Dear Paul - your tip seems like a life-saver. I gave it a quick try but
failed, not in that it didn't filled up the side chains well, but in that
the patched-up residues are now broken apart from its original polypeptide
chains.
Extensions -> All Molecule -> [Post MR] Fill Partial Residues...
I'm
On 23/05/2020 20:18, Yong Tang wrote:
Dear all, is there a way to "automatically" patch up the missing atoms
in the residues that otherwise are properly defined in a PDB entry.
For example, an Arginine is defined as Arginine but only has the beta
carbon on the side chain.
In Coot I could use
Try SWISS-MODEL.
Sent from Jack's iPhone
On May 23, 2020, at 6:24 PM, Eugene Osipov wrote:
Dear Yong,
you could use freely available Chimera.Use Tools->Structure Editing-> Dock
prep. in order to add missing side chains to your protein.
Another option - Protein preparation tool from Schroding
Dear Yong,
you could use freely available Chimera.Use Tools->Structure Editing-> Dock
prep. in order to add missing side chains to your protein.
Another option - Protein preparation tool from Schrodinger Suite. However,
it is non-free.
сб, 23 мая 2020 г. в 21:19, Yong Tang :
> Dear all, is there
Dear Maria -
Lipid diffraction resembles powder diffraction rather than discrete spots -
you can see examples in Cherezov's 2002 Biophys J article, for example - so
you wouldn't mistake them for protein diffraction. If not a case of
overlooked predictions as Kay suggests, you have probably crystall
Dear all, is there a way to "automatically" patch up the missing atoms in
the residues that otherwise are properly defined in a PDB entry. For
example, an Arginine is defined as Arginine but only has the beta carbon on
the side chain.
In Coot I could use the Extensions/Modeling/Residues with Missi
>
> I thought that some of the list members may be interested in the paper,
> titled "DSSR-enabled innovative schematics of 3D nucleic acid structures
> with PyMOL", recently published in _Nucleic Acids Research_ (
> https://doi.org/10.1093/nar/gkz1222).
*Sorry* about the wrong link to nar/gkz122
I thought that some of the list members may be interested in the paper,
titled "DSSR-enabled innovative schematics of 3D nucleic acid structures
with PyMOL", recently published in _Nucleic Acids Research_ (
https://doi.org/10.1093/nar/gkz1222). Among other things, DSSR can
dramatically simplify the
