Re: [PyMOL] Possible bug in set cartoon_cylindrical_helices
Hi Jason , Thanks to your example I figured it out and it seems like there is small problem with the status message text even when it fails. So if I had a created object obj01 This works: set cartoon_cylindrical_helices , 1, obj01 This does not work: set cartoon_cylindrical_helices , 1 , (obj01) In both cases pymol echoes a cartoon_cylindrical_helices set for 222 atoms in object obj01 in the status text. The only difference is the parentheses around the object. I guess the correct syntax is to not have the parentheses around the object name. Thanks for all your help Hari On Thu, Jun 17, 2010 at 8:14 PM, hari jayaram hari...@gmail.com wrote: Hi Jason , and Nat , I just tried it on my mac laptop and the set cartoon_cylindrical_helices works just as it should. Followng that I tried it on two separate ubuntu 64 bit boxes , running pymol version 1.2 and 1.3 and python version 2.5 and 2.6 , both of them dont do the right thing i.e allow the property to be set only for the object and instead propagate the property to all objects. I must admit that both of ubuntu builds were compiled by me , but everything is working just fine , other than this property setting as far as I know. Are your or anyone else seeing this on their machine. Thanks Hari On Thu, Jun 17, 2010 at 7:04 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Hari, The following, fetch 1cll 1ggz, async=0 set cartoon_cylindrical_helices, 1, 1cll as cartoon works just fine for me. Can you send me your PSE or pdb files? Are you setting anything else? Cheers, -- Jason On Thu, Jun 17, 2010 at 6:41 PM, hari jayaram hari...@gmail.com wrote: I am trying to show a molecule in ribbon representation , where all the helices except one helix are in ribbon form and a solitary helix is shown as a cylinder. Can someone confirm that set cartoon_cylindrical_helices , 1 , (obj01) Followed by show cartoon , (obj01). Does not show only (obj01) as a cylinder In my tests obj01 is the object created from a selection and then the property set for that object. But it seems that this does not just create a cylindrical helix for just that object. For some reason the cartoon_cylindrical_helices property is not handled the way other set properties are and that the object alone is not allowed to have a different value than the rest of the molecules. Thanks for your help in advance Hari -- 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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
Re: [PyMOL] Possible bug in set cartoon_cylindrical_helices
Hari, PyMOL has objects, which you access by writing objectName, selections which you access by (selectionName) and another level of selections that Warren was working on. While in many places you can use objectName or (objectName) to refer to your object, you cannot do this in all places. This is one. Cheers, -- Jason On Fri, Jun 18, 2010 at 9:55 AM, hari jayaram hari...@gmail.com wrote: Hi Jason , Thanks to your example I figured it out and it seems like there is small problem with the status message text even when it fails. So if I had a created object obj01 This works: set cartoon_cylindrical_helices , 1, obj01 This does not work: set cartoon_cylindrical_helices , 1 , (obj01) In both cases pymol echoes a cartoon_cylindrical_helices set for 222 atoms in object obj01 in the status text. The only difference is the parentheses around the object. I guess the correct syntax is to not have the parentheses around the object name. Thanks for all your help Hari On Thu, Jun 17, 2010 at 8:14 PM, hari jayaram hari...@gmail.com wrote: Hi Jason , and Nat , I just tried it on my mac laptop and the set cartoon_cylindrical_helices works just as it should. Followng that I tried it on two separate ubuntu 64 bit boxes , running pymol version 1.2 and 1.3 and python version 2.5 and 2.6 , both of them dont do the right thing i.e allow the property to be set only for the object and instead propagate the property to all objects. I must admit that both of ubuntu builds were compiled by me , but everything is working just fine , other than this property setting as far as I know. Are your or anyone else seeing this on their machine. Thanks Hari On Thu, Jun 17, 2010 at 7:04 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Hari, The following, fetch 1cll 1ggz, async=0 set cartoon_cylindrical_helices, 1, 1cll as cartoon works just fine for me. Can you send me your PSE or pdb files? Are you setting anything else? Cheers, -- Jason On Thu, Jun 17, 2010 at 6:41 PM, hari jayaram hari...@gmail.com wrote: I am trying to show a molecule in ribbon representation , where all the helices except one helix are in ribbon form and a solitary helix is shown as a cylinder. Can someone confirm that set cartoon_cylindrical_helices , 1 , (obj01) Followed by show cartoon , (obj01). Does not show only (obj01) as a cylinder In my tests obj01 is the object created from a selection and then the property set for that object. But it seems that this does not just create a cylindrical helix for just that object. For some reason the cartoon_cylindrical_helices property is not handled the way other set properties are and that the object alone is not allowed to have a different value than the rest of the molecules. Thanks for your help in advance Hari -- 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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
Re: [PyMOL] Possible bug in set cartoon_cylindrical_helices
Hi Hari, The following, fetch 1cll 1ggz, async=0 set cartoon_cylindrical_helices, 1, 1cll as cartoon works just fine for me. Can you send me your PSE or pdb files? Are you setting anything else? Cheers, -- Jason On Thu, Jun 17, 2010 at 6:41 PM, hari jayaram hari...@gmail.com wrote: I am trying to show a molecule in ribbon representation , where all the helices except one helix are in ribbon form and a solitary helix is shown as a cylinder. Can someone confirm that set cartoon_cylindrical_helices , 1 , (obj01) Followed by show cartoon , (obj01). Does not show only (obj01) as a cylinder In my tests obj01 is the object created from a selection and then the property set for that object. But it seems that this does not just create a cylindrical helix for just that object. For some reason the cartoon_cylindrical_helices property is not handled the way other set properties are and that the object alone is not allowed to have a different value than the rest of the molecules. Thanks for your help in advance Hari -- 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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
Re: [PyMOL] Possible bug in set cartoon_cylindrical_helices
Hi Jason , and Nat , I just tried it on my mac laptop and the set cartoon_cylindrical_helices works just as it should. Followng that I tried it on two separate ubuntu 64 bit boxes , running pymol version 1.2 and 1.3 and python version 2.5 and 2.6 , both of them dont do the right thing i.e allow the property to be set only for the object and instead propagate the property to all objects. I must admit that both of ubuntu builds were compiled by me , but everything is working just fine , other than this property setting as far as I know. Are your or anyone else seeing this on their machine. Thanks Hari On Thu, Jun 17, 2010 at 7:04 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Hari, The following, fetch 1cll 1ggz, async=0 set cartoon_cylindrical_helices, 1, 1cll as cartoon works just fine for me. Can you send me your PSE or pdb files? Are you setting anything else? Cheers, -- Jason On Thu, Jun 17, 2010 at 6:41 PM, hari jayaram hari...@gmail.com wrote: I am trying to show a molecule in ribbon representation , where all the helices except one helix are in ribbon form and a solitary helix is shown as a cylinder. Can someone confirm that set cartoon_cylindrical_helices , 1 , (obj01) Followed by show cartoon , (obj01). Does not show only (obj01) as a cylinder In my tests obj01 is the object created from a selection and then the property set for that object. But it seems that this does not just create a cylindrical helix for just that object. For some reason the cartoon_cylindrical_helices property is not handled the way other set properties are and that the object alone is not allowed to have a different value than the rest of the molecules. Thanks for your help in advance Hari -- 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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
