for my PhD thesis.
>> I'd like to find an automatic way to ensure that all of the
>> ray traced images have the same scale. Is there an easy way
>> to do this?
>>
>> Thanks! and all the best,
>>
>> --Buz
>>
>> --------------------------------------------------------------
>> ----------------
>> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las
>> Vegas, Nevada.
>> The future of the web can't happen without you.  Join us at
>> MIX09 to help pave the way to the Next Web now. Learn more
>> and register at
>> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009
> .visitmix.com/
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
> ------------------------------------------------------------------------------
> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas,  
> Nevada.
> The future of the web can't happen without you.  Join us at MIX09 to  
> help
> pave the way to the Next Web now. Learn more and register at
> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Dear All,

I'd like to mutate an ion in pymol from a potassium to a sodium. Is  
there an easy way to do this from the command line without having to  
edit the pdb file of the structure?

Also, when one displays an atom (for instance a K atom) using the  
spheres representation, is the radius of the sphere equal to the  
Pauling radius of the atom (under the assumption that it is ionized)?  
For K, it looks like it is.

Thanks! and all the best,

--Buz

Hi All
I have searched thru the archive and couldn't find an answer, to this.  I
would like to make pymol surface(s) colored by (1) hydrophobicity and (2)
concavity/convexity.
These are easily produced in grasp, so one possibility maybe to import
some type of grasp file.
Thanks in advance for suggestions, websites, or tutorials, etc.
Mark

Is it possible to add additional python modules to a MacPyMOL installation?

I am trying to install the PyNMR plugin:

http://maple.rsvs.ulaval.ca/mediawiki/index.php/PyNMR

And it requires the Numeric python module.  I have an external python
installation  built with the module, but it seems that MacPyMOL uses a
bundled python interpreter.

I tried setting the PYTHONPATH to the modules directory of my python 
build, but I get errors like this:

/programs/i386-mac/python/2.5.2/lib/python2.5/site-packages/Numeric/Numeric.py:91: RuntimeWarning: Python C API version mismatch for module multiarray: This Python has API version 1012, module multiarray has version 1013.

I poked around in the PyMOLX11Hybrid.app directories, but didn't see an
obvious place I could add a module installation.

Thanks.

-ben

--
Ben Eisenbraun
Structural Biology Grid                           Harvard Medical School
http://sbgrid.org                                 http://hms.harvard.edu

How large is large?

With enough RAM, PyMOL can do molecular surfaces up to perhap a hundred
thousand atoms or so, but above that, you probably need to fall back on
Gaussians as illustrated in the script below:

Cheers,
Warren

# load a whopping big PDB

load one_million_atoms.pdb, struct

spectrum count, selection=struct

# give ourselves a responsive UI

as spheres

set sphere_mode,1

# === now create a pseudo-fcalc map (a 3D volumetric scalar field) ===

# set the B-factors nice and high for smoothness

alter all, b=40

# ~10 A map resolution

set gaussian_resolution, 10

# ~10 A map spacing with a 10 A surrounding buffer
#  (you may need to vary this)

map_new map, gaussian, 10, struct, 10

# create a surface from the map

isosurface surf, map, 1.0

# now color the map based on the underlying protein

ramp_new ramp, struct, [0,10,10], [-1,-1,0]

color ramp, surf

disable ramp


--
DeLano Scientific LLC
Subscriber Support Services
mailto:su...@de...

 

> -----Original Message-----
> From: Crystal K. Chuang [mailto:CKC...@lb...] 
> Sent: Tuesday, December 16, 2008 5:11 PM
> To: pym...@li...
> Subject: [PyMOL] PyMol memory vs. computer memory
> 
> Hello,
> 
> When I try to add a surface to a very large structure and 
> PyMol gives me the error message  "PyMol just ran out of 
> memory and crashed...." am I receiving this message due to 
> limitations of the PyMol program, or do I need to install 
> more memory on my computer?
> 
> Thanks
> -Crystal
> 
> 
> 
> --------------------------------------------------------------
> ----------------
> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las 
> Vegas, Nevada.
> The future of the web can't happen without you.  Join us at 
> MIX09 to help pave the way to the Next Web now. Learn more 
> and register at 
> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009
.visitmix.com/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Hello,

When I try to add a surface to a very large structure and PyMol gives me the error message  "PyMol just ran out of memory and crashed...." am I receiving this message due to limitations of the PyMol program, or do I need to install more memory on my computer?

Thanks
-Crystal

Mark,
 
Sorry, but the current C code appears to be broken.  For future reference,
you should be able to do the following:
 
load $TUT/1hpv.pdb
 
# absolute linear scaling from the B factor
 
set cartoon_putty_transform, 7
 
# set a base radius of 1.0 (will be scaled based on B factors)
 
set cartoon_putty_radius, 1.0
 
# no limits on the scaling
 
set cartoon_putty_scale_min, -1
 
set cartoon_putty_scale_max, -1
 
# set the B factors
 
alter all, b=0.2
 
# display the cartoons appropriately
 
unset cartoon_smooth_loops
 
unset cartoon_flat_sheets
 
as cartoon
 
cartoon putty
 
# unfortunately, the above does not in fact work because there is a bug in
the code when all B factors are the same...you get a radius of 1 instead.
 
# regardless, setting non-identical B factors should currently work:
 
alter chain A, b=0.2
 
alter chain B, b=0.4
 
rebuild
 
Cheers,
Warren
 
--
DeLano Scientific LLC
Subscriber Support Services
mailto:su...@de...
 


  _____  

From: Mark A. White [mailto:ma...@ut...] 
Sent: Monday, December 15, 2008 3:34 PM
To: pym...@li...
Subject: [PyMOL] B-factor putty tube representation


Hi,

I would like to define the radius of the cartoon putty on absolute, rather
than a relative scale.  Is there any way to do this?  If I am comparing
rmsd, for example, I would like every image to be representative of the true
RMSD differences, rather than being a unique relative scale for each
comparison.

