Menu
▾
▴
pymol-users — Collaborative support and tips for PyMOL users
You can subscribe to this list here.
| 2001 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
(13) |
Nov
(22) |
Dec
(35) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2002 |
Jan
(33) |
Feb
(46) |
Mar
(56) |
Apr
(29) |
May
(56) |
Jun
(30) |
Jul
(64) |
Aug
(54) |
Sep
(86) |
Oct
(106) |
Nov
(50) |
Dec
(67) |
| 2003 |
Jan
(78) |
Feb
(98) |
Mar
(51) |
Apr
(95) |
May
(53) |
Jun
(103) |
Jul
(93) |
Aug
(64) |
Sep
(87) |
Oct
(93) |
Nov
(78) |
Dec
(86) |
| 2004 |
Jan
(83) |
Feb
(90) |
Mar
(64) |
Apr
(112) |
May
(103) |
Jun
(57) |
Jul
(101) |
Aug
(84) |
Sep
(92) |
Oct
(96) |
Nov
(86) |
Dec
(32) |
| 2005 |
Jan
(88) |
Feb
(108) |
Mar
(111) |
Apr
(107) |
May
(120) |
Jun
(134) |
Jul
(143) |
Aug
(129) |
Sep
(75) |
Oct
(171) |
Nov
(125) |
Dec
(65) |
| 2006 |
Jan
(95) |
Feb
(105) |
Mar
(114) |
Apr
(124) |
May
(87) |
Jun
(66) |
Jul
(88) |
Aug
(65) |
Sep
(71) |
Oct
(92) |
Nov
(94) |
Dec
(60) |
| 2007 |
Jan
(81) |
Feb
(84) |
Mar
(82) |
Apr
(68) |
May
(58) |
Jun
(80) |
Jul
(30) |
Aug
(47) |
Sep
(68) |
Oct
(92) |
Nov
(59) |
Dec
(17) |
| 2008 |
Jan
(69) |
Feb
(81) |
Mar
(60) |
Apr
(34) |
May
(47) |
Jun
(65) |
Jul
(46) |
Aug
(49) |
Sep
(84) |
Oct
(43) |
Nov
(33) |
Dec
(30) |
| 2009 |
Jan
(62) |
Feb
(48) |
Mar
(123) |
Apr
(73) |
May
(72) |
Jun
(69) |
Jul
(78) |
Aug
(72) |
Sep
(99) |
Oct
(82) |
Nov
(70) |
Dec
(53) |
| 2010 |
Jan
(112) |
Feb
(95) |
Mar
(127) |
Apr
(110) |
May
(135) |
Jun
(91) |
Jul
(91) |
Aug
(79) |
Sep
(136) |
Oct
(63) |
Nov
(38) |
Dec
(64) |
| 2011 |
Jan
(59) |
Feb
(109) |
Mar
(191) |
Apr
(130) |
May
(94) |
Jun
(90) |
Jul
(89) |
Aug
(127) |
Sep
(135) |
Oct
(113) |
Nov
(136) |
Dec
(140) |
| 2012 |
Jan
(158) |
Feb
(131) |
Mar
(151) |
Apr
(88) |
May
(121) |
Jun
(85) |
Jul
(82) |
Aug
(56) |
Sep
(55) |
Oct
(125) |
Nov
(87) |
Dec
(65) |
| 2013 |
Jan
(81) |
Feb
(64) |
Mar
(90) |
Apr
(77) |
May
(80) |
Jun
(92) |
Jul
(92) |
Aug
(70) |
Sep
(69) |
Oct
(60) |
Nov
(99) |
Dec
(50) |
| 2014 |
Jan
(89) |
Feb
(66) |
Mar
(52) |
Apr
(70) |
May
(68) |
Jun
(44) |
Jul
(68) |
Aug
(81) |
Sep
(152) |
Oct
(106) |
Nov
(74) |
Dec
(57) |
| 2015 |
Jan
(93) |
Feb
(48) |
Mar
(60) |
Apr
(107) |
May
(82) |
Jun
(64) |
Jul
(74) |
Aug
(38) |
Sep
(49) |
Oct
(99) |
Nov
(105) |
Dec
(51) |
| 2016 |
Jan
(68) |
Feb
(87) |
Mar
(55) |
Apr
(90) |
May
(68) |
Jun
(25) |
Jul
(25) |
Aug
(41) |
Sep
(35) |
Oct
(55) |
Nov
(24) |
Dec
(26) |
| 2017 |
Jan
(59) |
Feb
(49) |
Mar
(24) |
Apr
(50) |
May
(45) |
Jun
(63) |
Jul
(36) |
Aug
(26) |
Sep
(22) |
Oct
(23) |
Nov
(26) |
Dec
(29) |
| 2018 |
Jan
(17) |
Feb
(21) |
Mar
(30) |
Apr
(34) |
May
(24) |
Jun
(47) |
Jul
(65) |
Aug
(30) |
Sep
(24) |
Oct
(52) |
Nov
(21) |
Dec
(17) |
| 2019 |
Jan
(9) |
Feb
(39) |
Mar
(32) |
Apr
(22) |
May
(30) |
Jun
(69) |
Jul
(40) |
Aug
(48) |
Sep
(17) |
Oct
(26) |
Nov
(30) |
Dec
(19) |
| 2020 |
Jan
(32) |
Feb
(26) |
Mar
(16) |
Apr
(34) |
May
(50) |
Jun
(87) |
Jul
(51) |
Aug
(23) |
Sep
(25) |
Oct
(48) |
Nov
(32) |
Dec
(6) |
| 2021 |
Jan
(12) |
Feb
(31) |
Mar
(15) |
Apr
(31) |
May
(13) |
Jun
(13) |
Jul
(24) |
Aug
(9) |
Sep
(11) |
Oct
(28) |
Nov
(26) |
Dec
(25) |
| 2022 |
Jan
(47) |
Feb
(22) |
Mar
(22) |
Apr
(12) |
May
(4) |
Jun
(26) |
Jul
(17) |
Aug
(2) |
Sep
(13) |
Oct
(6) |
Nov
(13) |
Dec
(4) |
| 2023 |
Jan
(7) |
Feb
(6) |
Mar
(13) |
Apr
(2) |
May
(25) |
Jun
(13) |
Jul
(12) |
Aug
(10) |
Sep
(5) |
Oct
(13) |
Nov
(19) |
Dec
(7) |
| 2024 |
Jan
(3) |
Feb
(12) |
Mar
