Re: [PyMOL] weird visualization of a peptide structure
Annalisa, If bonds are not explicitly provided in the input file, then PyMOL infers bonding based on distance. Are the input coordinates valid? It looks like the atoms may be too close together in space... Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com _ From: annalisa bordogna [mailto:annalisa.bordo...@gmail.com] Sent: Thursday, December 18, 2008 6:40 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] weird visualization of a peptide structure Hi all, I have a little problem with the visualization of a peptide conformation: as you can see from the picture I enclose, the structure appears as if every atom is bound to every neighbour atom. What (and how) can I set in PyMOL, to visualize a correct structure? Thank you very much for your help. Best regards, Annalisa --- Annalisa Bordogna Ph.D. Student Università degli Studi di Milano - Bicocca Milano, IT
Re: [PyMOL] weird visualization of a peptide structure
Hi Andrew, thank you for your answer: now I have a clue! I knew that the structure is a NMR model, but what I didn't understand was that some atoms were repeated (with different coordinates). Now I have pruned my structure file and I can see a much more acceptable structure. Thank you very much, Annalisa 2008/12/19 Andrew Purkiss-Trew a.purk...@mail.cryst.bbk.ac.uk Hi Annalisa, Is the original coordinate file an NMR structure? It looks to me like there are several copies of each atom, which is consistent with the pdb file resulting from an NMR refinement. These will usually have several different models of the peptide, all consistent with the NMR data. You will need to extract just one set of coordinates and look at those. Which set of coordinates to use depends on the software used to generate the pdb, but look for the first or the 'best' model, the pdb header should tell you which is best. Hope this helps at bit Andrew Purkiss-Trew On Thu, 2008-12-18 at 15:40 +0100, annalisa bordogna wrote: Hi all, I have a little problem with the visualization of a peptide conformation: as you can see from the picture I enclose, the structure appears as if every atom is bound to every neighbour atom. What (and how) can I set in PyMOL, to visualize a correct structure? Thank you very much for your help. Best regards, Annalisa --- Annalisa Bordogna Ph.D. Student Università degli Studi di Milano - Bicocca Milano, IT -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] weird visualization of a peptide structure
Hi Annalisa, Is the original coordinate file an NMR structure? It looks to me like there are several copies of each atom, which is consistent with the pdb file resulting from an NMR refinement. These will usually have several different models of the peptide, all consistent with the NMR data. You will need to extract just one set of coordinates and look at those. Which set of coordinates to use depends on the software used to generate the pdb, but look for the first or the 'best' model, the pdb header should tell you which is best. Hope this helps at bit Andrew Purkiss-Trew On Thu, 2008-12-18 at 15:40 +0100, annalisa bordogna wrote: Hi all, I have a little problem with the visualization of a peptide conformation: as you can see from the picture I enclose, the structure appears as if every atom is bound to every neighbour atom. What (and how) can I set in PyMOL, to visualize a correct structure? Thank you very much for your help. Best regards, Annalisa --- Annalisa Bordogna Ph.D. Student Università degli Studi di Milano - Bicocca Milano, IT -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] weird visualization of a peptide structure
Hi all, I have a little problem with the visualization of a peptide conformation: as you can see from the picture I enclose, the structure appears as if every atom is bound to every neighbour atom. What (and how) can I set in PyMOL, to visualize a correct structure? Thank you very much for your help. Best regards, Annalisa --- Annalisa Bordogna Ph.D. Student Università degli Studi di Milano - Bicocca Milano, IT attachment: weird_peptide.png
