Sing, When producing a movie there are a couple settings that could result in a non-absolute white background. I encountered this awhile back and it's documented on the PyMOLWiki, here: http://pymolwiki.org/index.php/Ray#Modes.
Also, be sure to check out the two settings, ray_trace_mode (http://pymolwiki.org/index.php/Ray#Modes) and ray_opaque_background (http://pymolwiki.org/index.php/Ray_opaque_background), which directly affect your issue. Hope this helps, -- Jason On Tue, Jan 12, 2010 at 10:49 AM, Kin Sing Stephen Lee <[email protected]> wrote: > Dear all, > > I have a question regarding the movie setting. I was trying to make > movie from pymol. However, even I've set the background as white, the > movie that I saved has a grey background. I am wondering if there is > any trick to fix this. > > Thank you very much > > Sing > > On Jan 11, 2010, at 11:37 PM, pymol-users- > [email protected] wrote: > >> Send PyMOL-users mailing list submissions to >> [email protected] >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> or, via email, send a message with subject or body 'help' to >> [email protected] >> >> You can reach the person managing the list at >> [email protected] >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of PyMOL-users digest..." >> >> >> Today's Topics: >> >> 1. acquisition of PyMOL by Schrodinger (Thomas Stout) >> 2. PyMOL & Schrodinger (Jason Vertrees) >> 3. Re: acquisition of PyMOL by Schrodinger (Jason Vertrees) >> 4. select atoms near electron density (Michael Zimmermann) >> 5. Re: select atoms near electron density (Jason Vertrees) >> 6. Re: select atoms near electron density (Michael Lerner) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 8 Jan 2010 14:11:07 -0800 >> From: "Thomas Stout" <[email protected]> >> Subject: [PyMOL] acquisition of PyMOL by Schrodinger >> To: <[email protected]> >> Message-ID: >> <[email protected]> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> All -- >> >> from the PyMOL web site: >> >> >> ANNOUNCEMENT >> >> >> On January 8, 2010 Schr?dinger <http://www.schrodinger.com/> >> reached an agreement with the estate of the late Dr. Warren L. >> DeLano <http://www.jmdelano.com/> to acquire PyMOL. Schr?dinger >> will take over continued development and maintenance, as well as >> support and sales of PyMOL, including all current subscriptions. >> Schr?dinger will also continue to actively support the open-source >> community of PyMOL. >> >> Prior to Warren's tragic and unexpected passing, he had been working >> closely with Schr?dinger to progressively integrate PyMOL with Schr? >> dinger's graphical interface, Maestro. With a great sense of >> humility, we will work hard to pick up as best we can where Warren >> left off and will strive to honor his memory by continuing in the >> spirit and tradition of PyMOL. >> >> >> >> >> >> >> >> This email (including any attachments) may contain material >> that is confidential and privileged and is for the sole use of >> the intended recipient. Any review, reliance or distribution by >> others or forwarding without express permission is strictly >> prohibited. If you are not the intended recipient, please >> contact the sender and delete all copies. >> Exelixis, Inc. reserves the right, to the extent and under >> circumstances permitted by applicable law, to retain, monitor >> and intercept e-mail messages to and from its systems. >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> Message: 2 >> Date: Fri, 8 Jan 2010 17:20:20 -0500 >> From: Jason Vertrees <[email protected]> >> Subject: [PyMOL] PyMOL & Schrodinger >> To: pymol-users <[email protected]> >> Message-ID: >> <[email protected]> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> PyMOLers, >> >> After the tragic loss of Warren, his wife Beth has been working >> nonstop to preserve PyMOL, his legacy. Today, after nearly two months >> of deliberation, she has sold PyMOL and its intellectual property to >> Schrodinger (http://www.schrodinger.com/), a scientific software >> company. PyMOL has a new home! >> >> Also, Schrodinger has just hired me to help drive PyMOL forward. I >> worked with Warren for about two years and was working very closely >> with him up until his passing. My goal is to see that PyMOL lives on, >> continues to grow, and helps smart people do smart things. >> >> How this affects us: >> * PyMOL will still be open-source, just like now >> * PyMOL will have professional support >> * PyMOL will have professional development >> * The mailing list and wiki will continue be the main sources of >> communication and community-based support >> * Warren had ~20 different domain names -- all those will now point >> to pymol.org. If your favorite link is lost, please let me know ASAP, >> but please give us some time to arrange this >> >> I'm very excited for PyMOL and look forward to working with you all. >> >> Regards, >> >> -- Jason >> >> -- >> Jason Vertrees, PhD >> [email protected] >> >> PyMOL