(1) |
Apr
(13) |
May
(11) |
Jun
|
Jul
(20) |
Aug
(4) |
Sep
(4) |
Oct
(5) |
Nov
(4) |
Dec
(6) |
| 2025 |
Jan
(16) |
Feb
(8) |
Mar
(10) |
Apr
(6) |
May
(13) |
Jun
(7) |
Jul
(4) |
Aug
(1) |
Sep
(2) |
Oct
(1) |
Nov
|
Dec
|
|
From: Tsjerk W. <ts...@gm...> - 2005-07-26 10:56:03
|
If you just type=20 povray you'll get all command line options. Tsjerk On 7/25/05, andrea spitaleri <and...@gm...> wrote: > try povray +A0.3 file.pov > zero ---------^ >=20 > regards >=20 >=20 >=20 > Cameron Mura wrote: >=20 > > hi, > > Is there anything special I need to do/set to achieve antialiased > > images via pymol + POV-ray? > > To be more explicit, i'm using robert campbell's make_pov.py to have > > pymol dump the scene into a povray input file, and then ray-tracing w/ > > a minimalistic command-line (e.g., "povray +Iwhatever_pov.inp +W640 > > +H480")... all of this is w/ "antialias" set 'on' in pymol.. i'm > > unfamiliar w/ povray, so any tips or advice would be greatly appreciate= d. > > thanks, > > cameron > > > > > > ------------------------------------------------------- > > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > > from IBM. Find simple to follow Roadmaps, straightforward articles, > > informative Webcasts and more! Get everything you need to get up to > > speed, fast. http://ads.osdn.com/?ad_id=3D7477&alloc_id=3D16492&op=3Dcl= ick > > _______________________________________________ > > PyMOL-users mailing list > > PyM...@li... > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > >=20 >=20 >=20 > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_id=3D7477&alloc_id=3D16492&op=3Dclic= k > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
|
From: S. F. Y. <SY...@gn...> - 2005-07-25 23:41:36
|
Hi, I was trying to use the MovF and RotF functions in the 3-Buttion Editing mode using version 0.98. The molecule is deformed with one single atom being totally out of the place during the movement. Does anyone have the same problem? Thanks a lot, Frank |
|
From: Warren D. <wa...@de...> - 2005-07-25 18:41:55
|
PyMOL Users: One of the IT trade journals is doing a little piece on open-source business that will probably cover PyMOL/DeLano Scientific and they would like to talk with a some PyMOL users -- ideally paying subscribers from biotech, pharma, and academia. If you would like to participate, then please email me *today* (ASAP) if you feel comfortable going "on the record" regarding PyMOL, open-source, and drug-discovery, and would be willing to chat with a reporter over the phone. I'll need a phone number for him to reach you at over the next day or two. Thanks, Warren -- Warren L. DeLano, Ph.D. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 |
|
From: andrea s. <and...@gm...> - 2005-07-25 14:37:56
|
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> <html> <head> <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type"> <title></title> </head> <body bgcolor="#ffffff" text="#000000"> Hi <br> thanks to all for the links.<br> and something a bit closer to pymol? more focused on biological files...<br> <br> thanks again<br> <br> Regards<br> andrea<br> Jerome PANSANEL wrote: <blockquote cite="mid...