From: Ariel T. <tal...@ci...> - 2010-05-21 16:11:13
|
Hi there, I am trying to set stick transparency using the following command: set stick_transparency, 0.5, peg_1, but with no success. The problem is with the selection, because if I use instead, set stick_transparency, 0.5, then every thing represented with stick get 50% transparent. Can you help with this? I am using Pymol 1.2 under Ubuntu 10.04. Thanks a lot in advanced, Best regards, Ariel |
From: Matthew F. <Mat...@im...> - 2010-05-21 16:41:11
|
(I'm putting this back on-list) That's too bad. It worked for me: PyMOL 1.2r2, Windows XP. Can you set other properties of this object: color, stick_radius, etc.? - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems, a wholly owned subsidiary of Eli Lilly & Company 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 > -----Original Message----- > From: Ariel Talavera [mailto:tal...@ci...] > Sent: Friday, May 21, 2010 12:26 PM > To: Matthew Franklin > Subject: RE: [PyMOL] stick transparency > > Thanks for the very quick answer, but it didn't succeed. > > Best, > Ariel > > On Fri, 2010-05-21 at 11:18 -0500, Matthew Franklin wrote: > Hi Ariel - > > Try "set stick_transparency=0.5, peg_1" > > - Matt > > > -- > Matthew Franklin , Ph.D. > Senior Scientist, ImClone Systems, > a wholly owned subsidiary of Eli Lilly & Company > 180 Varick Street, 6th floor > New York, NY 10014 > phone:(917)606-4116 fax:(212)645-2054 > > > -----Original Message----- > > From: Ariel Talavera [mailto:tal...@ci...] > > Sent: Friday, May 21, 2010 12:01 PM > > To: pym...@li... > > Subject: [PyMOL] stick transparency > > > > Hi there, > > > > I am trying to set stick transparency using the following command: > > set stick_transparency, 0.5, peg_1, but with no success. The problem is > > with the selection, because if I use instead, set stick_transparency, > > 0.5, then every thing represented with stick get 50% transparent. Can > > you help with this? I am using Pymol 1.2 under Ubuntu 10.04. > > > > Thanks a lot in advanced, > > > > Best regards, > > Ariel > > Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you. |
From: Ariel T. <tal...@ci...> - 2010-05-21 16:45:48
|
Yes, it happen the same when setting other properties as you mentioned. Ariel On Fri, 2010-05-21 at 11:40 -0500, Matthew Franklin wrote: > (I'm putting this back on-list) > > That's too bad. It worked for me: PyMOL 1.2r2, Windows XP. Can you set other properties of this object: color, stick_radius, etc.? > > - Matt > > > > -- > Matthew Franklin , Ph.D. > Senior Scientist, ImClone Systems, > a wholly owned subsidiary of Eli Lilly & Company > 180 Varick Street, 6th floor > New York, NY 10014 > phone:(917)606-4116 fax:(212)645-2054 > > > > -----Original Message----- > > From: Ariel Talavera [mailto:tal...@ci...] > > Sent: Friday, May 21, 2010 12:26 PM > > To: Matthew Franklin > > Subject: RE: [PyMOL] stick transparency > > > > Thanks for the very quick answer, but it didn't succeed. > > > > Best, > > Ariel > > > > On Fri, 2010-05-21 at 11:18 -0500, Matthew Franklin wrote: > > Hi Ariel - > > > > Try "set stick_transparency=0.5, peg_1" > > > > - Matt > > > > > > -- > > Matthew Franklin , Ph.D. > > Senior Scientist, ImClone Systems, > > a wholly owned subsidiary of Eli Lilly & Company > > 180 Varick Street, 6th floor > > New York, NY 10014 > > phone:(917)606-4116 fax:(212)645-2054 > > > > > -----Original Message----- > > > From: Ariel Talavera [mailto:tal...@ci...] > > > Sent: Friday, May 21, 2010 12:01 PM > > > To: pym...@li... > > > Subject: [PyMOL] stick transparency > > > > > > Hi there, > > > > > > I am trying to set stick transparency using the following command: > > > set stick_transparency, 0.5, peg_1, but with no success. The problem is > > > with the selection, because if I use instead, set stick_transparency, > > > 0.5, then every thing represented with stick get 50% transparent. Can > > > you help with this? I am using Pymol 1.2 under Ubuntu 10.04. > > > > > > Thanks a lot in advanced, > > > > > > Best regards, > > > Ariel > > > > Confidentiality Note: > This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. > > Thank you. |
