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]