@pa..." type="cite"> <pre wrap="">Hello, You can find modules inside some software package, like: PyQuante (<a class="moz-txt-link-freetext" href="http://pyquante.sourceforge.net/">http://pyquante.sourceforge.net/</a>) FROWNS (<a class="moz-txt-link-freetext" href="http://frowns.sourceforge.net/">http://frowns.sourceforge.net/</a>) MMTK (<a class="moz-txt-link-freetext" href="http://starship.python.net/crew/hinsen/MMTK/">http://starship.python.net/crew/hinsen/MMTK/</a>) All these software are free software. Regards, Jerome PANSANEL -- Jerome PANSANEL <a class="moz-txt-link-freetext" href="http://www.alchem.org">http://www.alchem.org</a> Le Lundi 25 Juillet 2005 15:42, andrea spitaleri a écrit : </pre> <blockquote type="cite"> <pre wrap="">Hi all, I am using pymol also for python scripting and perlmol for perl scripting. They are both very nice. I am just wondering if there are some other useful python modules around for chemistry. Sorry for the OT. Regards, andrea ------------------------------------------------------- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. <a class="moz-txt-link-freetext" href="http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click">http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click</a> _______________________________________________ PyMOL-users mailing list <a class="moz-txt-link-abbreviated" href="mailto:PyM...@li...">PyM...@li...</a> <a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/pymol-users">https://lists.sourceforge.net/lists/listinfo/pymol-users</a> </pre> </blockquote> <pre wrap=""><!----> ------------------------------------------------------- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. <a class="moz-txt-link-freetext" href="http://ads.osdn.com/?ad_idt77&alloc_id492&op=click">http://ads.osdn.com/?ad_idt77&alloc_id492&op=click</a> _______________________________________________ PyMOL-users mailing list <a class="moz-txt-link-abbreviated" href="mailto:PyM...@li...">PyM...@li...</a> <a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/pymol-users">https://lists.sourceforge.net/lists/listinfo/pymol-users</a> </pre> </blockquote> <br> </body> </html> |
|
From: Jerome P. <j.p...@pa...> - 2005-07-25 14:15:44
|
Hello, You can find modules inside some software package, like: PyQuante (http://pyquante.sourceforge.net/) =46ROWNS (http://frowns.sourceforge.net/) MMTK (http://starship.python.net/crew/hinsen/MMTK/) All these software are free software. Regards, Jerome PANSANEL =2D- Jerome PANSANEL http://www.alchem.org Le Lundi 25 Juillet 2005 15:42, andrea spitaleri a =E9crit=A0: > Hi all, > I am using pymol also for python scripting and perlmol for perl > scripting. They are both very nice. > I am just wondering if there are some other useful python modules > around for chemistry. > Sorry for the OT. > > Regards, > > andrea > > > > > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_id=3D7477&alloc_id=3D16492&op=3Dclick > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
|
From: andrea s. <and...@gm...> - 2005-07-25 13:40:33
|
Hi all, I am using pymol also for python scripting and perlmol for perl scripting. They are both very nice. I am just wondering if there are some other useful python modules around for chemistry. Sorry for the OT. Regards, andrea |
|
From: <li...@ul...> - 2005-07-25 11:14:33
|
On Sunday 24 July 2005 05:42, yi zhang wrote:
> cmd.symexp('sym', 'obj', 'obj',10 )
>
> of course, I can manually save each symmetry-related
> molecule to *.pdb file by clicking save molecule
> button, but how can I write a script to save all of
> them or part of them? the symmetry-related objects
> are not appendable.