From: Ariel T. <tal...@ci...> - 2010-05-21 16:48:18
|
Hi again, Actually it seems that for some reason the comma after the value (0.5) invalidate the command line. Ariel On Fri, 2010-05-21 at 11:40 -0500, Matthew Franklin wrote: > (I'm putting this back on-list) > > That's too bad. It worked for me: PyMOL 1.2r2, Windows XP. Can you set other properties of this object: color, stick_radius, etc.? > > - Matt > > > > -- > Matthew Franklin , Ph.D. > Senior Scientist, ImClone Systems, > a wholly owned subsidiary of Eli Lilly & Company > 180 Varick Street, 6th floor > New York, NY 10014 > phone:(917)606-4116 fax:(212)645-2054 > > > > -----Original Message----- > > From: Ariel Talavera [mailto:tal...@ci...] > > Sent: Friday, May 21, 2010 12:26 PM > > To: Matthew Franklin > > Subject: RE: [PyMOL] stick transparency > > > > Thanks for the very quick answer, but it didn't succeed. > > > > Best, > > Ariel > > > > On Fri, 2010-05-21 at 11:18 -0500, Matthew Franklin wrote: > > Hi Ariel - > > > > Try "set stick_transparency=0.5, peg_1" > > > > - Matt > > > > > > -- > > Matthew Franklin , Ph.D. > > Senior Scientist, ImClone Systems, > > a wholly owned subsidiary of Eli Lilly & Company > > 180 Varick Street, 6th floor > > New York, NY 10014 > > phone:(917)606-4116 fax:(212)645-2054 > > > > > -----Original Message----- > > > From: Ariel Talavera [mailto:tal...@ci...] > > > Sent: Friday, May 21, 2010 12:01 PM > > > To: pym...@li... > > > Subject: [PyMOL] stick transparency > > > > > > Hi there, > > > > > > I am trying to set stick transparency using the following command: > > > set stick_transparency, 0.5, peg_1, but with no success. The problem is > > > with the selection, because if I use instead, set stick_transparency, > > > 0.5, then every thing represented with stick get 50% transparent. Can > > > you help with this? I am using Pymol 1.2 under Ubuntu 10.04. > > > > > > Thanks a lot in advanced, > > > > > > Best regards, > > > Ariel > > > > Confidentiality Note: > This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. > > Thank you. |
From: Michael Z. <mic...@ia...> - 2010-05-21 19:11:04
|
Hi Ariel, Commands like setting transparency (for surfaces, spheres, sticks, etc) act on objects, not selections. Does something like the following work for you? fetch 1t3r, async=0 hide everything show cartoon create lig, resn 017 show sticks, lig set stick_transparency, 0.7,lig show sticks, byres (lig around 5) and not resn 017 For me, this shows the ligand as transparent sticks and nearby residues as solid sticks. Mike Z On Fri, May 21, 2010 at 11:50 AM, Ariel Talavera <tal...@ci...>wrote: > Hi again, > > Actually it seems that for some reason the comma after the value (0.5) > invalidate the command line. > > Ariel > > On Fri, 2010-05-21 at 11:40 -0500, Matthew Franklin wrote: > > (I'm putting this back on-list) > > > > That's too bad. It worked for me: PyMOL 1.2r2, Windows XP. Can you set > other properties of this object: color, stick_radius, etc.? > > > > - Matt > > > > > > > > -- > > Matthew Franklin , Ph.D. > > Senior Scientist, ImClone Systems, > > a wholly owned subsidiary of Eli Lilly & Company > > 180 Varick Street, 6th floor > > New York, NY 10014 > > phone:(917)606-4116 fax:(212)645-2054 > > > > > > > -----Original Message----- > > > From: Ariel Talavera [mailto:tal...