Hi Charles, It is better to reply on the mailing list as this will ensure that the discussions are archived. That way, many biologists will be able to search for answers to their questions before posting themselves ;)
The font settings can be controlled with 'set'. If you type 'set label' in the Tcl/Tk gui or in the main window (messages screen) and then press TAB, you will get a list of settings related to label appearance. However, a better option might be to browse the pymol wiki, where you can also find examples of the commands. Unfortunately, the labels settings do not contain images to illustrate the effects, but maybe you'd be interested to make that contribution ;) As a side note, I think that the non-programmers using Pymol and in need of examples should usually have the wiki loaded in the background for reference. It contains a fairly complete account of commands, settings and examples, and is still being extended. O yes, sorry to have forgotten the quotes. Cheers, Tsjerk On 3/24/09, Charles David Stout <d...@scripps.edu> wrote: > Dear Tsjerk, > > Thank you for the reply and explanation. > > I entered: > >label chain B and resn trp and resi 42 and name ca, 'Trp42' > and it works (after I remembered to try the quotes, not in your email > example). > > This syntax is logical. What I meant by 'obscure' is that for a > non-programmer, it is hard to get to it exactly right without a specific > example. > Since you have many biologists using your program, I would suggest > providing more specific examples in the help file. > > The label come up white and small; can the color, font size, or position be > controlled? > > Thanks > C. D. Stout > 3-23-09 > > > > Tsjerk Wassenaar wrote: > > > Hi Charles, > > > > What do you mean with obscure? I've always thought the examples were > > clear enough. It'd be more helpful if you could give more of your > > ideas of what is obscure about the help and what would be needed to > > improve it. But the syntax is > > > > label selection, expression > > > > Now selections may be slightly obscure when starting out, but no more > > than with any other language. The c-alpha atom of tryptophan 42 of > > chain B is simply 'chain B and resn trp and resi 42 and name ca'. And > > if you want to label 'Trp42', it's just that: > > > > label chain B and resn trp and resi 42 and name ca, Trp42 > > > > There's another way to do the selection, but this one's most > > intuitive. You might also give the expression as 'resn + resi', which > > is particularly better when dealing with series of atoms. > > > > Cheers, > > > > Tsjerk > > > > On Sat, Mar 21, 2009 at 8:00 AM, Charles David Stout <d...@scripps.edu> > wrote: > > > > > > > It's a hassle to always add labels to PyMol figures in Photoshop > > > > > > How do you do this in PyMol? e.g. I want to label 'Trp42' next to its > > > alpha-carbon (on chain B). > > > The examples in the help manual are obscure. > > > Thanks > > > C. D. Stout > > > 3-20-09 > > > > > > > ------------------------------------------------------------------------------ > > > Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are > > > powering Web 2.0 with engaging, cross-platform capabilities. Quickly and > > > easily build your RIAs with Flex Builder, the Eclipse(TM)based > development > > > software that enables intelligent coding and step-through debugging. > > > Download the free 60 day trial. > http://p.sf.net/sfu/www-adobe-com > > > _______________________________________________ > > > PyMOL-users mailing list > > > PyMOL-users@lists.sourceforge.net > > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > > > > > > > > > > > > > > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