I have used something like this in the past:
#--------------
# get symmetry mates
objs = [ n for n in cmd.get_names() if n[0:3]=="sym" ]
for obj in objs:
if cmd.get_type(obj)!="object:molecule":
print "Something's wrong!"
else:
cmd.save(obj+".pdb",obj)
#--------------
Hope this helps,
--
Lieven Buts
Ultrastructure Laboratory
Vrije Universiteit Brussel
|
|
From: andrea s. <and...@gm...> - 2005-07-25 08:21:54
|
try povray +A0.3 file.pov zero ---------^ regards Cameron Mura wrote: > hi, > Is there anything special I need to do/set to achieve antialiased > images via pymol + POV-ray? > To be more explicit, i'm using robert campbell's make_pov.py to have > pymol dump the scene into a povray input file, and then ray-tracing w/ > a minimalistic command-line (e.g., "povray +Iwhatever_pov.inp +W640 > +H480")... all of this is w/ "antialias" set 'on' in pymol.. i'm > unfamiliar w/ povray, so any tips or advice would be greatly appreciated. > thanks, > cameron > > > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
|
From: Cameron M. <cm...@uc...> - 2005-07-25 06:30:19
|
hi, Is there anything special I need to do/set to achieve antialiased images via pymol + POV-ray? To be more explicit, i'm using robert campbell's make_pov.py to have pymol dump the scene into a povray input file, and then ray-tracing w/ a minimalistic command-line (e.g., "povray +Iwhatever_pov.inp +W640 +H480")... all of this is w/ "antialias" set 'on' in pymol.. i'm unfamiliar w/ povray, so any tips or advice would be greatly appreciated. thanks, cameron |
|
From: <ag...@po...> - 2005-07-24 19:15:06
|
Hello! I'm again writing about the same problem. Is there any way to get the frames of the animated zoom, center, or orient? I tried through python and it didn't work, then I tried to do it directly from pymol with the following commands: mclear mset 1 x100 mdo 1:load 1aoi.pdb mdo 10: hide everything, all mdo 20: show cartoon, 1aoi mdo 30: move x, -50; move y, -50 mdo 50: orient visible, animate=3 mpng frames/frame and it's still not working. I get the frames up to 49th and then it says "MoviePNG-Error: Missing rendered image". Is there anyone who can help me this time? I would really appreciate, thanks! Aga |
|
From: yi z. <zha...@ya...> - 2005-07-24 03:43:24
|
Hi, everyone,
I used symexp command in pymol to generate
symmetry-related molecule, something like:
cmd.symexp('sym', 'obj', 'obj',10 )
of course, I can manually save each symmetry-related
molecule to *.pdb file by clicking save molecule
button, but how can I write a script to save all of
them or part of them? the symmetry-related objects
are not appendable.
thanks!
