Hi Bala, Recently, I added a new python script to the PyMOLWiki. Search for "modevectors" or "arrows" and you should find the method for drawing arrows with TONS of examples. I'm not sure if that's what you are looking for but you should be able to find your answer amidst the script.
Sean > From: pymol-users-requ...@lists.sourceforge.net > Subject: PyMOL-users Digest, Vol 35, Issue 6 > To: pymol-users@lists.sourceforge.net > Date: Tue, 14 Apr 2009 11:49:04 +0000 > > Send PyMOL-users mailing list submissions to > pymol-users@lists.sourceforge.net > > 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 > pymol-users-requ...@lists.sourceforge.net > > You can reach the person managing the list at > pymol-users-ow...@lists.sourceforge.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of PyMOL-users digest..." > > > Today's Topics: > > 1. Re: (Simple) unit cell construction (Warren DeLano) > 2. creating arrows (Bala subramanian) > 3. PyMOLWIki Survey (Jason Vertrees) > 4. advice for the novice movie maker (Thomas S. Leyh, Ph. D.) > 5. Alignment of states (Young-Tae Lee) > 6. Re: advice for the novice movie maker (Simon Kolstoe) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 9 Apr 2009 18:35:08 -0700 > From: "Warren DeLano" <war...@delsci.com> > Subject: Re: [PyMOL] (Simple) unit cell construction > To: "Roger Rowlett" <rrowl...@mail.colgate.edu>, > <pymol-users@lists.sourceforge.net> > Message-ID: > <896b75251ba19745a529b1b867893fa50eb...@planet.delsci.local> > Content-Type: text/plain; charset="us-ascii" > > Roger, > > Sorry Roger, this isn't possible at present, but it will be in the > future... > > Cheers, > Warren > ________________________________________ > From: Roger Rowlett [mailto:rrowl...@mail.colgate.edu] > Sent: Wednesday, April 08, 2009 8:18 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] (Simple) unit cell construction > > Is there a relatively simply way to get pymol to populate a unit cell > with exactly the correct number of copies of the asymmetric unit, i.e., > similar to the Uppsala software factory utility XPAND or the "Build > Crystallographic Symmetry" command in SPDBV? Ideally, it would be > helpful to perform the symmetry operations on the ASU, and then have the > ability to translate errant symmetry copies by +/- a,b, or c to get an > intelligent packing of the unit cell box. > > The "symexp" command is contact-distance controlled, and is better for > inspecting crystal packing than for creating nice "fluff" images of unit > cells. > > > Cheers, > > -- > ________________________________________ > Roger S. Rowlett > Professor > Colgate University Presidential Scholar > Department of Chemistry > Colgate University > 13 Oak Drive > Hamilton, NY 13346 > > tel: (315)-228-7245 > ofc: (315)-228-7395 > fax: (315)-228-7935 > email: rrowl...@mail.colgate.edu > > > > > ------------------------------ > > Message: 2 > Date: Fri, 10 Apr 2009 13:12:49 +0200 > From: Bala subramanian <bala.biophys...@gmail.com> > Subject: [PyMOL] creating arrows > To: pymol-users@lists.sourceforge.net > Message-ID: > <288df32a0904100412g5cc7dbb1mf1a8f7250974...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Friends, > > I have to draw arrows through the phosphate atoms of my DNA, Is there any > way that can make it in pymol. Kindly give me some suggestions if it is > possible. > > > Thanks, > Bala > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 3 > Date: Fri, 10 Apr 2009 17:16:07 -0400 > From: Jason Vertrees <j...@cs.dartmouth.edu> > Subject: [PyMOL] PyMOLWIki Survey > To: pymol-users@lists.sourceforge.net > Message-ID: <49dfb717.2020...@cs.dartmouth.edu> > Content-Type: text/plain; charset=ISO-8859-1 > > PyMOLers, > > The PyMOLWiki is thriving, we serve over 3800 pages a day, but I feel we > still need to make more improvements. So, I'd like to hear your > thoughts about the PyMOLWiki -- what you like about it, how we can > improve it, and where it's lacking. > > Please take the short survey. You will help make the wiki a better > place for us all. Follow the link to take the survey: > > http://www.surveymonkey.com/s.aspx?sm=NPHgdFVCWobsztKtjr5s5g_3d_3d > > You can also access the survey from the PyMOLWiki Main Page. > > > Cheers, > > -- Jason > > -- > > Jason Vertrees, PhD > > Dartmouth College : j...@cs.dartmouth.edu > Boston University : jas...@bu.edu > > PyMOLWiki : http://www.pymolwiki.org/ > > > > ------------------------------ > > Message: 4 > Date: Mon, 13 Apr 2009 17:30:49 -0400 > From: "Thomas S. Leyh, Ph. D." <l...@aecom.yu.edu> > Subject: [PyMOL] advice for the novice movie maker > To: <pymol-users@lists.sourceforge.net> > Message-ID: <49f407702f954648ba918a7ffb312...