Re: [PyMOL] New to PyMol. Want to extract sequence from .pse file w/ colors.
Hi Shane,
I have a script which saves a colored sequence in HTML format. See
attachment.
Example usage:
run save_colored_fasta.py
save_colored_fasta seq.html
It should be possible to copypaste the colored sequence from your
browser to excel.
Cheers,
Thomas
Shane Neeley wrote, On 02/27/12 01:45:
Hi Pymol Network,
I would appreciate someones help in extracting the sequence in the
viewer above the protein. I have gone through the sequence and
changed AAs to different colors based on their position. I would
ideally like to be able to copy that sequence with the colors that
they are coded so that I could export it to an excel file. Is this
possible?
Thanks very much.
Shane
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
'''
(c) 2012 Thomas Holder, MPI for Developmental Biology
License: BSD-2-Clause
'''
from pymol import cmd
def save_colored_fasta(filename, selection='(all)', gapped=1, quiet=1):
'''
DESCRIPTION
Save a html file with colored (by C-alpha atoms) fasta sequence.
USAGE
save_colored_fasta filename [, selection [, gapped ]]
'''
from pymol.exporting import _resn_to_aa as one_letter
from pymol import Scratch_Storage
gapped = int(gapped)
selection = '(%s) and guide' % (selection)
html = []
stored = Scratch_Storage()
def callback(resv, resn, color):
if stored.resv is None:
stored.resv = resv - (resv % 70)
if gapped:
while stored.resv+1 resv:
callback(stored.resv+1, '-', 25)
stored.resv += 1
if stored.resv % 70 == 1:
html.append(('/font\nbr%4d font' % (resv)).replace(' ', 'nbsp;'))
stored.color = None
c = cmd.get_color_tuple(color)
color = '#%02x%02x%02x' % (c[0]*255, c[1]*255, c[2]*255)
aa = one_letter.get(resn, '-')
if color != stored.color:
html.append('/fontfont color=' + color + '')
stored.color = color
html.append(aa)
for obj in cmd.get_object_list(selection):
for chain in cmd.get_chains('model %s and (%s)' % (obj, selection)):
sele = 'model %s and chain %s and (%s)' % (obj, chain, selection)
html.append('\nbrgt;%s_%sfont' % (obj, chain))
stored.resv = None if gapped else 0
stored.color = None
cmd.iterate(sele, 'callback(resv, resn, color)', space=locals())
html.append('/font')
handle = open(filename, 'w')
print handle, 'htmlbody style=font-family:monospace'
print handle, ''.join(html)
print handle, '/body/html'
handle.close()
cmd.extend('save_colored_fasta', save_colored_fasta)
cmd.auto_arg[1].update([
('save_colored_fasta', cmd.auto_arg[0]['zoom']),
])
# vi: ts=4:sw=4:smarttab:expandtab
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[PyMOL] Little coordinate cross in Pymol?
Dear all, is it possible to show in Pymol a little coordinate cross with axes x,y,z, for example like in VMD, please? I have a protein made from dummy atoms and there is no unit cell. I just want to show clearly which plane is shown when presenting the model in my document. Thank you for your help. Kind regards Gudrun Lotze -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ 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] Little coordinate cross in Pymol?
http://pymolwiki.org/index.php/Axes -David On Feb 27, 2012, at 5:38 AM, Gudrun Lotze gudrun.lo...@gmx.net wrote: Dear all, is it possible to show in Pymol a little coordinate cross with axes x,y,z, for example like in VMD, please? I have a protein made from dummy atoms and there is no unit cell. I just want to show clearly which plane is shown when presenting the model in my document. Thank you for your help. Kind regards Gudrun Lotze -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ 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 -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ 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] Little coordinate cross in Pymol?