yi
__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
http://mail.yahoo.com
|
|
From: Warren D. <wa...@de...> - 2005-07-22 17:20:00
|
Laura Reissue the mset commmand. mclear actually clears the image cache...not the commmand list -- how confusing! Cheers, Warren -- Warren L. DeLano, Ph.D. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 =20 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf Of=20 > Laura Grell > Sent: Friday, July 22, 2005 7:49 AM > To: pym...@li... > Subject: [PyMOL] Clearing Frames >=20 > Hi all!! >=20 > I was wondering if there was a way to clear out all the=20 > settings for frames of a movie without having to=20 > reinitializie the window. I've tried using mclear but that=20 > doesn't seem to do anything. Thanks!! >=20 > Laura Grell >=20 > _________________________________________________________________ > Don't just search. Find. Check out the new MSN Search!=20 > http://search.msn.click-url.com/go/onm00200636ave/direct/01/ >=20 >=20 >=20 > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration=20 > Strategies from IBM. Find simple to follow Roadmaps,=20 > straightforward articles, informative Webcasts and more! Get=20 > everything you need to get up to speed, fast.=20 > http://ads.osdn.com/?ad_id=3D7477&alloc_id=3D16492&op=3Dclick > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 >=20 >=20 |
|
From: Laura G. <pee...@ho...> - 2005-07-22 14:41:31
|
Hi all!! I was wondering if there was a way to clear out all the settings for frames of a movie without having to reinitializie the window. I've tried using mclear but that doesn't seem to do anything. Thanks!! Laura Grell _________________________________________________________________ Dont just search. Find. Check out the new MSN Search! http://search.msn.click-url.com/go/onm00200636ave/direct/01/ |
|
From: Tsjerk W. <ts...@gm...> - 2005-07-22 08:17:06
|
Hi Doug, Well, you could write a function average(Object1, Object2, ...) which would return an object containing the average structure and the fluctuations from this average in the b-factor field.., I think :) Might be a useful feature, so if I'll find some time... (but feel free to try to beat my to it ;)) Cheers, Tsjerk On 7/21/05, Douglas Kojetin <djk...@un...> wrote: > Many thanks for the suggestion. I worked something up using CNS/ > python scripts -- but if anyone comes up with an all PyMOL > alternative, please share with the list! >=20 > Doug >=20 > On Jul 20, 2005, at 1:18 PM, Cartailler, Jean-Philippe wrote: >=20 >=20 >=20 > > > > One way to do this would be to calculate RMSD between your models > > (using > > whatever package) and replace the B-factor column with those values > > (make sure you respect the PDB format (B-factors are in columns 61 > > - 66, > > with first column as "1" - see > > http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_62.html for > > details), load that into pymol, and voila. If the effect isn't > > enough, > > you could always multiply your RMS values by some value (eg. 10). > > Good > > luck! > > > > JP Cartailler > > > > > > -----Original Message----- > > From: pym...@li... > > [mailto:pym...@li...] On Behalf Of Douglas > > Kojetin > > Sent: Tuesday, July 19, 2005 3:48 PM > > To: pymol > > Subject: [PyMOL] putty/sausage NMR figure > > > > Hello All- > > > > From what I've read, the 'cartoon putty' command uses the PDB B- > > factor > > value to determine the appearance of the sausage diagram. How can > > I use > > the 'cartoon putty' command with NMR structures in a way that > > represents > > the structure ensemble, similar to that as the MOLMOL sausage diagram? > > > > Thanks, > > Doug > > > > > > ------------------------------------------------------- > > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > > from IBM. Find simple to follow Roadmaps, straightforward articles, > > informative Webcasts and more! Get everything you need to get up to > > speed, fast. http://ads.osdn.com/?ad_id=3D7477&alloc_id=3D16492&op=3Dcl= ick > > _______________________________________________ > > PyMOL-users mailing list > > PyM...@li... > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > ------------------------------------------------------- > > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > > from IBM. Find simple to follow Roadmaps, straightforward articles, > > informative Webcasts and more! Get everything you need to get up to > > speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=3Dclick > > _______________________________________________ > > PyMOL-users mailing list > > PyM...@li... > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > >=20 >=20 >=20 >=20 >=20 > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&opclick > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
|
From: Sarina <sa...@ac...> - 2005-07-21 21:44:36
|
For the purposes of illustrating how a protein domain moves when ligands bind, it would be great if there were a way to create a PyMOL surface that is both simple and smooth. I tried decreasing the surface quality to -3, which makes a simplified surface, but it has pointed corners. Has anyone done this? Many Thanks, Sarina Bromberg |
|
From: Andreas F. <an...@bi...> - 2005-07-21 19:32:09
|
Warren, what's up with this? Pymol and one-button mouse?? What's next?=20
Pymol on abacus?
Wouldn't it rather be time to remind Apple to provide ergonomic equipment=
?