Product Manager >> Schr?dinger LLC >> >> >> >> ------------------------------ >> >> Message: 3 >> Date: Fri, 8 Jan 2010 17:28:37 -0500 >> From: Jason Vertrees <[email protected]> >> Subject: Re: [PyMOL] acquisition of PyMOL by Schrodinger >> To: Thomas Stout <[email protected]> >> Cc: pymol-users <[email protected]> >> Message-ID: >> <[email protected]> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> Tom, >> >> Man you guys are quick. Here's the rest of Schrodinger's press >> release: >> >> Under the agreement, Schr?dinger will take over continued development >> and maintenance, as well as support and sales of PyMOL, including all >> current subscriptions. Schr?dinger will also continue to actively >> support the open-source community of PyMOL. "Warren really enjoyed >> working with the folks at Schr?dinger," said Ms. Beth Pehrson, the >> late Dr. DeLano's wife, "I know this is what Warren wanted for PyMOL's >> future." >> >> -- Jason >> >> -- >> Jason Vertrees, PhD >> [email protected] >> >> PyMOL Product Manager >> Schrodinger LLC >> >> >> >> >> On Fri, Jan 8, 2010 at 5:11 PM, Thomas Stout <[email protected]> >> wrote: >>> >>> All -- >>> >>> from the PyMOL web site: >>> >>> >>> ANNOUNCEMENT >>> >>> On January 8, 2010 Schr?dinger reached an agreement with the estate >>> of the >>> late Dr. Warren L. DeLano to acquire PyMOL. Schr?dinger will take >>> over >>> continued development and maintenance, as well as support and sales >>> of >>> PyMOL, including all current subscriptions. Schr?dinger will also >>> continue >>> to actively support the open-source community of PyMOL. >>> >>> Prior to Warren's tragic and unexpected passing, he had been >>> working closely >>> with Schr?dinger to progressively integrate PyMOL with Schr?dinger's >>> graphical interface, Maestro. With a great sense of humility, we >>> will work >>> hard to pick up as best we can where Warren left off and will >>> strive to >>> honor his memory by continuing in the spirit and tradition of PyMOL. >>> >>> >>> >>> >>> >>> >>> >>> This email (including any attachments) may contain material >>> that is confidential and privileged and is for the sole use of >>> the intended recipient. Any review, reliance or distribution by >>> others or forwarding without express permission is strictly >>> prohibited. If you are not the intended recipient, please >>> contact the sender and delete all copies. >>> Exelixis, Inc. reserves the right, to the extent and under >>> circumstances permitted by applicable law, to retain, monitor >>> and intercept e-mail messages to and from its systems. >>> >>> >>> ------------------------------------------------------------------------------ >>> This SF.Net email is sponsored by the Verizon Developer Community >>> Take advantage of Verizon's best-in-class app development support >>> A streamlined, 14 day to market process makes app distribution fast >>> and easy >>> Join now and get one step closer to millions of Verizon customers >>> http://p.sf.net/sfu/verizon-dev2dev >>> _______________________________________________ >>> PyMOL-users mailing list ([email protected]) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/[email protected] >>> >> >> >> >> ------------------------------ >> >> Message: 4 >> Date: Fri, 8 Jan 2010 18:05:07 -0600 >> From: Michael Zimmermann <[email protected]> >> Subject: [PyMOL] select atoms near electron density >> To: pymol-users <[email protected]> >> Message-ID: >> <[email protected]> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> Dear PyMol users, >> >> I wonder if anyone knows a way to select atoms that are near a region >> of electron density. >> >> Say I have a binding pocket in atomic detail, but the ligand binds >> transiently and non-specifically, so I just have an approximate >> electron density could for it. Is it possible to select atoms in an >> object that are near to these density levels? Alternatively, can you >> turn a map into an object that can be used in this way (fill it with >> dummy atoms)? >> >> Thank you, >> >> Michael Zimmermann >> >> >> >> ------------------------------ >> >> Message: 5 >> Date: Sat, 9 Jan 2010 04:20:34 -0500 >> From: Jason Vertrees <[email protected]> >> Subject: Re: [PyMOL] select atoms near electron density >> To: Michael Zimmermann <[email protected]> >> Cc: pymol-users <[email protected]> >> Message-ID: >> <[email protected]> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> Michael, >> >> I don't think this is possible with PyMOL. Distance measures are >> calculated from objects. >> >> -- Jason >> >> -- >> Jason Vertrees, PhD >> [email protected] >> >> PyMOL Product Manager >> Schrodinger, Inc. >> >> >> >> On Fri, Jan 8, 2010 at 7:05 PM, Michael Zimmermann <[email protected] >> > wrote: >>> Dear PyMol users, >>> >>> I wonder if anyone knows a way to select atoms that are near a region >>> of electron density. >>> >>> Say I have a binding pocket in atomic detail, but the ligand