RE: [PyMOL] homologous alignments?
Camille, If I understand your question, you're looking for the setting which creates a discrete color transition at the edges of helices and strands, instead of blending. It is: set cartoon_discrete_colors, on For example color grey, name ca color yellow, ss s and name ca color red, ss h and name ca set cartoon_discrete_colors, on Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of cami...@mrc-lmb.cam.ac.uk > Sent: Monday, January 19, 2004 7:37 AM > To: Warren L. DeLano > Cc: 'Michael Bovee'; pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] homologous alignments? > > Hello, >I am unable to read the archive at the moment so can anyone tell > me the command that allows colouring of the edge of helices and strands > (usually grey). I think this was posted recently but I don't have it in > any of my saved scripts. > > Many thanks, > Camille > > Dr Camille Shammas > Medical Research Council Laboratory of Molecular Biology Hills Road, > Cambridge CB2 2QH, UK. > Tel: +44 (0)1223 402407 > Mobile: 07812035842 > E-mail: cami...@mrc-lmb.cam.ac.uk > > > > --- > The SF.Net email is sponsored by EclipseCon 2004 > Premiere Conference on Open Tools Development and Integration See the > breadth of Eclipse activity. February 3-5 in Anaheim, CA. > http://www.eclipsecon.org/osdn > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] homologous alignments?
Hello, I am unable to read the archive at the moment so can anyone tell me the command that allows colouring of the edge of helices and strands (usually grey). I think this was posted recently but I don't have it in any of my saved scripts. Many thanks, Camille Dr Camille Shammas Medical Research Council Laboratory of Molecular Biology Hills Road, Cambridge CB2 2QH, UK. Tel: +44 (0)1223 402407 Mobile: 07812035842 E-mail: cami...@mrc-lmb.cam.ac.uk
RE: [PyMOL] homologous alignments?
Michael, Welcome to PyMOL! I don't think PyMOL is a replacement for SPDV -- the feature sets are distinct, and you should be able to use both together. Yes, I think "align" is what you want. After... load x.pdb load y.pdb This would do an all-matched-atoms alignment: align x, y And this would do a CA-only alignment: align xca, yca To see which atoms are aligned, add and object name: align xca, yca, object=alignment Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Michael Bovee Sent: Friday, November 07, 2003 3:31 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] homologous alignments? Hi there, I'm switching to pymol from swiss pdb viewer because I simply needed better quality final images, but one of the coolest features of spdbv was the 'magic fit' where a single mouse click would superpose overall alignment of, say, the same protein from two different bacterial organisms (obviously high homology situation) opened in two different 'layers'. In pymol, it looks like the 'align' command is what I want (don't know if pymol uses the layers analogy), but I'm having difficulty understanding if I am to use parentheses and brackets as shown in the refman.pdf, and the use of this punctuation style doesnt seem to be defined in the pdf. USAGE align (source), (target) [,cutoff [,cycles [,gap [,extend \ [,skip [,object [,matrix [, quiet (This style of outlining command formats is probably old hat to programmers, but that's not me.) So, is this the right command for superposition alignments in pymol, after loading pdb files x and y, for instance? Sorry for such a basic question; its getting late and I'm floundering :0) Thank you, --Michael