Andreas
ps. I would be interested in hearing if anyone has found an ingenious=20
use for the dozens of shiny slick white shrink-wrapped one-button mice=20
that accumulate in departments that use Mac.
--=20
>>> Andreas F=F6rster <<<
8 rue Doudart de Lagr=E9e, 38000 Grenoble
++33.(0)438.866201 and ++33.(0)456.452000
b5foan at skype and yahoo messenger
docandreas.blogspot.com
|
|
From: Xavier D. <Xav...@st...> - 2005-07-21 19:26:08
|
Thanks everybody. Framed (<http://www.likelysoft.com/framed/>) works fine. x -- Xavier Deupi, Ph.D. Department of Molecular and Cellular Physiology Beckman Center for Molecular and Genetic Medicine (B161) 279 Campus Drive, Stanford University School of Medicine Stanford, CA 94305 (USA) E-mail: Xav...@st... Phone: +1 (650) 725-6497 Fax : +1 (650) 725-8021 |
|
From: Douglas K. <djk...@un...> - 2005-07-21 14:53:41
|
Many thanks for the suggestion. I worked something up using CNS/=20 python scripts -- but if anyone comes up with an all PyMOL =20 alternative, please share with the list! Doug On Jul 20, 2005, at 1:18 PM, Cartailler, Jean-Philippe wrote: > > One way to do this would be to calculate RMSD between your models =20 > (using > whatever package) and replace the B-factor column with those values > (make sure you respect the PDB format (B-factors are in columns 61 =20 > - 66, > with first column as "1" - see > http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_62.html for > details), load that into pymol, and voila. If the effect isn't =20 > enough, > you could always multiply your RMS values by some value (eg. 10). =20 > Good > luck! > > JP Cartailler > > > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf Of Douglas > Kojetin > Sent: Tuesday, July 19, 2005 3:48 PM > To: pymol > Subject: [PyMOL] putty/sausage NMR figure > > Hello All- > > =46rom what I've read, the 'cartoon putty' command uses the PDB B- =20= > factor > value to determine the appearance of the sausage diagram. How can =20 > I use > the 'cartoon putty' command with NMR structures in a way that =20 > represents > the structure ensemble, similar to that as the MOLMOL sausage diagram? > > Thanks, > Doug > > > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_id=3D7477&alloc_id=3D16492&op=3Dcli= ck > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=3Dclick > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > |
|
From: Reinhold P. <rp...@ha...> - 2005-07-21 07:58:05
|
Sorry, I was not aware that this required QT Pro... Anyway, if you =20 want free, there's that too: <http://www.likelysoft.com/framed/> =20 Works very well. HTH, -Reinhold On Jul 20, 2005, at 14:46, Gilleain Torrance wrote: > Of course, this assumes you have purchased a QuickTime Pro (tm) key =20= > for =A320 > ($25)... > > gilleain > > > On 20/7/05 23:44, "Reinhold Penner" <rp...@ha...> wrote: > > >> Xavier, >> >> since you're on a Mac, it's easy enough to just fire up QuickTime >> Player and select File->Open Image Sequence. This will prompt you to >> select the first png file in a folder and load all other pngs with >> the same base name in that folder. Then simply export these frames as >> a movie with any of the available quicktime codecs at a frame rate >> you like. It's totally simple. >> >> HTH, -Reinhold >> >> On Jul 20, 2005, at 12:14 PM, Xavier Deupi wrote: >> >> >>> Hi, >>> >>> I've produced a series of png files using PyMOL, and I want to >>> compress them to produce a movie. I was considering to use mencoder >>> (following the suggestions in the PyMOL wiki), but I'm having some >>> problems in running it under MacOSX >>> >>> Briefly, mencoder complains because it can't find the mpng codec. I >>> downloaded a codecs.conf file and copied to ~/.mplayer, but it >>> doesn't help. >>> >>> Are any of you using mencoder in a mac? If so, I'd like to get some >>> advice. >>> >>> Thanks in advance, >>> >>> Xavier >>> >>> --=20 >>> Xavier Deupi, Ph.D. >>> Department of Molecular and Cellular Physiology >>> Beckman Center for Molecular and Genetic Medicine (B161) >>> 279 Campus Drive, Stanford University School of Medicine >>> Stanford, CA 94305 (USA) >>> >>> E-mail: Xav...