@ci...] > > > Sent: Friday, May 21, 2010 12:26 PM > > > To: Matthew Franklin > > > Subject: RE: [PyMOL] stick transparency > > > > > > Thanks for the very quick answer, but it didn't succeed. > > > > > > Best, > > > Ariel > > > > > > On Fri, 2010-05-21 at 11:18 -0500, Matthew Franklin wrote: > > > Hi Ariel - > > > > > > Try "set stick_transparency=0.5, peg_1" > > > > > > - Matt > > > > > > > > > -- > > > Matthew Franklin , Ph.D. > > > Senior Scientist, ImClone Systems, > > > a wholly owned subsidiary of Eli Lilly & Company > > > 180 Varick Street, 6th floor > > > New York, NY 10014 > > > phone:(917)606-4116 fax:(212)645-2054 > > > > > > > -----Original Message----- > > > > From: Ariel Talavera [mailto:tal...@ci...] > > > > Sent: Friday, May 21, 2010 12:01 PM > > > > To: pym...@li... > > > > Subject: [PyMOL] stick transparency > > > > > > > > Hi there, > > > > > > > > I am trying to set stick transparency using the following command: > > > > set stick_transparency, 0.5, peg_1, but with no success. The problem > is > > > > with the selection, because if I use instead, set stick_transparency, > > > > 0.5, then every thing represented with stick get 50% transparent. Can > > > > you help with this? I am using Pymol 1.2 under Ubuntu 10.04. > > > > > > > > Thanks a lot in advanced, > > > > > > > > Best regards, > > > > Ariel > > > > > > Confidentiality Note: > > This e-mail, and any attachment to it, contains privileged and > confidential information intended only for the use of the individual(s) or > entity named on the e-mail. If the reader of this e-mail is not the intended > recipient, or the employee or agent responsible for delivering it to the > intended recipient, you are hereby notified that reading it is strictly > prohibited. If you have received this e-mail in error, please immediately > return it to the sender and delete it from your system. > > > > Thank you. > > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Michael Zimmermann Ph.D. student in Bioinformatics and Computational Biology Department of Biochemistry, Biophysics and Molecular Biology Iowa State University |
From: Michael Z. <mic...@ia...> - 2010-05-21 19:13:07
|
Sorry, I didn't mention that I use 1.2r1 on xinXP It could be a version difference if the command does not work correctly for you. On Fri, May 21, 2010 at 11:50 AM, Ariel Talavera <tal...@ci...>wrote: > Hi again, > > Actually it seems that for some reason the comma after the value (0.5) > invalidate the command line. > > Ariel > > On Fri, 2010-05-21 at 11:40 -0500, Matthew Franklin wrote: > > (I'm putting this back on-list) > > > > That's too bad. It worked for me: PyMOL 1.2r2, Windows XP. Can you set > other properties of this object: color, stick_radius, etc.? > > > > - Matt > > > > > > > > -- > > Matthew Franklin , Ph.D. > > Senior Scientist, ImClone Systems, > > a wholly owned subsidiary of Eli Lilly & Company > > 180 Varick Street, 6th floor > > New York, NY 10014 > > phone:(917)606-4116 fax:(212)645-2054 > > > > > > > -----Original Message----- > > > From: Ariel Talavera [mailto:tal...@ci...] > > > Sent: Friday, May 21, 2010 12:26 PM > > > To: Matthew Franklin > > > Subject: RE: [PyMOL] stick transparency > > > > > > Thanks for the very quick answer, but it didn't succeed. > > > > > > Best, > > > Ariel > > > > > > On Fri, 2010-05-21 at 11:18 -0500, Matthew Franklin wrote: > > > Hi Ariel - > > > > > > Try "set stick_transparency=0.5, peg_1" > > > > > > - Matt > > > > > > > > > -- > > > Matthew Franklin , Ph.D. > > > Senior Scientist, ImClone Systems, > > > a wholly owned subsidiary of Eli Lilly & Company > > > 180 Varick Street, 6th floor > > > New York, NY 10014 > > > phone:(917)606-4116 fax:(212)645-2054 > > > > > > > -----Original Message----- > > > > From: Ariel Talavera [mailto:tal...@ci...] > > > > Sent: Friday, May 21, 2010 12:01 PM > > > > To: pym...