binds >>> transiently and non-specifically, so I just have an approximate >>> electron density could for it. ?Is it possible to select atoms in an >>> object that are near to these density levels? ?Alternatively, can you >>> turn a map into an object that can be used in this way (fill it with >>> dummy atoms)? >>> >>> Thank you, >>> >>> Michael Zimmermann >>> >>> ------------------------------------------------------------------------------ >>> This SF.Net email is sponsored by the Verizon Developer Community >>> Take advantage of Verizon's best-in-class app development support >>> A streamlined, 14 day to market process makes app distribution fast >>> and easy >>> Join now and get one step closer to millions of Verizon customers >>> http://p.sf.net/sfu/verizon-dev2dev >>> _______________________________________________ >>> PyMOL-users mailing list ([email protected]) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/[email protected] >>> >> >> >> >> ------------------------------ >> >> Message: 6 >> Date: Mon, 11 Jan 2010 23:37:40 -0500 >> From: Michael Lerner <[email protected]> >> Subject: Re: [PyMOL] select atoms near electron density >> To: Jason Vertrees <[email protected]> >> Cc: pymol-users <[email protected]> >> Message-ID: >> <[email protected]> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Yes, I believe this is the case. >> >> -Michael >> >> On Sat, Jan 9, 2010 at 4:20 AM, Jason Vertrees <[email protected] >> >wrote: >> >>> Michael, >>> >>> I don't think this is possible with PyMOL. Distance measures are >>> calculated from objects. >>> >>> -- Jason >>> >>> -- >>> Jason Vertrees, PhD >>> [email protected] >>> >>> PyMOL Product Manager >>> Schrodinger, Inc. >>> >>> >>> >>> On Fri, Jan 8, 2010 at 7:05 PM, Michael Zimmermann <[email protected] >>> > >>> wrote: >>>> Dear PyMol users, >>>> >>>> I wonder if anyone knows a way to select atoms that are near a >>>> region >>>> of electron density. >>>> >>>> Say I have a binding pocket in atomic detail, but the ligand binds >>>> transiently and non-specifically, so I just have an approximate >>>> electron density could for it. Is it possible to select atoms in an >>>> object that are near to these density levels? Alternatively, can >>>> you >>>> turn a map into an object that can be used in this way (fill it with >>>> dummy atoms)? >>>> >>>> Thank you, >>>> >>>> Michael Zimmermann >>>> >>>> >>> ------------------------------------------------------------------------------ >>>> This SF.Net email is sponsored by the Verizon Developer Community >>>> Take advantage of Verizon's best-in-class app development support >>>> A streamlined, 14 day to market process makes app distribution >>>> fast and >>> easy >>>> Join now and get one step closer to millions of Verizon customers >>>> http://p.sf.net/sfu/verizon-dev2dev >>>> _______________________________________________ >>>> PyMOL-users mailing list ([email protected]) >>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> Archives: http://www.mail-archive.com/[email protected] >>>> >>> >>> >>> ------------------------------------------------------------------------------ >>> This SF.Net email is sponsored by the Verizon Developer Community >>> Take advantage of Verizon's best-in-class app development support >>> A streamlined, 14 day to market process makes app distribution fast >>> and >>> easy >>> Join now and get one step closer to millions of Verizon customers >>> http://p.sf.net/sfu/verizon-dev2dev >>> _______________________________________________ >>> PyMOL-users mailing list ([email protected]) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/[email protected] >>> >> >> >> >> -- >> Michael Lerner, Ph.D. >> IRTA Postdoctoral Fellow >> Laboratory of Computational Biology NIH/NHLBI >> 5635 Fishers Lane, Room T909, MSC 9314 >> Rockville, MD 20852 (UPS/FedEx/Reality) >> Bethesda MD 20892-9314 (USPS) >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> ------------------------------------------------------------------------------ >> This SF.Net email is sponsored by the Verizon Developer Community >> Take advantage of Verizon's best-in-class app development support >> A streamlined, 14 day to market process makes app distribution fast >> and easy >> Join now and get one step closer to millions of Verizon customers >> http://p.sf.net/sfu/verizon-dev2dev >> >> ------------------------------ >> >> _______________________________________________ >> PyMOL-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> >> End of PyMOL-users Digest, Vol 44, Issue 4 >> ****************************************** > > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > PyMOL-users mailing list ([email protected]) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/[email protected] > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) [email protected] (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev _______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
