Your responses are tantalizing. In what way are the files not correct?
As Garib says, the N+ is not chiral (and hence @ should not be needed).
Paul.
On 09/05/12 20:13, Shya Biswas wrote:
does not give correct files needed to insert special symbol @ after N+
Shya
On Wed, May 9, 2012 at 2:57
does not give correct files needed to insert special symbol @ after N+
Shya
On Wed, May 9, 2012 at 2:57 PM, Pavel Afonine wrote:
> Shya,
>
> Elbow command:
>
> phenix.elbow --smiles="O=C(C[N+]23CN1CN(CN(C1)C2)C3)c45c45"
>
> will give you CIF and PDB files. I just tried, it took 5 minutes
Shya,
Elbow command:
phenix.elbow --smiles="O=C(C[N+]23CN1CN(CN(C1)C2)C3)c45c45"
will give you CIF and PDB files. I just tried, it took 5 minutes to
calculate them on my mac.
Pavel
On Wed, May 9, 2012 at 9:08 AM, Shya Biswas wrote:
> Hi all,
> I am having trouble generating a pdb and
Interesting: N+ does not seem to be chiral. Three out of four carbons attached
to it seem to be equivalent.
Garib
On 9 May 2012, at 18:13, Shya Biswas wrote:
> The following seems to work with phenix:
> O=C(C[N@+]23CN1CN(CN(C1)C2)C3)c45c45
> Shya
>
> On Wed, May 9, 2012 at 12:15 PM, Bo
The following seems to work with phenix:
O=C(C[N@+]23CN1CN(CN(C1)C2)C3)c45c45
Shya
On Wed, May 9, 2012 at 12:15 PM, Bosch, Juergen wrote:
> Is that your molecule ?
>
> On May 9, 2012, at 12:08 PM, Shya Biswas wrote:
>
> O=C(C[N+]23CN1CN(CN(C1)C2)C3)c45c45
>
>
> ..
Hi Paul
The pdb file that you send me does not have the right geometry, have tried
phenix elbow, same problem not the right geometry however in consultation
with Nigel it looks like a special symbol had to be inserted in smiles, he
send me a file that looks like correct.
thanks to all who helped,
S
On 09/05/12 17:08, Shya Biswas wrote:
Hi all,
I am having trouble generating a pdb and cif file from the following
smiles string:
O=C(C[N+]23CN1CN(CN(C1)C2)C3)c45c45
Prodrg fails to run when i draw the molecule in JME editor was
wondering if anyone knows a better program which does th
..@gmail.com>>
Date: Wed, 9 May 2012 12:08:39 -0400
To: mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: [ccp4bb] pdb and cif file generation from smiles string
Hi all,
I am having trouble generating a pdb and cif file from the following smiles
string:
O=C(C[N+]23CN1CN(CN(C1)C2)C3)c45c45
multiple ways of getting there:
I used Picto (OpenEye)
But you can also search PubChem with your smile string and find a perfect match
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=437043&loc=ec_rcs
If you look around you will find what you need on that web page.
Jürgen
On May 9, 2012,
Is that what you are looking for?libcheck cn generate it (JLigand should be able). grade should also generate from smiles.Garib
1.cif
Description: Binary data
1.pdb
Description: Binary data
On 9 May 2012, at 17:08, Shya Biswas wrote:Hi all,I am having trouble generating a pdb and cif file from t
Is that your molecule ?
[cid:FDC217A8-8891-4163-88FE-3886A27C2823@sph.ad.jhsph.edu]
On May 9, 2012, at 12:08 PM, Shya Biswas wrote:
O=C(C[N+]23CN1CN(CN(C1)C2)C3)c45c45
..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistr
Hi all,
I am having trouble generating a pdb and cif file from the following smiles
string:
O=C(C[N+]23CN1CN(CN(C1)C2)C3)c45c45
Prodrg fails to run when i draw the molecule in JME editor was wondering if
anyone knows a better program which does this kind of job.
thanks in advance,
shya
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