RE: [PyMOL] adding residues
Sergio, PyMOL probably isn't the best tool for doing this, but it can be done: To add to a free N-terminus, pick (ctrl-middle-click) the N-terminal nitrogen, and then press Alt-Letter (on Macs, Option-Letter) for the amino acid you want: For example: Alt-G adds a glycine To add onto the C-terminus, pick the C-terminal carbon, and do the same. If you'd like to remove hydrogens after you're done, type remove hydro Or select "Auto-remove hydrogens" from the Setting menu. Cheers, Warren > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Sergio Modesto Vechi > Sent: Friday, March 26, 2004 11:42 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] adding residues > > Hi all, > > > I load my protein pdb file and I'm trying to add the missing > residues to this molecule. Anyone knows how to do it? > > Thanks in advance, > > > Sergio. > > > > --- > This SF.Net email is sponsored by: IBM Linux Tutorials Free > Linux tutorial presented by Daniel Robbins, President and CEO > of GenToo technologies. Learn everything from fundamentals to > system > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
Re: [PyMOL] adding residues
Oi Sergio, You should pick (PkAt) either the atom N or C depending towards which end you want to extend the chain: N ==> to extend the N-terminus C ==> to extend the C-terminus and then select the residue you want to add from the Build->Residue menu. Um abraco, Zac On Fri, 26 Mar 2004, Sergio Modesto Vechi wrote: | Hi all, | | | I load my protein pdb file and I'm trying to add the missing residues to | this molecule. Anyone knows how to do it? | | Thanks in advance, | | | Sergio. | | | | --- | This SF.Net email is sponsored by: IBM Linux Tutorials | Free Linux tutorial presented by Daniel Robbins, President and CEO of | GenToo technologies. Learn everything from fundamentals to system | administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click | ___ | PyMOL-users mailing list | PyMOL-users@lists.sourceforge.net | https://lists.sourceforge.net/lists/listinfo/pymol-users | Ezequiel Panepucci, Ph.D. - Laboratory of Prof. Axel Brunger HHMI - Stanford University Phone: 650-736-1714 Cell: 650-714-9414
[PyMOL] adding residues
Hi all, I load my protein pdb file and I'm trying to add the missing residues to this molecule. Anyone knows how to do it? Thanks in advance, Sergio.
RE: [PyMOL] opaque interiors flag
Ken, set ray_interior_color, color-name eg: set ray_interior_color, grey30 To restore default: set ray_interior_color, -1 Cheers, Warren > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Kenneth Dale Westover > Sent: Friday, March 26, 2004 8:27 AM > To: PyMOL-users@lists.sourceforge.net > Subject: [PyMOL] opaque interiors flag > > Anyone know the command (for scripting) to set the opaque > interiors flag? > In the GUI it's under Display > Rendering > Opaque Interiors. > > Thanks, > Ken > > > --- > This SF.Net email is sponsored by: IBM Linux Tutorials Free > Linux tutorial presented by Daniel Robbins, President and CEO > of GenToo technologies. Learn everything from fundamentals to > system > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
RE: [PyMOL] CGO shading
On Thu, 2004-03-25 at 18:38, Warren DeLano wrote: > You need to provide normal vectors too. Otherwise OpenGL & the > raytracer won't be able to light them correctly. OK, that works fine now. If anyone else is interested in making CGO 'walls', a simple script is now on my PyMOL page (it's called walls.py) http://www.ebi.ac.uk/~gareth/pymol/ Gareth > > -Original Message- > > From: pymol-users-ad...@lists.sourceforge.net > > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > > Gareth Stockwell > > Sent: Thursday, March 25, 2004 10:04 AM > > To: pymol-users > > Subject: [PyMOL] CGO shading > > > > > > Hi there, > > > > Does anyone know how to get CGO objects to be properly shaded? > > > > For example, if I create two triangles which lie in > > perpendicular planes... > > > > obj = [ > > > > BEGIN, TRIANGLES, > > > > COLOR, 1, 0, 0, > > VERTEX, 0, 0, 0, > > VERTEX, 1, 0, 0, > > VERTEX, 1, 1, 0, > > > > COLOR, 1, 0, 0, > > VERTEX, 0, 0, 0, > > VERTEX, 1, 0, 0, > > VERTEX, 1, 0, 1, > > > > END > > ] > > > > cmd.load_cgo(obj,'triangles') > > > > > > ... the colour of both triangles looks identical, in either > > OpenGL or ray-traced rendering. > > > > I want to use CGOs to create 'floor' and 'walls' as a > > backdrop to ray-traced images, to give better perspective. > > At the moment, I have to manually set the shade of each wall > > in order to get it to look right. > > > > Details of my setup: > > PyMOL version 0.95 beta, running on Linux > > GL_VENDOR: 2d3D, Inc > > GL_RENDERER: Mesa DRI Intel(R) 845G 20021115 > > GL_VERSION: 1.2 Mesa 4.0.4 > > > > Cheers, > > Gareth > > -- --- Gareth Stockwell EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD gar...@ebi.ac.uk Tel 01223 492548 http://www.ebi.ac.uk/~gareth
[PyMOL] opaque interiors flag
Anyone know the command (for scripting) to set the opaque interiors flag? In the GUI it's under Display > Rendering > Opaque Interiors. Thanks, Ken
RE: [PyMOL] embeding pymol in a web page
Einat, On Thu, 2004-03-25 at 18:50, Warren DeLano wrote: > For web-page embeddable molecular graphics today, look to Jmol: > http://jmol.sourceforge.net Another alternative is the AstexViewer Java applet - free, but unfortunately closed source. http://www.astex-technology.com/AstexViewer/visualisation/index.html The MSD at EBI have developed an extended version, in use here: http://www.ebi.ac.uk/msd-srv/apps/Viewer/ViewerServlet?id=1atp It has some nice features, like showing the sequence of the protein and allowing you to zoom in on a residue when clicked in the sequence. I'm not sure about the licence position on the EBI version though; if you're interested, I'm sure someone from the MSD group could help out. Gareth -- --- Gareth Stockwell EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD gar...@ebi.ac.uk Tel 01223 492548 http://www.ebi.ac.uk/~gareth