I notice that others have also asked about this in the past, but I did not
see a response on the Pymol-Users Email Archive.  Maybe there are new
features in 1.1 that address this?

[PyMOL] putty tube representation From: Evan Kantrowitz
<evan.kantrowitz@bc...> - 2007-08-09 21:37 
Attachments: HTML-Email.html
<http://sourceforge.net/mailarchive/attachment.php?list_name=pymol-users&mes
sag...@bc...&counter=1>       I am
making tube representations as a comparison between two 
structures. I have the rmsd in the b-factor field.
1) If I do a putty representation it works. How does the program 
decide on the width variation of the tube?
2) How can this be reset?
I want to do this so when I compare two different rmsd plots the 
width of lets say 1 rms is the same in both figures.

Any help would be apprecipated.
-------------------------------------------------------------------
Evan R. Kantrowitz, 
Ph.D 
evan.kantrowitz
Boston 
College 




Yours sincerely,

Mark A. White, Ph.D.
Assistant Professor, Dept. Biochemistry and Molecular Biology, 
Manager, Sealy Center for Structural Biology and Molecular Biophysics X-ray
Crystallography Laboratory,
Basic Science Building, Room 6.660 C
University of Texas Medical Branch
Galveston, TX 77555-0647
Tel. (409) 747-4747
Cell. (409) 539-9138
Fax. (409) 747-4745
mailto://white@xray.utmb.edu
http://xray.utmb.edu
http://xray.utmb.edu/~white


	

Hi Buz,

You can use "center" as a selection name for input with zoom, along with a
distance value.

zoom center, distance

e.g.

# first, get the object you want in the center of the screen

orient

# then zoom the viewer by a fixed amount about the center point

zoom center, 10

# you may also wish to move the clipping planes in/out to avoid cutting into
any of the molecular representations:

clip atoms, 4, selection=all

# also, depending upon the application, you might want to disable
perspective

set orthoscopic

# get rid of background pixels

unset opaque_background

# render

ray

# and save

save struct001.png

Cheers,
Warren


--
DeLano Scientific LLC
Subscriber Support Services
mailto:su...@de...

 

> -----Original Message-----
> From: Buz Barstow [mailto:bu...@ma...] 
> Sent: Monday, December 15, 2008 11:42 AM
> To: pym...@li...
> Subject: [PyMOL] Ray Tracing A Protein Gallery
> 
> Dear All,
> 
> I'm making a gallery of protein molecules for my PhD thesis. 
> I'd like to find an automatic way to ensure that all of the 
> ray traced images have the same scale. Is there an easy way 
> to do this?
> 
> Thanks! and all the best,
> 
> --Buz
> 
> --------------------------------------------------------------
> ----------------
> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las 
> Vegas, Nevada.
> The future of the web can't happen without you.  Join us at 
> MIX09 to help pave the way to the Next Web now. Learn more 
> and register at 
> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009
.visitmix.com/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Hi,

I would like to define the radius of the cartoon putty on absolute,
rather than a relative scale.  Is there any way to do this?  If I am
comparing rmsd, for example, I would like every image to be
representative of the true RMSD differences, rather than being a unique
relative scale for each comparison.

I notice that others have also asked about this in the past, but I did
not see a response on the Pymol-Users Email Archive.  Maybe there are
new features in 1.1 that address this?

[PyMOL] putty tube representation
From: Evan Kantrowitz <evan.kantrowitz@bc...> - 2007-08-09 21:37 
Attachments: HTML-Email.html      
I am making tube representations as a comparison between two 
structures. I have the rmsd in the b-factor field.
1) If I do a putty representation it works. How does the program 
decide on the width variation of the tube?
2) How can this be reset?
I want to do this so when I compare two different rmsd plots the 
width of lets say 1 rms is the same in both figures.

Any help would be apprecipated.
-------------------------------------------------------------------
Evan R. Kantrowitz, 
Ph.D 
evan.kantrowitz
Boston 
College 



Yours sincerely,

Mark A. White, Ph.D.
Assistant Professor, Dept. Biochemistry and Molecular Biology, 
Manager, Sealy Center for Structural Biology and Molecular Biophysics
X-ray Crystallography Laboratory,
Basic Science Building, Room 6.660 C
University of Texas Medical Branch
Galveston, TX 77555-0647
Tel. (409) 747-4747
Cell. (409) 539-9138
Fax. (409) 747-4745
mailto://white@xray.utmb.edu
http://xray.utmb.edu
http://xray.utmb.edu/~white

On Mon, Dec 15, 2008 at 11:41 AM, Buz Barstow <bu...@ma...> wrote:

> I'm making a gallery of protein molecules for my PhD thesis. I'd like
> to find an automatic way to ensure that all of the ray traced images
> have the same scale. Is there an easy way to do this?
>

Translate every model so that the center is at the origin, then use the
set_view command to apply the same viewing matrix for each model.  (You can
still rotate the models, just don't zoom.)  I'm not sure if there's already
a simple way to do the translation from within PyMOL, but it should be quite
straightforward using cctbx or CNS or something similar.

-Nat

Dear All,

I'm making a gallery of protein molecules for my PhD thesis. I'd like  
to find an automatic way to ensure that all of the ray traced images  
have the same scale. Is there an easy way to do this?

Thanks! and all the best,

--Buz

Hi,

Does anybody have suggestions for the simplest way to script loading an
apbs grid and displaying the molecular surface colored by charge
(possibly changing the low/high values as well)?
I can do this interactively, but have come up blank trying to script this.

Thanks,

Pete