From: Yarrow M. <ama...@uc...> - 2012-05-17 19:11:19
|
Hello, This seems to be a simple problem but I can't figure out how to change the outline width of the ray_trace in ray_trace_mode, 1. I want to make it thicker so that when I ray_trace it doesn't look so small. -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 |
From: Thomas H. <sp...@us...> - 2012-05-17 19:36:50
|
Hi Yarrow, you are looking for the "ray_trace_gain" setting. http://pymolwiki.org/index.php/Ray_Trace_Gain Cheers, Thomas Yarrow Madrona wrote, On 05/17/12 21:11: > Hello, > > This seems to be a simple problem but I can't figure out how to change the > outline width of the ray_trace in ray_trace_mode, 1. I want to make it > thicker so that when I ray_trace it doesn't look so small. -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: Yarrow M. <ama...@uc...> - 2012-05-17 19:46:09
|
Hi Thomas, I have tried this. It works well for sticks but puts a lot of cross hatching patterns in the cartoon representation. I would like to ray_trace a transparent or white cartoon without the hatching (looks like shading drawn with ink) -Yarrow > Hi Yarrow, > > you are looking for the "ray_trace_gain" setting. > > http://pymolwiki.org/index.php/Ray_Trace_Gain > > Cheers, > Thomas > > Yarrow Madrona wrote, On 05/17/12 21:11: >> Hello, >> >> This seems to be a simple problem but I can't figure out how to change >> the >> outline width of the ray_trace in ray_trace_mode, 1. I want to make it >> thicker so that when I ray_trace it doesn't look so small. > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > > -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 |
From: Jason V. <jas...@sc...> - 2012-05-17 22:29:05
|
Yarrow, What about ray_trace_mode set to 2? Cheers, -- Jason On Thu, May 17, 2012 at 8:46 PM, Yarrow Madrona <ama...@uc...> wrote: > Hi Thomas, > > I have tried this. It works well for sticks but puts a lot of cross > hatching patterns in the cartoon representation. I would like to ray_trace > a transparent or white cartoon without the hatching (looks like shading > drawn with ink) > > -Yarrow > >> Hi Yarrow, >> >> you are looking for the "ray_trace_gain" setting. >> >> http://pymolwiki.org/index.php/Ray_Trace_Gain >> >> Cheers, >> Thomas >> >> Yarrow Madrona wrote, On 05/17/12 21:11: >>> Hello, >>> >>> This seems to be a simple problem but I can't figure out how to change >>> the >>> outline width of the ray_trace in ray_trace_mode, 1. I want to make it >>> thicker so that when I ray_trace it doesn't look so small. >> >> -- >> Thomas Holder >> MPI for Developmental Biology >> Spemannstr. 35 >> D-72076 Tübingen >> >> > > > -- > Yarrow Madrona > > Graduate Student > Molecular Biology and Biochemistry Dept. > University of California, Irvine > Natural Sciences I, Rm 2403 > Irvine, CA 92697 > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > 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 Schrödinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Yarrow M. <ama...@uc...> - 2012-05-17 22:38:41
|
Same thing happens. I get cross hatches with ray_trace_mode set at two and the gain anything above 0. Without the gain I don't get cross hatches but the outline is very faint for ray tracing at 3000x3000. > Yarrow, > > What about ray_trace_mode set to 2? > > Cheers, > > -- Jason > > On Thu, May 17, 2012 at 8:46 PM, Yarrow Madrona <ama...@uc...> wrote: >> Hi Thomas, >> >> I have tried this. It works well for sticks but puts a lot of cross >> hatching patterns in the cartoon representation. I would like to >> ray_trace >> a transparent or white cartoon without the hatching (looks like shading >> drawn with ink) >> >> -Yarrow >> >>> Hi Yarrow, >>> >>> you are looking for the "ray_trace_gain" setting. >>> >>> http://pymolwiki.org/index.php/Ray_Trace_Gain >>> >>> Cheers, >>> Thomas >>> >>> Yarrow Madrona wrote, On 05/17/12 21:11: >>>> Hello, >>>> >>>> This seems to be a simple problem but I can't figure out how to change >>>> the >>>> outline width of the ray_trace in ray_trace_mode, 1. I want to make it >>>> thicker so that when I ray_trace it doesn't look so small. >>> >>> -- >>> Thomas Holder >>> MPI for Developmental Biology >>> Spemannstr. 35 >>> D-72076 Tübingen >>> >>> >> >> >> -- >> Yarrow Madrona >> >> Graduate Student >> Molecular Biology and Biochemistry Dept. >> University of California, Irvine >> Natural Sciences I, Rm 2403 >> Irvine, CA 92697 >> >> >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. >> Discussions >> will include endpoint security, mobile security and the latest in >> malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> 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 > Schrödinger, LLC > > (e) Jas...@sc... > (o) +1 (603) 374-7120 > > -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 |