@stratosphere> > Content-Type: text/plain; charset="iso-8859-1" > > Hello everyone, > > I'm trying to assess the best way to begin making molecular movies with > Pymol. It seems eMovie is higly rated. I understand it is a Pymol plug-in, > however I gave this a run on my PC (Vista) only to discover, ultimately > through Warren, that that approach won't work, a Mac is required. (This came > a surprise since, in in their TRENDS article, the eMovie author's claim that > it runs under windows.) I have access to an iMac (duo 2 core, OS 10.5), and > I wonder whether this is the preferred path. Further, there is the issue of > which Pymol version to downloaded. Finally, is a Pymol build with rigimole > required - this is a special (expert) build that requires unix-like, > command-line fluency. > > Thanks a bunch, > > Tom Leyh > > -------------- next part -------------- > An HTML attachment was scrubbed... > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: Thomas S. Leyh.vcf > Type: text/x-vcard > Size: 418 bytes > Desc: not available > > ------------------------------ > > Message: 5 > Date: Mon, 13 Apr 2009 18:41:12 -0700 > From: Young-Tae Lee <yt...@scripps.edu> > Subject: [PyMOL] Alignment of states > To: pymol-users@lists.sourceforge.net > Message-ID: <27fc7003-1cd0-42a4-86d8-3b8d93a38...@scripps.edu> > Content-Type: text/plain; charset="us-ascii" > > Dear all, > > I am working on making a movie showing protein movements, for example > from A -> B -> C -> D. I obtained calculated intermediate states > between A-B, B-C, C-D from the morph server at Yale. Unfortunately, > the last coordinate from one morphing step and the first coordinate > from the next morphing step were not aligned, although I uploaded the > aligned coordinates of A, B, C, and D to the morph server. I would > like to know how to align the coordinates properly so that movie > would show continuous movement of molecule from A to D. > > Thanks, > Young-Tae > > Young-Tae Lee, Ph. D. > Research Associate > David Goodin lab > Dept. of Molecular Biology > The Scripps Research Institute > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 6 > Date: Tue, 14 Apr 2009 12:48:22 +0100 > From: Simon Kolstoe <s.kols...@ucl.ac.uk> > Subject: Re: [PyMOL] advice for the novice movie maker > To: "Thomas S. Leyh, Ph. D." <l...@aecom.yu.edu> > Cc: pymol-users@lists.sourceforge.net > Message-ID: <0710ffaa-e50d-4b0e-a17f-4ece65382...@ucl.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > Dear Tom, > > I use eMovie quite a bit on a mac (Macbook Pro 10.5.6) and think it is > definitely the easiest to use molecular movie software BUT... > > 1. It was designed for the free PyMol 0.99 and doesn't work so well > with newer versions. > 2. It is extremely buggy - crashes, flickering windows, components not > doing what they say they do etc.. > > So, although PyMol is my favorite picture making software (I used it > to make a front cover of Nature once), it is not so good when it comes > to making movies. PyMol's movies commands are not straight forward and > whilst although eMovie is a great concept to fix this problem, it > fails a bit in its application. It would be fantastic if Warren was > able to incorporate some of the eMovie code in future releases of PyMol! > > Simon > > > On 13 Apr 2009, at 22:30, Thomas S. Leyh, Ph. D. wrote: > > > Hello everyone, > > > > I'm trying to assess the best way to begin making molecular > > movies with Pymol. It seems eMovie is higly rated. I understand it > > is a Pymol plug-in, however I gave this a run on my PC (Vista) only > > to discover, ultimately through Warren, that that approach won't > > work, a Mac is required. (This came a surprise since, in in their > > TRENDS article, the eMovie author's claim that it runs under > > windows.) I have access to an iMac (duo 2 core, OS 10.5), and I > > wonder whether this is the preferred path. Further, there is the > > issue of which Pymol version to downloaded. Finally, is a Pymol > > build with rigimole required - this is a special (expert) build that > > requires unix-like, command-line fluency. > > > > Thanks a bunch, > > > > Tom Leyh > > <Thomas S. Leyh.vcf> > > ------------------------------------------------------------------------------ > > This SF.net email is sponsored by: > > High Quality Requirements in a Collaborative Environment. > > Download a free trial of Rational Requirements Composer Now! > > http://p.sf.net/sfu/www-ibm-com_______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by: > High Quality Requirements in a Collaborative Environment. > Download a free trial of Rational Requirements Composer Now! > http://p.sf.net/sfu/www-ibm-com > > ------------------------------ > > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > End of PyMOL-users Digest, Vol 35, Issue 6 > ****************************************** _________________________________________________________________ Create a cool, new character for your Windows Live™ Messenger. http://go.microsoft.com/?linkid=9656621