@li... > > > > Subject: [PyMOL] stick transparency > > > > > > > > Hi there, > > > > > > > > I am trying to set stick transparency using the following command: > > > > set stick_transparency, 0.5, peg_1, but with no success. The problem > is > > > > with the selection, because if I use instead, set stick_transparency, > > > > 0.5, then every thing represented with stick get 50% transparent. Can > > > > you help with this? I am using Pymol 1.2 under Ubuntu 10.04. > > > > > > > > Thanks a lot in advanced, > > > > > > > > Best regards, > > > > Ariel > > > > > > Confidentiality Note: > > This e-mail, and any attachment to it, contains privileged and > confidential information intended only for the use of the individual(s) or > entity named on the e-mail. If the reader of this e-mail is not the intended > recipient, or the employee or agent responsible for delivering it to the > intended recipient, you are hereby notified that reading it is strictly > prohibited. If you have received this e-mail in error, please immediately > return it to the sender and delete it from your system. > > > > Thank you. > > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Michael Zimmermann Ph.D. student in Bioinformatics and Computational Biology Department of Biochemistry, Biophysics and Molecular Biology Iowa State University |
From: Jason V. <jas...@sc...> - 2010-05-22 18:46:01
|
Hi all, Don't worry it's still there, just under a different command. Stick_color, stick_transparency, etc are properties of bonds, so it's best to now use 'set_bond' intead of 'set'. For example, set_bond stick_transparency, 0.5, objectName Cheers, -- Jason On Fri, May 21, 2010 at 3:13 PM, Michael Zimmermann <mic...@ia...> wrote: > Sorry, I didn't mention that I use 1.2r1 on xinXP > It could be a version difference if the command does not work correctly for > you. > > On Fri, May 21, 2010 at 11:50 AM, Ariel Talavera <tal...@ci...> > wrote: >> >> Hi again, >> >> Actually it seems that for some reason the comma after the value (0.5) >> invalidate the command line. >> >> Ariel >> >> On Fri, 2010-05-21 at 11:40 -0500, Matthew Franklin wrote: >> > (I'm putting this back on-list) >> > >> > That's too bad. It worked for me: PyMOL 1.2r2, Windows XP. Can you set >> > other properties of this object: color, stick_radius, etc.? >> > >> > - Matt >> > >> > >> > >> > -- >> > Matthew Franklin , Ph.D. >> > Senior Scientist, ImClone Systems, >> > a wholly owned subsidiary of Eli Lilly & Company >> > 180 Varick Street, 6th floor >> > New York, NY 10014 >> > phone:(917)606-4116 fax:(212)645-2054 >> > >> > >> > > -----Original Message----- >> > > From: Ariel Talavera [mailto:tal...@ci...] >> > > Sent: Friday, May 21, 2010 12:26 PM >> > > To: Matthew Franklin >> > > Subject: RE: [PyMOL] stick transparency >> > > >> > > Thanks for the very quick answer, but it didn't succeed. >> > > >> > > Best, >> > > Ariel >> > > >> > > On Fri, 2010-05-21 at 11:18 -0500, Matthew Franklin wrote: >> > > Hi Ariel - >> > > >> > > Try "set stick_transparency=0.5, peg_1" >> > > >> > > - Matt >> > > >> > > >> > > -- >> > > Matthew Franklin , Ph.D. >> > > Senior Scientist, ImClone Systems, >> > > a wholly owned subsidiary of Eli Lilly & Company >> > > 180 Varick Street, 6th floor >> > > New York, NY 10014 >> > > phone:(917)606-4116 fax:(212)645-2054 >> > > >> > > > -----Original Message----- >> > > > From: Ariel Talavera [mailto:tal...@ci...] >> > > > Sent: Friday, May 21, 2010 12:01 PM >> > > > To: pym...@li... >> > > > Subject: [PyMOL] stick transparency >> > > > >> > > > Hi there, >> > > > >> > > > I am trying to set stick transparency using the following command: >> > > > set stick_transparency, 0.5, peg_1, but with no success. The problem >> > > > is >> > > > with the selection, because if I use instead, set >> > > > stick_transparency, >> > > > 0.5, then every thing represented with stick get 50% transparent. >> > > > Can >> > > > you help with this? I am using Pymol 1.2 under Ubuntu 10.04. >> > > > >> > > > Thanks a lot in advanced, >> > > > >> > > > Best regards, >> > > > Ariel >> > > > >> > Confidentiality Note: >> > This e-mail, and any