issues with visualization of saxs models in chimera
Dear Chimera team, I am a user from your software and I would like to have a superimposition of some crystallographic structures in a recent saxs pdb model I obtained. However, I cannot visualize the saxs pdb file with Chimera. Would you have any tips or inputs how can I do this? Thank you very much in advance for all your help, Kind regards, Anabel
Hi Anabel, SAXS "PDB" files frequently have atoms that lie exactly on a grid, which causes some calculations in Chimera to fail. If you can prevent Chimera from trying to create bonds and/or "missing segment" pseudobonds between your "atoms", then those problematic calculations don't happen. The easiest way to do this is to change all your ATOM records into HETATM records. Make sure to keep the columns the same, so actually change "ATOM " (i.e. and the two trailing spaces) into "HETATM". --Eric Eric Pettersen UCSF Computer Graphics Lab
On Oct 20, 2020, at 7:35 AM, Anabel Pacios Michelena <anabel.pacios_michelena@uni-wuerzburg.de> wrote:
Dear Chimera team,
I am a user from your software and I would like to have a superimposition of some crystallographic structures in a recent saxs pdb model I obtained. However, I cannot visualize the saxs pdb file with Chimera. Would you have any tips or inputs how can I do this?
Thank you very much in advance for all your help,
Kind regards,
Anabel _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Anabel, Unclear what you mean by "cannot visualize" ... maybe you just need to display the points, e.g. command "display". Also maybe these points are supposed to be spheres with specific radii assigned by the SAXS software, whereas the PDB file only gives center dot coordinates. You can display the points with those radii if you can figure out from the SAXS software what the radii are supposed to be. For example if it is open as model #0 and you find out that the sphere radii are supposed to be 4.5 angstroms, commands: display #0 repr sphere #0 vdwdefine 4.5 #0 (However, this is all a guess. Usually if you are asking about problems with some file, you would need to attach that file to allow us to say anything useful.) The above would give you a bunch of spheres. Usually when I see a SAXS model in a paper, it is a surface. You would still need to use "vdwdefine" to set the proper sphere size first, but then you could hide them and show a surface. Continuing the example above: ~display #0 surface #0 surftransparency 50 #0 Or, you could try to make a map from the SAXS model with "molmap" command but I don't know what parameters you would need to use for resolution, etc. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 20, 2020, at 7:35 AM, Anabel Pacios Michelena <anabel.pacios_michelena@uni-wuerzburg.de> wrote:
Dear Chimera team, I am a user from your software and I would like to have a superimposition of some crystallographic structures in a recent saxs pdb model I obtained. However, I cannot visualize the saxs pdb file with Chimera. Would you have any tips or inputs how can I do this? Thank you very much in advance for all your help, Kind regards, Anabel
participants (3)
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Anabel Pacios Michelena -
Elaine Meng -
Eric Pettersen