Dear all, I used the following script David pointed out: from pymol.cgo import * from pymol import cmd w = 0.06 # cylinder width l = 0.75 # cylinder length h = 0.25 # cone hight d = w * 1.618 # cone base diameter obj = [CYLINDER, 0.0, 0.0, 0.0, l, 0.0, 0.0, w, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, CYLINDER, 0.0, 0.0, 0.0, 0.0, l, 0.0, w, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, CYLINDER, 0.0, 0.0, 0.0, 0.0, 0.0, l, w, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, CONE, l, 0.0, 0.0, h+l, 0.0, 0.0, d, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 1.0, CONE, 0.0, l, 0.0, 0.0, h+l, 0.0, d, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 1.0, CONE, 0.0, 0.0, l, 0.0, 0.0, h+l, d, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 1.0, 1.0] cmd.load_cgo(obj, 'axes') The axes appear, but the screen in pymol is now split into two sections with the cross covering one part. Is there a chance to move the cross closer to the model in one screen section? A bit like shown in picture on page http://pymolwiki.org/index.php/Axes . Kind regards Gudrun Am 27.02.2012 um 12:01 schrieb David Hall: http://pymolwiki.org/index.php/Axes -David On Feb 27, 2012, at 5:38 AM, Gudrun Lotze gudrun.lo...@gmx.net wrote: Dear all, is it possible to show in Pymol a little coordinate cross with axes x,y,z, for example like in VMD, please? I have a protein made from dummy atoms and there is no unit cell. I just want to show clearly which plane is shown when presenting the model in my document. Thank you for your help. Kind regards Gudrun Lotze -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ 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 -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ 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] pymol 1.4.1 (incentive), segfault upon help-about
Hi Jason, I just installed pymol 1.5.0.3 on our linux machines and the segfault in libtcl8.5.so upon help-about is still present. Do you have any hint when this will be fixed? Best regards, Joachim -- Dr. rer. nat. Joachim Greipel Med. Hochschule Hannover Biophys. Chem. OE 4350 Carl-Neuberg-Str. 1 30625 Hannover Germany Fon: +49-511-532-3718 Fax: +49-511-532-16-3718 -Ursprüngliche Nachricht- Von: Jason Vertrees [mailto:jason.vertr...@schrodinger.com] Gesendet: Donnerstag, 19. Mai 2011 17:53 An: Greipel, Joachim Dr. Cc: pymol-users@lists.sourceforge.net; h...@schrodinger.com Betreff: Re: [PyMOL] pymol 1.4.1 (incentive), segfault upon help-about Hi Joachim, I always get a segmentation fault, when I click help-about to see the version details of pymol. The respective entry in /var/log/messages is: pymol.exe[4991]: segfault at 3e0019b ip f74857a0 sp f3bab9a8 error 4 in libtcl8.5.so[f741+ed0 00] Indeed on a few Linux distros, there is a crash when selecting Help About. We're trying to track down the cause. The error happens in our pure Python code and the segfault happens in the libtcl8.5 shared library. If you're checking for the PyMOL version number, please use get_version in the meantime. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 smime.p7s Description: S/MIME cryptographic signature -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ 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] Little coordinate cross in Pymol?
Hi Gudrun, On 02/27/2012 01:36 PM, Gudrun Lotze wrote: The axes appear, but the screen in pymol is now split into two sections with the cross covering one part. Is there a chance to move the cross closer to the model in one screen section? A bit like shown in picture on page http://pymolwiki.org/index.php/Axes . You can drag the axes object with the mouse. In the right panel, click on A drag and then use Shift+MiddleMouseButton to drag it. If you prefer the command line over mouse, you could use translate and rotate commands: http://pymolwiki.org/index.php/Translate http://pymolwiki.org/index.php/Rotate Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ 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] pymol 1.4.1 (incentive), segfault upon help-about
Try install tkinter Tkinter uses tcl 8.4 (something...) Troels Emtekær Linnet Lyongade 24. 4.mf, 2300 København S Mobil: +45 60210234 2012/2/27 greipel.joac...@mh-hannover.de Hi Jason, I just installed pymol 1.5.0.3 on our linux machines and the segfault in libtcl8.5.so upon help-about is still present. Do you have any hint when this will be fixed? Best regards, Joachim -- Dr. rer. nat. Joachim Greipel Med. Hochschule Hannover Biophys. Chem. OE 4350 Carl-Neuberg-Str. 1 30625 Hannover Germany Fon: +49-511-532-3718 Fax: +49-511-532-16-3718 -Ursprüngliche Nachricht- Von: Jason Vertrees [mailto:jason.vertr...@schrodinger.com] Gesendet: Donnerstag, 19. Mai 2011 17:53 An: Greipel, Joachim Dr. Cc: pymol-users@lists.sourceforge.net; h...@schrodinger.com Betreff: Re: [PyMOL] pymol 1.4.1 (incentive), segfault upon help-about Hi Joachim, I always get a segmentation fault, when I click help-about to see the version details of pymol. The respective entry in /var/log/messages is: pymol.exe[4991]: segfault at 3e0019b ip f74857a0 sp f3bab9a8 error 4 in libtcl8.5.so[f741+ed0 00] Indeed on a few Linux distros, there is a crash when selecting Help About. We're trying to track down the cause. The error happens in our pure Python code and the segfault happens in the libtcl8.5 shared library. If you're checking for the PyMOL version number, please use get_version in the meantime. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ 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 -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ 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] Little coordinate cross in Pymol?
