Re: [PyMOL] Viewport and ray
Dear Tsjerk, thank you very much for your help. I apologise for this question but could not find in the WIKI help for this. I noticed just now I have to get the width and height correct so everything fits into the frame. Then nothing is cut off in the final image. Thank you again! Kind regards Gudrun Am 29.03.2012 um 12:19 schrieb Tsjerk Wassenaar: > Hi Gudrun, > > If you raytrace an image it is written to disk and loaded into the > viewport. If the imge is larger than the viewport it is displayed > smaller with the real resolution mentioned underneath. If you save the > image, using 'png', it is saved in the large format, without the black > padding. > > Cheers, > > Tsjerk > > On Thu, Mar 29, 2012 at 1:12 PM, Gudrun Lotze wrote: >> Dear Pymol-Experts, >> a while ago I had problems with the ray command. It always showed me a black >> frame with mentioning at the bottom the image size. >> The group advised me to use viewport. >> >> viewport 800, 600 >> >> ray 800, 600 >> >> >> This works and I don't get this black frame, however if I try different >> values, for example 1200, 1000 I still get the black frame. Everything fits >> nicely on the screen and I don't know where this black box comes really in >> the other cases. >> I would like to use a higher resolution than 800, 600 without the black box. >> >> Thank you very much for your help. >> Kind regards >> Gudrun >> >> >> -- >> This SF email is sponsosred by: >> Try Windows Azure free for 90 days Click Here >> http://p.sf.net/sfu/sfd2d-msazure >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > * Groningen Institute for Biomolecular Research and Biotechnology > * Zernike Institute for Advanced Materials > University of Groningen > The Netherlands -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ 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] Viewport and ray
Dear Pymol-Experts, a while ago I had problems with the ray command. It always showed me a black frame with mentioning at the bottom the image size. The group advised me to use viewport. viewport 800, 600 ray 800, 600 This works and I don't get this black frame, however if I try different values, for example 1200, 1000 I still get the black frame. Everything fits nicely on the screen and I don't know where this black box comes really in the other cases. I would like to use a higher resolution than 800, 600 without the black box. Thank you very much for your help. Kind regards Gudrun -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ 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] Axes.py question
Thank you very much! Really cool!
Gudrun
Am 28.03.2012 um 17:38 schrieb Jason Vertrees:
> Hi Gudrun,
>
> The quickest way would be to center the camera on your selection/protein:
>
> # create the axes
>
> run axes.py
>
> # put camera center at center of protein geometry
>
> orient 6lys
>
> x = cmd.get_position()
>
> # move the axes
>
> cmd.set_object_ttt("axes", [1, 0, 0, x[0], 0, 1, 0, x[1], 0, 0, 1,
> x[2], 0, 0, 0, 1])
>
> Cheers,
>
> -- Jason
>
> On Wed, Mar 28, 2012 at 9:00 AM, Gudrun Lotze wrote:
>> Dear all,
>>
>> I used the second script from page http://www.pymolwiki.org/index.php/Axes
>> to draw those axes.
>>
>> However they are not plotted within my 6Lys.pdb file, those axes are located
>> next to the crystal structure. I honestly don't know whee is the center of
>> 6Lys.pdb, but is there a chance to bring 6Lys.pdb and axes.py with regard to
>> their centers into one point, please? Basically, the axes.py sits in the
>> center of the molecule.
>> Is there a defined way to achieve this without random try & fail
>> translations, please?
>>
>> Thank you for your help.
>> Kind regards
>> Gudrun
>> --
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>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrödinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
--
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[PyMOL] Axes.py question
Dear all, I used the second script from page http://www.pymolwiki.org/index.php/Axes to draw those axes. However they are not plotted within my 6Lys.pdb file, those axes are located next to the crystal structure. I honestly don't know whee is the center of 6Lys.pdb, but is there a chance to bring 6Lys.pdb and axes.py with regard to their centers into one point, please? Basically, the axes.py sits in the center of the molecule. Is there a defined way to achieve this without random try & fail translations, please? Thank you for your help. Kind regards Gudrun -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ 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] Line thickness for show as cell
Dear all, Thank you very much for your help. It worked :-) Kind regards Gudrun -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ 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] Line thickness for show as cell
Dear all, How can I draw a thicker line when using show as cell, please? I would like to have the cell lines thicker, please. At the moment I cannot find an entry in the Pymol wiki. Kind regards and thank you for your help. Gudrun -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ 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] 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 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
[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
[PyMOL] Question about ray
Dear Pymol-Users, I tried to ray my protein to get a good looking picture. I tried set ray_trace_mode, 0 and ray 1200, 1200. I always go a square around my protein and parts where not visible. How can I get rid of that black border line and how can I ray my protein so it is on the whole page visible and not in a box cut off. Thank you and kind regards Gudrun Lotze -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo ___ 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