@st... >>> Phone: +1 (650) 725-6497 >>> Fax : +1 (650) 725-8021 >>> >>> >>> >>> ------------------------------------------------------- >>> SF.Net email is sponsored by: Discover Easy Linux Migration =20 >>> Strategies >>> from IBM. Find simple to follow Roadmaps, straightforward articles, >>> informative Webcasts and more! Get everything you need to get up to >>> speed, fast. http://ads.osdn.com/?ad_id=3D7477&alloc_id=3D16492&op=3Dc= lick >>> _______________________________________________ >>> PyMOL-users mailing list >>> PyM...@li... >>> https://lists.sourceforge.net/lists/listinfo/pymol-users >>> >>> >> >> >> >> ------------------------------------------------------- >> SF.Net email is sponsored by: Discover Easy Linux Migration =20 >> Strategies >> from IBM. Find simple to follow Roadmaps, straightforward articles, >> informative Webcasts and more! Get everything you need to get up to >> speed, fast. http://ads.osdn.com/?ad_id=3D7477&alloc_id=3D16492&op=3Dcl= ick >> _______________________________________________ >> PyMOL-users mailing list >> PyM...@li... >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> > > > > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=CCk > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
|
From: Gilleain T. <gil...@ho...> - 2005-07-21 00:47:43
|
Of course, this assumes you have purchased a QuickTime Pro (tm) key for =A320 ($25)... gilleain On 20/7/05 23:44, "Reinhold Penner" <rp...@ha...> wrote: > Xavier, >=20 > since you're on a Mac, it's easy enough to just fire up QuickTime > Player and select File->Open Image Sequence. This will prompt you to > select the first png file in a folder and load all other pngs with > the same base name in that folder. Then simply export these frames as > a movie with any of the available quicktime codecs at a frame rate > you like. It's totally simple. >=20 > HTH, -Reinhold >=20 > On Jul 20, 2005, at 12:14 PM, Xavier Deupi wrote: >=20 >> Hi, >>=20 >> I've produced a series of png files using PyMOL, and I want to >> compress them to produce a movie. I was considering to use mencoder >> (following the suggestions in the PyMOL wiki), but I'm having some >> problems in running it under MacOSX >>=20 >> Briefly, mencoder complains because it can't find the mpng codec. I >> downloaded a codecs.conf file and copied to ~/.mplayer, but it >> doesn't help. >>=20 >> Are any of you using mencoder in a mac? If so, I'd like to get some >> advice. >>=20 >> Thanks in advance, >>=20 >> Xavier >>=20 >> --=20 >> Xavier Deupi, Ph.D. >> Department of Molecular and Cellular Physiology >> Beckman Center for Molecular and Genetic Medicine (B161) >> 279 Campus Drive, Stanford University School of Medicine >> Stanford, CA 94305 (USA) >>=20 >> E-mail: Xav...@st... >> Phone: +1 (650) 725-6497 >> Fax : +1 (650) 725-8021 >>=20 >>=20 >>=20 >> ------------------------------------------------------- >> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies >> from IBM. Find simple to follow Roadmaps, straightforward articles, >> informative Webcasts and more! Get everything you need to get up to >> speed, fast. http://ads.osdn.com/?ad_id=3D7477&alloc_id=3D16492&op=3Dclick >> _______________________________________________ >> PyMOL-users mailing list >> PyM...@li... >> https://lists.sourceforge.net/lists/listinfo/pymol-users >>=20 >=20 >=20 >=20 > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_id=3D7477&alloc_id=3D16492&op=3Dclick > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 |
|
From: Reinhold P. <rp...@ha...> - 2005-07-20 22:45:06
|