attachment to it, contains privileged and >> > confidential information intended only for the use of the individual(s) or >> > entity named on the e-mail. If the reader of this e-mail is not the intended >> > recipient, or the employee or agent responsible for delivering it to the >> > intended recipient, you are hereby notified that reading it is strictly >> > prohibited. If you have received this e-mail in error, please immediately >> > return it to the sender and delete it from your system. >> > >> > Thank you. >> >> >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... > > > > -- > Michael Zimmermann > Ph.D. student in Bioinformatics and Computational Biology > Department of Biochemistry, Biophysics and Molecular Biology > Iowa State University > > ------------------------------------------------------------------------------ > > > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Maia C. <ch...@ua...> - 2010-05-23 22:55:54
|
I would like to show coordination bonds between Mg ion and its ligands (oxygens) as broken lines, the distance of Mg-O bond is between 1.9-2.2 A. Maia |
From: Nathaniel E. <nat...@gm...> - 2010-05-23 23:08:54
|
On Sun, May 23, 2010 at 3:55 PM, Maia Cherney <ch...@ua...> wrote: > I would like to show coordination bonds between Mg ion and its ligands > (oxygens) as broken lines, the distance of Mg-O bond is between 1.9-2.2 A. > dist elem mg, (all within 2.2 of elem mg) Might need to try a slightly longer length to catch everything. -Nat |
From: Maia C. <ch...@ua...> - 2010-05-24 01:41:00
|
I found a similar command dist 1, elem mg, elem o, 2.2 Nathaniel Echols wrote: > On Sun, May 23, 2010 at 3:55 PM, Maia Cherney <ch...@ua... > <mailto:ch...@ua...>> wrote: > > I would like to show coordination bonds between Mg ion and its ligands > (oxygens) as broken lines, the distance of Mg-O bond is between > 1.9-2.2 A. > > > dist elem mg, (all within 2.2 of elem mg) > > Might need to try a slightly longer length to catch everything. > > -Nat > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |
From: Maia C. <ch...@ua...> - 2010-05-24 02:08:17
|
Thank you for your help. However, I have 4 Mg ions in the au, so all Mg ions (and all coordinated ligands) got connected. I need only coordination for one Mg. Maia Nathaniel Echols wrote: > On Sun, May 23, 2010 at 3:55 PM, Maia Cherney <ch...@ua... > <mailto:ch...@ua...>> wrote: > > I would like to show coordination bonds between Mg ion and its ligands > (oxygens) as broken lines, the distance of Mg-O bond is between > 1.9-2.2 A. > > > dist elem mg, (all within 2.2 of elem mg) > > Might need to try a slightly longer length to catch everything. > > -Nat > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |
From: Nathaniel E. <nat...@gm...> - 2010-05-24 01:45:20
|
On Sun, May 23, 2010 at 6:33 PM, Maia Cherney <ch...@ua...> wrote: > Thank you for your help. However, I have 4 Mg ions in the au, so all Mg > ions (and all coordinated ligands) got connected. I need only coordination > for one Mg. > Then you need to qualify the selection with the residue number, and repeat up to 4 times. Same principle still applies, though: dist (elem mg and resid 341), (all within 2.2 of (elem mg and resid 341)) this particular example may be unnecessarily verbose if the residue number is unique. -Nat |
From: Ariel T. <tal...@ci...> - 2010-05-24 14:16:38
|
