Hi everybody, I'm using SiteComp to detect differences in binding affinities between two similar structures. The _clusters.pdb file produced by SiteComp is a standard PDB file in which the grid points corresponding to the difference clusters are represented by hydrogen atoms. They can be treated as any molecule in Chimera. Usually I find it useful to represent them as a mesh surface. Usually, I load in Chimera the protein.pdb, the ligand.pdb and the _clusters.pdb. After this, I select the _clusters.pdb and show it as mesh or solid using Actions-> Surface. In some cases, I fail to render the surface, or to be precise only one part of the clusters is rendered. I understand that this is a frequent problem with this type of discontinuous pdb. I'm attaching one such file and I would be grateful for any help Best regards George
Hi George, Sometimes by making small changes in the surface calculation parameters, you can get it to work, but there is no guaranteed fix. Here is some text from an earlier post to chimera-users@cgl.ucsf.edu on this topic: ---------------------------------------------- The first thing to do is make sure you have a fairly recent version of Chimera, say 1.4 from Dec 2009 or newer. Although we have not eliminated the failures, we have made some improvements that reduce their frequency. Sometimes when there is an error, it can still fall back to a "single component" calculation. The problem may be in some inside bubble, whereas the "single component" is the main outer surface. If that's what happened, but it still looks like you got the surface you want, you can ignore the message. If you didn't get any surface, however, there are several things to try, as mentioned in several previous posts (links below). Unfortunately none is a magic bullet that works in all situations. <http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-April/003816.html> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-September/003096.html> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002417.html> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/002954.html> --------------------------------------------- Different things may work for different structures, and for some, you may not be able to find any fix. Best, Elaine On Jul 6, 2012, at 8:20 AM, George Tzotzos wrote:
Hi everybody,
I'm using SiteComp to detect differences in binding affinities between two similar structures. The _clusters.pdb file produced by SiteComp is a standard PDB file in which the grid points corresponding to the difference clusters are represented by hydrogen atoms. They can be treated as any molecule in Chimera.
Usually I find it useful to represent them as a mesh surface. Usually, I load in Chimera the protein.pdb, the ligand.pdb and the _clusters.pdb. After this, I select the _clusters.pdb and show it as mesh or solid using Actions-> Surface. In some cases, I fail to render the surface, or to be precise only one part of the clusters is rendered.
I understand that this is a frequent problem with this type of discontinuous pdb. I'm attaching one such file and I would be grateful for any help
Best regards George
Hi George, You might want to use the "molmap" command to create a Gaussian surface instead of a solvent excluded surface. For example if _clusters.pdb is model #2 and you want a 5 Angstrom resolution surface use: molmap #2 5 This never fails. It sums a Gaussian centered at each atom and computes a contour surface. Tom
Hi everybody,
I'm using SiteComp to detect differences in binding affinities between two similar structures. The _clusters.pdb file produced by SiteComp is a standard PDB file in which the grid points corresponding to the difference clusters are represented by hydrogen atoms. They can be treated as any molecule in Chimera.
Usually I find it useful to represent them as a mesh surface. Usually, I load in Chimera the protein.pdb, the ligand.pdb and the _clusters.pdb. After this, I select the _clusters.pdb and show it as mesh or solid using Actions-> Surface. In some cases, I fail to render the surface, or to be precise only one part of the clusters is rendered.
I understand that this is a frequent problem with this type of discontinuous pdb. I'm attaching one such file and I would be grateful for any help
Best regards
George
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Hi Tom, Many thanks for this. Much appreciated. Thanks also to Elaine for her suggestions. Have a good weekend George On Jul 6, 2012, at 6:41 PM, Tom Goddard wrote:
Hi George,
You might want to use the "molmap" command to create a Gaussian surface instead of a solvent excluded surface. For example if _clusters.pdb is model #2 and you want a 5 Angstrom resolution surface use:
molmap #2 5
This never fails. It sums a Gaussian centered at each atom and computes a contour surface.
Tom
Hi everybody,
I'm using SiteComp to detect differences in binding affinities between two similar structures. The _clusters.pdb file produced by SiteComp is a standard PDB file in which the grid points corresponding to the difference clusters are represented by hydrogen atoms. They can be treated as any molecule in Chimera.
Usually I find it useful to represent them as a mesh surface. Usually, I load in Chimera the protein.pdb, the ligand.pdb and the _clusters.pdb. After this, I select the _clusters.pdb and show it as mesh or solid using Actions-> Surface. In some cases, I fail to render the surface, or to be precise only one part of the clusters is rendered.
I understand that this is a frequent problem with this type of discontinuous pdb. I'm attaching one such file and I would be grateful for any help
Best regards
George
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi George, One more idea: just show the cluster as atoms in the sphere representation. From your description, SiteComp makes them hydrogens, so that would initially just use the hydrogen radius in Chimera. However, you could set the "VDW" radii (and thus sphere size) of those fake atoms to whatever value you like. For example, if your cluster.pdb file is open as model 2, set the radii of its atoms to 2.5 angstroms: rep sphere #2 vdwdef 2.5 #2 The atom spheres can't be shown as mesh, but you could make them transparent, for example: color 1,0,0,.5 #2 Elaine On Jul 6, 2012, at 9:43 AM, George Tzotzos wrote:
Hi Tom,
Many thanks for this. Much appreciated.
Thanks also to Elaine for her suggestions.
Have a good weekend
George
On Jul 6, 2012, at 6:41 PM, Tom Goddard wrote:
Hi George,
You might want to use the "molmap" command to create a Gaussian surface instead of a solvent excluded surface. For example if _clusters.pdb is model #2 and you want a 5 Angstrom resolution surface use:
molmap #2 5
This never fails. It sums a Gaussian centered at each atom and computes a contour surface.
Tom
Hi everybody,
I'm using SiteComp to detect differences in binding affinities between two similar structures. The _clusters.pdb file produced by SiteComp is a standard PDB file in which the grid points corresponding to the difference clusters are represented by hydrogen atoms. They can be treated as any molecule in Chimera.
Usually I find it useful to represent them as a mesh surface. Usually, I load in Chimera the protein.pdb, the ligand.pdb and the _clusters.pdb. After this, I select the _clusters.pdb and show it as mesh or solid using Actions-> Surface. In some cases, I fail to render the surface, or to be precise only one part of the clusters is rendered.
I understand that this is a frequent problem with this type of discontinuous pdb. I'm attaching one such file and I would be grateful for any help
Best regards
George
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Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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participants (3)
-
Elaine Meng -
George Tzotzos -
Tom Goddard