[Avogadro-Discuss] UNL after using Fill Unit Cell
Hi all, I am trying to recreate the unit cell assemblage of 4z1r (visible using the PDB NGL viewer on the website). After importing my structure and checking the unit cell dimensions, I set the space group (5 c 2y c 1 2 1 as determined using Maestro) then select “Fill Unit Cell”. Visually, everything looks good. But unfortunately, all means of identifying the atom and the corresponding residue is lost in the exported pdb and matching/replicated atoms as listed together rather than in their corresponding residue order. I plan on importing this into Gromacs, but in its current state the .pdb file is impossible to read. E.g., HETATM1 N UNL 1 3.631 3.685 8.676 1.00 0.00 N HETATM2 N UNL 2 165.943 3.685 16.225 1.00 0.00 N HETATM3 N UNL 3 89.418 10.655 8.676 1.00 0.00 N HETATM4 N UNL 4 80.156 10.655 16.225 1.00 0.00 N HETATM5 C UNL 5 4.854 4.502 8.763 1.00 0.00 C HETATM6 C UNL 6 164.720 4.502 16.138 1.00 0.00 C HETATM7 C UNL 7 90.640 11.472 8.763 1.00 0.00 C HETATM8 C UNL 8 78.933 11.472 16.138 1.00 0.00 C HETATM9 C UNL 9 6.049 3.864 8.047 1.00 0.00 C HETATM 10 C UNL10 163.525 3.864 16.854 1.00 0.00 C HETATM 11 C UNL11 91.836 10.833 8.047 1.00 0.00 C HETATM 12 C UNL12 77.738 10.833 16.854 1.00 0.00 C HETATM 13 O HOH13 5.956 2.719 7.616 1.00 0.00 O HETATM 14 O HOH14 163.618 2.719 17.285 1.00 0.00 O HETATM 15 O HOH15 91.743 9.688 7.616 1.00 0.00 O HETATM 16 O HOH16 77.831 9.688 17.285 1.00 0.00 O Any idea how to fix this? I’m beginning to think the only way around this would be to import my asymmetric unit structure into Gromacs, replicate the protein, identify the x,y,z location of a central atom from within Avogadro of one of the three replicated molecules, and perform some basic maths to translate the copies. Thanks Anthony Dr Anthony Nash Department of Chemistry University College London Skeletal Tissue Dynamics Group Committee member of London Matrix Group @LondonMatrixGrp -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
[Avogadro-Discuss] displaying multiple NBO orbitals
Hi all, Apologies if this has been covered before; I've looked but with no success. I have loaded in my Gaussian formatted checkpoint file and I have identified the three NBOs involved in hydrogen bonding between an organic molecule and a single explicit water molecule. Unfortunately it seems that I can only display one orbital at anyone time. I wish to render the LP (the one of the two with the most interaction energy from the second order...) and the (O-H)* delocalised orbital. Avogadro 1.1.1 QT version 4.8.6 Anthony advice is greatly appreciated. Thanks Anthony -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
[Avogadro-Discuss] HBond display can't change colours.
Hi all, Just installed Avogadro 1.1.1 app and lib version on Mac yosemite 10.10.1. Unless I am missing something very obvious I can't change hydrogen bonds to a different color. They always remain yellow even when I select custom color. I am able to change hydrogen bond width so I know the software can act on them. I have tried enabling and disabling hydrogen bonds between changing colours, I have even tried the other Colour by options with no change. Any help would be appreciated. Thanks Anthony Dr Anthony Nash Department of Chemistry University College London -- Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