Xavier, since you're on a Mac, it's easy enough to just fire up QuickTime Player and select File->Open Image Sequence. This will prompt you to select the first png file in a folder and load all other pngs with the same base name in that folder. Then simply export these frames as a movie with any of the available quicktime codecs at a frame rate you like. It's totally simple. HTH, -Reinhold On Jul 20, 2005, at 12:14 PM, Xavier Deupi wrote: > Hi, > > I've produced a series of png files using PyMOL, and I want to > compress them to produce a movie. I was considering to use mencoder > (following the suggestions in the PyMOL wiki), but I'm having some > problems in running it under MacOSX > > Briefly, mencoder complains because it can't find the mpng codec. I > downloaded a codecs.conf file and copied to ~/.mplayer, but it > doesn't help. > > Are any of you using mencoder in a mac? If so, I'd like to get some > advice. > > Thanks in advance, > > Xavier > > -- > Xavier Deupi, Ph.D. > Department of Molecular and Cellular Physiology > Beckman Center for Molecular and Genetic Medicine (B161) > 279 Campus Drive, Stanford University School of Medicine > Stanford, CA 94305 (USA) > > E-mail: Xav...@st... > Phone: +1 (650) 725-6497 > Fax : +1 (650) 725-8021 > > > > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
|
From: Xavier D. <Xav...@st...> - 2005-07-20 22:14:40
|
Hi, I've produced a series of png files using PyMOL, and I want to compress them to produce a movie. I was considering to use mencoder (following the suggestions in the PyMOL wiki), but I'm having some problems in running it under MacOSX Briefly, mencoder complains because it can't find the mpng codec. I downloaded a codecs.conf file and copied to ~/.mplayer, but it doesn't help. Are any of you using mencoder in a mac? If so, I'd like to get some advice. Thanks in advance, Xavier -- Xavier Deupi, Ph.D. Department of Molecular and Cellular Physiology Beckman Center for Molecular and Genetic Medicine (B161) 279 Campus Drive, Stanford University School of Medicine Stanford, CA 94305 (USA) E-mail: Xav...@st... Phone: +1 (650) 725-6497 Fax : +1 (650) 725-8021 |
|
From: Joel T. <joe...@ot...> - 2005-07-20 21:03:34
|
Check out the post on "High end graphics". This will solve the problem.=20 Basically you can ray-trace your molecule at a resolution bigger tahn=20 teh screen size and then cut it down afterwards effectively generating a = high resolution graphic from a 72 dpi starting point Cheers J Kolli, Madhavi wrote: > Hi, > > I=92ve just started using PyMol for making some figures. I=92m very hap= py=20 > that it is so easy to use. However the resolution of my pictures is=20 > very bad even after rendering them. When I print them they are very=20 > pixellated. I=92m sure there is something I=92m not doing right. Any he= lp,=20 > suggestions will be appreciated. > > Thanks. > > Regards, > > Madhavi Kolli > > Graduate Student > > UMass Medical School Worcester > --=20 Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand =20 Pukenga Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti Aotearoa Ph / Waea +64 3 4797293=20 Fax / Waeawhakaahua +64 3 4797034 |
|
From: Kolli, M. <Mad...@um...> - 2005-07-20 17:40:54
|
Hi, I've just started using PyMol for making some figures. I'm very happy that it is so easy to use. However the resolution of my pictures is very bad even after rendering them. When I print them they are very pixellated. I'm sure there is something I'm not doing right. Any help, suggestions will be appreciated. Thanks. Regards, Madhavi Kolli Graduate Student UMass Medical School Worcester |
|
From: Warren D. <wa...@de...> - 2005-07-20 17:34:00
|
Mac Users: We strongly recommend (require?) use of a three-button mouse with MacPyMOL and PyMOLX11Hybrid. However, it is possible to use MacPyMOL in a limited way on Macs that have a single button mouse thanks to some built-in mouse remapping in the Mac OS X GLUT implementation. Her is how that works... If the Mac is hooked up to a 1-button mouse (only) when MacPyMOL or HybridX11PyMOL are launched, then Mac OS X itself will furnish translations as follows: Rotate: Click & Drag XY-Translate: Option-Click & Dreg Zoom: Control-Click & Drag Select: Click & Release Box-Select: Shift-Click & Drag Box-Deselect: Shift-Option-Click & Drag Clipping: Control-Shift-Click & Drag with... - near plane controlled by vertical motion - far plane controlled by horizontal motion Note that not all mouse actions are possible with a one-button mouse. For example, I don't think molecular editing is possible with a one-button mouse. Cheers, Warren -- Warren L. DeLano, Ph.D. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 |
115 messages has been excluded from this view by a project administrator.