Dear Gudrun, I have no experience with PyMOL on Mac. Maybe this helps: http://pymolwiki.org/index.php/Mouse_Controls Deselecting objects does not help, because by default you transform in camera space, which affects all objects. What you need is transformation in model space, which is achieved by A drag or A drag matrix for a particular object. Here an example to use the command line: translate [10,0,0], object=axes Hope that helps. Cheers, Thomas On 02/27/2012 03:21 PM, Gudrun Lotze wrote: Dear Thomas Thank you for your reply. The mouse dragging does not work because the Mac starts to move windows in a very beautiful way which I never came across. :-) So I used a 2-button mouse. But there is still a problem. The dummy atom model and the three axes object are always moving together when dragging around. Even when I deselect the model, drag the cross, and re-select the model, the model has moved as well. May I have to shift the cross within the script? Kind regards Gudrun Am 27.02.2012 um 12:50 schrieb Thomas Holder: Hi Gudrun, On 02/27/2012 01:36 PM, Gudrun Lotze wrote: The axes appear, but the screen in pymol is now split into two sections with the cross covering one part. Is there a chance to move the cross closer to the model in one screen section? A bit like shown in picture on page http://pymolwiki.org/index.php/Axes . You can drag the axes object with the mouse. In the right panel, click on A drag and then use Shift+MiddleMouseButton to drag it. If you prefer the command line over mouse, you could use translate and rotate commands: http://pymolwiki.org/index.php/Translate http://pymolwiki.org/index.php/Rotate Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ 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] Question about ray tracing, set_view, surface smoothness
Dear all, I wish to ray trace my object so it looks nice. I have chosen a mesh as surface representation. I did viewport 1024, 768 ray 1024, 768 But the mesh is black afterwards and not anymore blue. Is there a chance to keep the color and have less dominant lines for the mesh? Is there a chance to view the object in question for example in the XY, YZ plane? Are there somewhere easy rotation matrix available? I tried to bring my object manually into the YZ plane view, for example, but it works only halfhearted. It would be nice to be able to tell pymol in a very easy way which view I would like to see the object. Thank you for your patience. Kind regards Gudrun -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ 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] Question about ray tracing, set_view, surface smoothness
Hi Gudrun, But the mesh is black afterwards and not anymore blue. You may want to check your light position, or try a slighter blue. Is there a chance to keep the color and have less dominant lines for the mesh? I'm not artistically skilled enough to know about less dominant lines, but the mesh_width setting can be used to make thinner (or thicker) lines. Is there a chance to view the object in question for example in the XY, YZ plane? Are there somewhere easy rotation matrix available? I tried to bring my object manually into the YZ plane view, for example, but it works only halfhearted. It would be nice to be able to tell pymol in a very easy way which view I would like to see the object. The turn/rotate commands can be used fairly easily for 90 degree turns; but I'm not sure if that's what you're asking about. Pete -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ 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
