Re: [ccp4bb] Ligand building

[Barone, Matthias]

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 need of a restraint file, or build a ligand from 
scratch. Adding atoms, change their H-counts, chirality, or adding bonds 
between two atoms is rather fast. Minimize the molecule either in vacuum or 
dock it right there on its substrate. If you need coot later on, store a pdb 
file and

- create the restraints file via prodrg server 
(http://prodrg1.dyndns.org/submit.html). Its up to you to disable EM at this 
point to retain the conformation of your molecule

- pre-load the cif file in coot and then load the pdb file that comes along 
with the prodrg run (prodrg might change atom names, so work with its outputs 
from now on)


If you need help in moloc, send me a message. Its not a WYSIWYG layout but has 
some big advantages over coot in terms of picking and moving single chains, 
fragments or group of atoms.

cheers,

Matthias


Dr. Matthias Barone

AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin

Germany
Phone: +49 (0)30 94793-284


From: CCP4 bulletin board  on behalf of Hari shankar 
<465d10db143e-dmarc-requ...@jiscmail.ac.uk>
Sent: Saturday, June 13, 2020 6:50:51 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Ligand building

Hi all,

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 new to this and 
unaware of how to solve this issue. Could I get some suggestions on how to 
start this?

2. Alternatively, I was trying to use eLBOW from phenix but it seems to only 
build ligands but unable to delete atoms. Is there another program or option 
for me to delete sections of the ligand and geometrical optimise them in phenix?

Thanks
Hari



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Re: [ccp4bb] Ligand building

[Tomas Malinauskas]

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
<465d10db143e-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hi all,
>
> 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 new to this 
> and unaware of how to solve this issue. Could I get some suggestions on how 
> to start this?
>
> 2. Alternatively, I was trying to use eLBOW from phenix but it seems to only 
> build ligands but unable to delete atoms. Is there another program or option 
> for me to delete sections of the ligand and geometrical optimise them in 
> phenix?
>
> Thanks
> Hari
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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Re: [ccp4bb] Ligand building

[Paul Emsley]

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” as an error message on my Windows. I am 
new to this and unaware of how to solve this issue. Could I get some 
suggestions on how to start this?




In CCP4i2: Task menu -> Ligands -> Make Ligand -> New Job -> Run -> 
{sketch} -> Close the window




that should be:

Task menu -> Ligands -> Make Ligand -> New Job -> Run -> {sketch} -> 
Apply -> Close the window




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Re: [ccp4bb] Ligand building

[Paul Emsley]

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 new 
to this and unaware of how to solve this issue. Could I get some 
suggestions on how to start this?




In CCP4i2: Task menu -> Ligands -> Make Ligand -> New Job -> Run -> 
{sketch} -> Close the window


In Coot: Calculate -> Ligand Builder -> {sketch} -> Apply

You can use File -> Fetch Molecule... or File -> Import Molecule... to 
either fetch (from the aether) or import (from a mmcif file in the 
monomer library) a previously described molecule.




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Re: [ccp4bb] Ligand building in real space

[Paul Emsley]

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 molecular editor is 2D).  If you want to use Coot I 
would do as Johannes says, use File -> Get Monomer.


PG4 (first choice), PGE, PEG, PE8. These are fun to refine in Coot, they 
wriggle around.


I think that SMILES is a bit of side-issue.



I am already using Polder and omit maps that confirm these are not noise.



:-)

Paul.

Re: [ccp4bb] Ligand building in real space

[Johannes Cramer]

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 think you must have ccp4 installed, for this to work, but I am not 100%
sure.

Cheers,
Johannes


2017-04-10 9:44 GMT+02:00 Mohamed Noor :

> Dear all
>
> Is it possible to directly build a ligand in real space (in Coot?) and
> then generate a SMILES string for restraint generation. I have some unknown
> blobs in my density where they look like PEG molecules but these do not
> really fit the density (local CC of 0.7).
>
> I am already using Polder and omit maps that confirm these are not noise.
>
> Thanks.
> Mohamed
>