Hi all, Thanks a lot. It worked great. Cheers, Ariel On Sat, 2010-05-22 at 13:45 -0500, Jason Vertrees wrote: > Hi all, > > Don't worry it's still there, just under a different command. > Stick_color, stick_transparency, etc are properties of bonds, so it's > best to now use 'set_bond' intead of 'set'. For example, > > set_bond stick_transparency, 0.5, objectName > > Cheers, > > -- Jason > > > On Fri, May 21, 2010 at 3:13 PM, Michael Zimmermann > <mic...@ia...> wrote: > > Sorry, I didn't mention that I use 1.2r1 on xinXP > > It could be a version difference if the command does not work correctly for > > you. > > > > On Fri, May 21, 2010 at 11:50 AM, Ariel Talavera <tal...@ci...> > > wrote: > >> > >> Hi again, > >> > >> Actually it seems that for some reason the comma after the value (0.5) > >> invalidate the command line. > >> > >> Ariel > >> > >> On Fri, 2010-05-21 at 11:40 -0500, Matthew Franklin wrote: > >> > (I'm putting this back on-list) > >> > > >> > That's too bad. It worked for me: PyMOL 1.2r2, Windows XP. Can you set > >> > other properties of this object: color, stick_radius, etc.? > >> > > >> > - Matt > >> > > >> > > >> > > >> > -- > >> > Matthew Franklin , Ph.D. > >> > Senior Scientist, ImClone Systems, > >> > a wholly owned subsidiary of Eli Lilly & Company > >> > 180 Varick Street, 6th floor > >> > New York, NY 10014 > >> > phone:(917)606-4116 fax:(212)645-2054 > >> > > >> > > >> > > -----Original Message----- > >> > > From: Ariel Talavera [mailto:tal...@ci...] > >> > > Sent: Friday, May 21, 2010 12:26 PM > >> > > To: Matthew Franklin > >> > > Subject: RE: [PyMOL] stick transparency > >> > > > >> > > Thanks for the very quick answer, but it didn't succeed. > >> > > > >> > > Best, > >> > > Ariel > >> > > > >> > > On Fri, 2010-05-21 at 11:18 -0500, Matthew Franklin wrote: > >> > > Hi Ariel - > >> > > > >> > > Try "set stick_transparency=0.5, peg_1" > >> > > > >> > > - Matt > >> > > > >> > > > >> > > -- > >> > > Matthew Franklin , Ph.D. > >> > > Senior Scientist, ImClone Systems, > >> > > a wholly owned subsidiary of Eli Lilly & Company > >> > > 180 Varick Street, 6th floor > >> > > New York, NY 10014 > >> > > phone:(917)606-4116 fax:(212)645-2054 > >> > > > >> > > > -----Original Message----- > >> > > > From: Ariel Talavera [mailto:tal...@ci...] > >> > > > Sent: Friday, May 21, 2010 12:01 PM > >> > > > To: pym...@li... > >> > > > Subject: [PyMOL] stick transparency > >> > > > > >> > > > Hi there, > >> > > > > >> > > > I am trying to set stick transparency using the following command: > >> > > > set stick_transparency, 0.5, peg_1, but with no success. The problem > >> > > > is > >> > > > with the selection, because if I use instead, set > >> > > > stick_transparency, > >> > > > 0.5, then every thing represented with stick get 50% transparent. > >> > > > Can > >> > > > you help with this? I am using Pymol 1.2 under Ubuntu 10.04. > >> > > > > >> > > > Thanks a lot in advanced, > >> > > > > >> > > > Best regards, > >> > > > Ariel > >> > > > > >> > Confidentiality Note: > >> > This e-mail, and any attachment to it, contains privileged and > >> > confidential information intended only for the use of the individual(s) or > >> > entity named on the e-mail. If the reader of this e-mail is not the intended > >> > recipient, or the employee or agent responsible for delivering it to the > >> > intended recipient, you are hereby notified that reading it is strictly > >> > prohibited. If you have received this e-mail in error, please immediately > >> > return it to the sender and delete it from your system. > >> > > >> > Thank you. > >> > >> > >> > >> > >> ------------------------------------------------------------------------------ > >> > >> _______________________________________________ > >> PyMOL-users mailing list (PyM...@li...) > >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > >> Archives: http://www.mail-archive.com/pym...@li... > > > > > > > > -- > > Michael Zimmermann > > Ph.D. student in Bioinformatics and Computational Biology > > Department of Biochemistry, Biophysics and Molecular Biology > > Iowa State University > > > > ------------------------------------------------------------------------------ > > > > > > _______________________________________________ > > PyMOL-users mailing list (PyM...@li...) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pym...@li... > > > > > |