[PyMOL] how to create a custom rainbow according to residue number
Dear All, I'm using Pymol1.4 in windows and I have a protein build-up by 6 domains organized in pairs in an anti-parallel fashion ( i.e. if A and V are the domains: AV AV AV) (the domains are structurally homologous but the sequence is different). I want to color the two domains in different colors (i.e. A green and V blue) but then I want this colors to be in a gradient according to the sequence (i.e. A should be colored from light green to dark green and V colored from light blue to dark blue). As I understood one cannot create new color schemes in the spectrum command (if yes I would just color them individually) am i right? For that reason I'm thinking of creating a ramp that I would color with that color scheme, for this i need to create a selection containing the residue number of the residues involved. Is there a way to directly create a list of residue number in Pymol ? Best Afonso ### Afonso Duarte ITQB-UNL Portugal -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] how to create a custom rainbow according to residue number
Hi Afonso, this should do the job: http://pymolwiki.org/index.php/Spectrumany Example: PyMOL run spectrumany.py PyMOL spectrumany resi, lime green forest, chain A+C+E PyMOL spectrumany resi, lightblue blue density, chain B+D+F Hope that helps. Cheers, Thomas Afonso Duarte wrote, On 09/04/12 15:15: Dear All, I'm using Pymol1.4 in windows and I have a protein build-up by 6 domains organized in pairs in an anti-parallel fashion ( i.e. if A and V are the domains: AV AV AV) (the domains are structurally homologous but the sequence is different). I want to color the two domains in different colors (i.e. A green and V blue) but then I want this colors to be in a gradient according to the sequence (i.e. A should be colored from light green to dark green and V colored from light blue to dark blue). As I understood one cannot create new color schemes in the spectrum command (if yes I would just color them individually) am i right? For that reason I'm thinking of creating a ramp that I would color with that color scheme, for this i need to create a selection containing the residue number of the residues involved. Is there a way to directly create a list of residue number in Pymol ? Best Afonso ### Afonso Duarte ITQB-UNL Portugal -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] how to create a custom rainbow according to residue number
Hi Thomas, Thanks! indeed it does the job! Cheers Afonso On Tue, Sep 4, 2012 at 3:00 PM, Thomas Holder spel...@users.sourceforge.net wrote: Hi Afonso, this should do the job: http://pymolwiki.org/index.php/Spectrumany Example: PyMOL run spectrumany.py PyMOL spectrumany resi, lime green forest, chain A+C+E PyMOL spectrumany resi, lightblue blue density, chain B+D+F Hope that helps. Cheers, Thomas Afonso Duarte wrote, On 09/04/12 15:15: Dear All, I'm using Pymol1.4 in windows and I have a protein build-up by 6 domains organized in pairs in an anti-parallel fashion ( i.e. if A and V are the domains: AV AV AV) (the domains are structurally homologous but the sequence is different). I want to color the two domains in different colors (i.e. A green and V blue) but then I want this colors to be in a gradient according to the sequence (i.e. A should be colored from light green to dark green and V colored from light blue to dark blue). As I understood one cannot create new color schemes in the spectrum command (if yes I would just color them individually) am i right? For that reason I'm thinking of creating a ramp that I would color with that color scheme, for this i need to create a selection containing the residue number of the residues involved. Is there a way to directly create a list of residue number in Pymol ? Best Afonso ### Afonso Duarte ITQB-UNL Portugal -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
