Hi all, I would like to build a cage model using cage builder, but the problem is that I need to use different polygons than available in the pop-up window of cage builder. My question is: is there any option to use for example octagons, decagons or even more-gons? Thank in advance Artur =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Artur BIELA, PhD Scientific Assistant Bionanoscience and Biochemistry Laboratory Malopolska Centre of Biotechnology Jagiellonian University 7A, Gronostajowa Street 30-387 Krakow Poland Department of Cell Biology and Imaging Institute of Zoology and Biomedical Research Jagiellonian University Gronostajowa 9 30-387 Krakow artur.biela@uj.edu.pl http://www.mcb.uj.edu.pl/en_GB/heddle-laboratory publons<https://publons.com/mashlets?el=badgeCont570&rid=M-3954-2019> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Hi Artur, Sorry, there is no option for polygons with N sides >7 in the Cage Builder tool. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/cagebuilder/cagebuilder.html> You can create arbitrary polygon objects and other shapes in the BILD input format (a simple text file), but in that case you have to specify the vertex coordinates yourself — it doesn’t automatically form enclosed cages. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 5, 2019, at 1:10 AM, Artur Biela <artur.biela@uj.edu.pl> wrote:
Hi all,
I would like to build a cage model using cage builder, but the problem is that I need to use different polygons than available in the pop-up window of cage builder. My question is: is there any option to use for example octagons, decagons or even more-gons?
Thank in advance Artur
Hi Artur, You can modify one line of the Cage Builder python code in your copy of Chimera to create buttons to make polygons with more sides. The file to modify is chimera/share/CageBuilder/gui.py or on Mac Chimera.app/Contents/Resources/share/CageBuilder/gui.py and the line to modify is apb = [('%d' % n , lambda n=n: self.attach_polygons(n)) for n in range(3,8)] which you could change replacing 8 by 16 to get apb = [('%d' % n , lambda n=n: self.attach_polygons(n)) for n in range(3,16)] which would create buttons in the Cage Builder panel for polygons with 3 through 15 sides. After you edit the file with a text editor (keep the indentation of the line the same as this is important in Python), then restart Chimera and it will have the new buttons. Tom
On Sep 5, 2019, at 1:10 AM, Artur Biela <artur.biela@uj.edu.pl> wrote:
Hi all,
I would like to build a cage model using cage builder, but the problem is that I need to use different polygons than available in the pop-up window of cage builder. My question is: is there any option to use for example octagons, decagons or even more-gons?
Thank in advance Artur
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Artur BIELA, PhD Scientific Assistant Bionanoscience and Biochemistry Laboratory Malopolska Centre of Biotechnology Jagiellonian University 7A, Gronostajowa Street 30-387 Krakow Poland
Department of Cell Biology and Imaging Institute of Zoology and Biomedical Research Jagiellonian University Gronostajowa 9 30-387 Krakow
artur.biela@uj.edu.pl <mailto:artur.biela@uj.edu.pl> http://www.mcb.uj.edu.pl/en_GB/heddle-laboratory <http://www.mcb.uj.edu.pl/en_GB/heddle-laboratory> publons <https://publons.com/mashlets?el=badgeCont570&rid=M-3954-2019> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
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Thank you Tom, Everything is working now perfectly. Best, Artur =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Artur BIELA, PhD Scientific Assistant Bionanoscience and Biochemistry Laboratory Malopolska Centre of Biotechnology Jagiellonian University 7A, Gronostajowa Street 30-387 Krakow Poland Department of Cell Biology and Imaging Institute of Zoology and Biomedical Research Jagiellonian University Gronostajowa 9 30-387 Krakow artur.biela@uj.edu.pl http://www.mcb.uj.edu.pl/en_GB/heddle-laboratory publons<https://publons.com/mashlets?el=badgeCont570&rid=M-3954-2019> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Od: Tom Goddard<mailto:goddard@sonic.net> Wysłano: czwartek, 5 września 2019 19:55 Do: Artur Biela<mailto:artur.biela@uj.edu.pl> DW: chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> Temat: Re: [Chimera-users] cage builder Hi Artur, You can modify one line of the Cage Builder python code in your copy of Chimera to create buttons to make polygons with more sides. The file to modify is chimera/share/CageBuilder/gui.py or on Mac Chimera.app/Contents/Resources/share/CageBuilder/gui.py and the line to modify is apb = [('%d' % n , lambda n=n: self.attach_polygons(n)) for n in range(3,8)] which you could change replacing 8 by 16 to get apb = [('%d' % n , lambda n=n: self.attach_polygons(n)) for n in range(3,16)] which would create buttons in the Cage Builder panel for polygons with 3 through 15 sides. After you edit the file with a text editor (keep the indentation of the line the same as this is important in Python), then restart Chimera and it will have the new buttons. Tom On Sep 5, 2019, at 1:10 AM, Artur Biela <artur.biela@uj.edu.pl<mailto:artur.biela@uj.edu.pl>> wrote: Hi all, I would like to build a cage model using cage builder, but the problem is that I need to use different polygons than available in the pop-up window of cage builder. My question is: is there any option to use for example octagons, decagons or even more-gons? Thank in advance Artur =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Artur BIELA, PhD Scientific Assistant Bionanoscience and Biochemistry Laboratory Malopolska Centre of Biotechnology Jagiellonian University 7A, Gronostajowa Street 30-387 Krakow Poland Department of Cell Biology and Imaging Institute of Zoology and Biomedical Research Jagiellonian University Gronostajowa 9 30-387 Krakow artur.biela@uj.edu.pl<mailto:artur.biela@uj.edu.pl> http://www.mcb.uj.edu.pl/en_GB/heddle-laboratory publons<https://publons.com/mashlets?el=badgeCont570&rid=M-3954-2019> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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Artur Biela -
Elaine Meng -
Tom Goddard