From: Jason V. <jas...@sc...> - 2012-05-18 09:00:49
|
Yarrow, You can also try setting "ray_trace_slope_factor" to something large like 5. Cheers, -- Jason On Thursday, May 17, 2012, Yarrow Madrona wrote: > Same thing happens. I get cross hatches with ray_trace_mode set at two and > the gain anything above 0. Without the gain I don't get cross hatches but > the outline is very faint for ray tracing at 3000x3000. > > > > Yarrow, > > > > What about ray_trace_mode set to 2? > > > > Cheers, > > > > -- Jason > > > > On Thu, May 17, 2012 at 8:46 PM, Yarrow Madrona <ama...@uc...<javascript:;>> > wrote: > >> Hi Thomas, > >> > >> I have tried this. It works well for sticks but puts a lot of cross > >> hatching patterns in the cartoon representation. I would like to > >> ray_trace > >> a transparent or white cartoon without the hatching (looks like shading > >> drawn with ink) > >> > >> -Yarrow > >> > >>> Hi Yarrow, > >>> > >>> you are looking for the "ray_trace_gain" setting. > >>> > >>> http://pymolwiki.org/index.php/Ray_Trace_Gain > >>> > >>> Cheers, > >>> Thomas > >>> > >>> Yarrow Madrona wrote, On 05/17/12 21:11: > >>>> Hello, > >>>> > >>>> This seems to be a simple problem but I can't figure out how to change > >>>> the > >>>> outline width of the ray_trace in ray_trace_mode, 1. I want to make it > >>>> thicker so that when I ray_trace it doesn't look so small. > >>> > >>> -- > >>> Thomas Holder > >>> MPI for Developmental Biology > >>> Spemannstr. 35 > >>> D-72076 Tübingen > >>> > >>> > >> > >> > >> -- > >> Yarrow Madrona > >> > >> Graduate Student > >> Molecular Biology and Biochemistry Dept. > >> University of California, Irvine > >> Natural Sciences I, Rm 2403 > >> Irvine, CA 92697 > >> > >> > >> > >> > >> > ------------------------------------------------------------------------------ > >> Live Security Virtual Conference > >> Exclusive live event will cover all the ways today's security and > >> threat landscape has changed and how IT managers can respond. > >> Discussions > >> will include endpoint security, mobile security and the latest in > >> malware > >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > >> _______________________________________________ > >> PyMOL-users mailing list (PyM...@li...<javascript:;> > ) > >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > >> Archives: http://www.mail-archive.com/pym...@li... > > > > > > > > -- > > Jason Vertrees, PhD > > PyMOL Product Manager > > Schrödinger, LLC > > > > (e) Jas...@sc... <javascript:;> > > (o) +1 (603) 374-7120 > > > > > > > -- > Yarrow Madrona > > Graduate Student > Molecular Biology and Biochemistry Dept. > University of California, Irvine > Natural Sciences I, Rm 2403 > Irvine, CA 92697 > > > > -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: H. A. S. <ad...@st...> - 2012-05-18 16:26:35
|
Hi all, If you open a c-alpha pdb (3ixz for example) in PyMol, you can show the c-alphas as spheres, or you can show a cartoon as a tube (ribbon like) but you can make a traditional flat faced PyMol cartoon. Yet when you open the same pdb in JMol it shows the traditional PyMol cartoon as the default. :P Why can't PyMol show the traditional cartoon like JMol does? and if JMol is faking the traditional cartoon, why can't we get PyMol to also fake the traditional cartoon? :) Thanks for any insight. Adam H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 |
From: Jason V. <jas...@sc...> - 2012-05-18 16:32:08
|
Hi Adam, set cartoon_trace_atoms set cartoon_throw, 1 If you want secondary structures, then you'll need to assign them using the 'alter' command. Cheers, -- Jason On Fri, May 18, 2012 at 5:13 PM, H. Adam Steinberg <ad...@st...> wrote: > Hi all, > > If you open a c-alpha pdb (3ixz for example) in PyMol, you can show the > c-alphas as spheres, or you can show a cartoon as a tube (ribbon like) but > you can make a traditional flat faced PyMol cartoon. Yet when you open the > same pdb in JMol it shows the traditional PyMol cartoon as the default. :P > > Why can't PyMol show the traditional cartoon like JMol does? and if JMol is > faking the traditional cartoon, why can't we get PyMol to also fake the > traditional cartoon? :) > > Thanks for any insight. > > Adam > > H. Adam Steinberg > 7904 Bowman Rd > Lodi, WI 53555 > 608/592-2366 > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > 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 Schrödinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |