From: Robert C. <Rob...@ca...> - 2006-08-02 13:30:33
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Hi. I want to make a figure showing a cutaway surface representation of a large complex showing a channel containing a peptide helix. If I show the surface and cartoon representations respectively and fiddle around with the clipping and slabing I can't get it so that the channel is 'open' without clipping part of the helix. Is it possible to make an image of the cutaway surface and superimpose the helix? Sorry if that's confusing! Cheers, Rob |
From: EPF (E. P. Friis) <EP...@no...> - 2006-08-02 14:05:44
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Hi Rob A bit confusing :-) But the trick in such cases is usually to duplicate your object, and show the cutaway surface on the original and the cartoon/helix/etc on the copy. The cutaway surface is often easier to create by box-selecting (with the mouse) everything but the part that should be left open, and then show surface of the selection Also confusing? :-) Cheers Esben On Wed, 2006-08-02 at 15:30, Robert Court wrote: > Hi. > > I want to make a figure showing a cutaway surface representation of a large > complex showing a channel containing a peptide helix. If I show the surface > and cartoon representations respectively and fiddle around with the clipping > and slabing I can't get it so that the channel is 'open' without clipping > part of the helix. > > Is it possible to make an image of the cutaway surface and superimpose the > helix? > > Sorry if that's confusing! > > Cheers, > > Rob > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys -- and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: Marc B. <br...@mp...> - 2006-08-03 15:11:12
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hello, is there any way to find out which atoms are discarded during the refinement cycles of the "align" command? regards, marc |
From: Michael L. <mgl...@gm...> - 2006-08-03 15:25:27
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This is not a great answer, but do you know about the object parameter for the align command? I often type something like align struct1, struct2, object=alignment and then just look at which things were included/excluded. -michael On 8/3/06, Marc Bruning <br...@mp...> wrote: > hello, > > is there any way to find out which atoms are discarded during the refinement > cycles of the "align" command? > > regards, > marc > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys -- and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Marc B. <br...@mp...> - 2006-08-04 09:46:12
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the problem in this case is to recognize the rejected atoms by eye, if you align about 400 c-alphas with average RMSDs of 0.2A. a printable list would be more helpful. but i guess this is not possible. but thanks a lot for your answer. On Thursday 03 August 2006 17:25, you wrote: > This is not a great answer, but do you know about the object parameter > for the align command? I often type something like > > align struct1, struct2, object=alignment > > and then just look at which things were included/excluded. > > -michael > > On 8/3/06, Marc Bruning <br...@mp...> wrote: > > hello, > > > > is there any way to find out which atoms are discarded during the > > refinement cycles of the "align" command? > > > > regards, > > marc > > > > ------------------------------------------------------------------------- > > Take Surveys. Earn Cash. Influence the Future of IT > > Join SourceForge.net's Techsay panel and you'll get the chance to share > > your opinions on IT & business topics through brief surveys -- and earn > > cash > > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > > _______________________________________________ > > PyMOL-users mailing list > > PyM...@li... > > https://lists.sourceforge.net/lists/listinfo/pymol-users |