Re: [PyMOL] weird visualization of a peptide structure
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:supp...@delsci.com _ From: annalisa bordogna [mailto:annalisa.bordo...@gmail.com] Sent: Thursday, December 18, 2008 6:40 AM To: pymol-users@lists.sourceforge.net 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
Re: [PyMOL] Mutating an Ion in Pymol and Displaying van der waals Radii
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:supp...@delsci.com > -Original Message- > From: Buz Barstow [mailto:b...@mac.com] > Sent: Thursday, December 18, 2008 2:30 PM > To: pymol-users@lists.sourceforge.net > 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 > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] surface properties
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:supp...@delsci.com > -Original Message- > From: Mark Collins [mailto:mnc2...@columbia.edu] > Sent: Thursday, December 18, 2008 7:38 AM > To: pymol-users@lists.sourceforge.net > 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 > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] adding python modules for MacPyMOL
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:supp...@delsci.com > -Original Message- > From: Ben Eisenbraun [mailto:b...@crystal.harvard.edu] > Sent: Wednesday, December 17, 2008 9:53 AM > To: pymol-users@lists.sourceforge.net > 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 > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Ray Tracing A Protein Gallery
> 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:b...@mac.com] > Sent: Thursday, December 18, 2008 3:27 PM > To: pymol-users@lists.sourceforge.net > 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:supp...@delsci.com > > > > > > > >> -Original Message- > >> From: Buz Barstow [mailto:b...@mac.com] > >> Sent: Monday, December 15, 2008 11:42 AM > >> To: pymol-users@lists.sourceforge.net > >> 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 > >> PyMOL-users@lists.sourceforge.net > >> 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 > > PyMOL-users@lists.sourceforge.net > > 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://a
Re: [PyMOL] weird visualization of a peptide structure
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 > 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 > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > >
Re: [PyMOL] weird visualization of a peptide structure
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 > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] surface properties
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:supp...@delsci.com -Original Message- From: Mark Collins [mailto:mnc2...@columbia.edu] Sent: Thursday, December 18, 2008 7:38 AM To: pymol-users@lists.sourceforge.net 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 PyMOL-users@lists.sourceforge.net 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 PyMOL-users@lists.sourceforge.net 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: a...@biotec.tu-dresden.de
[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
Re: [PyMOL] cmd.scene('*')
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:malcolm.da...@bms.com]
> Sent: Friday, December 19, 2008 3:46 PM
> To: pymol-users@lists.sourceforge.net
> 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
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>
