Hi Hari
If I understood you correctly, you want to modify and subsequently dock it onto
a complex structure, right? For me, the following workflow turned out to be
most straightfwd:
- build it in MOLOC (http://www.moloc.ch/). It lets you very easily modify an
existing molecule without the
Hi Hari,
I typically draw formulae using ChemDraw online, export SMILES and use
them to get PDBs/CIFs from Grade web server (Global Phasing). Both
ChemDraw and Grade web servers are free to use.
Hope that helps,
Tomas
On Sat, Jun 13, 2020 at 6:01 PM Hari shankar
On 13/06/2020 18:16, Paul Emsley wrote:
On 13/06/2020 17:50, Hari shankar wrote:
I want to build a ligand that does not exist in reality (or be able
to modify an existing ligand as per choice).
1. JLigand in the ccp4 suite seems to work only on java and gives me
an “configuration problem”
On 13/06/2020 17:50, Hari shankar wrote:
I want to build a ligand that does not exist in reality (or be able to
modify an existing ligand as per choice).
1. JLigand in the ccp4 suite seems to work only on java and gives me
an “configuration problem” as an error message on my Windows. I am
To answer your question...
On 10/04/17 08:44, Mohamed Noor wrote:
Is it possible to directly build a ligand in real space (in Coot?) and then
generate a SMILES string for restraint generation.
I think that you are describing a 3D editor. It is not possible to do
this in Coot (Coot's
Hey Mohamed,
I am not sure, if this is what you want, but you can import different PEG
molecules from coot's "File-> Get monomer". A list of different length PEGs
three letter codes can be found on page 1278 of this paper:
Naschberger et al., (2016) http://doi.org/10.1107/S205979831601723X.
I
