With due respect ! I want to ask that,
If it is protonated at neutral pH, what about the local pka of the active
site key residues involved ? would not it make any difference if it adds
extra H-atom and actual case is different when the reaction is carried out
?
With Kind regards
Prem
On Fri, A
Hi Remie,
PyMOL by default sorts atoms based on their identifiers (segment, chain,
residue number). Could it be that your file has segment identifiers? Try this
after loading your file:
PyMOL>alter all, segi=""
PyMOL>sort
Cheers,
Thomas
On 07 Aug 2014, at 19:08, CCP4BB automatic digest syst
Hi,
A trick that has worked for me a few times is to skip the regularization stage in Jligand, although some may argue that it's "illegal". If your ligand/cofactor has a decent geometry without regularization it may well work for you too.
Cheers,
Boaz
Boaz Shaanan, P
Hi Dr. Gruene,
Thanks for your input.
I have actually checked pdb and the chains are listed in the order A, B then C;
except for the LinkR between the ligand units and between some amino acids
where there are gaps (those link records were towards the top), so I moved
those LinkR corresponding
Dear Remie,
did you check (with a text editor) the PDB file saved from coot if it actually
reordered the chains inside the file? Maybe chain C is still listed first, and
maybe this is what pymol takes as order.
Regards,
Tim
On Thu, Aug 07, 2014 at 11:19:42AM -0400, Remie Fawaz-Touma wrote:
> Hi
Thanks Ian.
Is it possible to force Jligand to keep only two hydrogens in this case?
I tried setting the N's charge to 0, but it reverts back to 1 after
regularization.
Thanks,
Abhinav
__
Abhinav Kumar, Ph.D.
The Joint Center for Structural Genomics
MS99, SL
Hi, I would say three: aliphatic amines such as the one you show are weak
bases so at neutral pH the protonated form predominates. Aromatic amines
are obviously trickier.
Cheers
-- Ian
On 7 August 2014 17:37, Abhinav Kumar wrote:
> Hi,
>
> I am making a ligand in Jligand (figure attached) a
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Hi,
I am making a ligand in Jligand (figure attached) and have a question
about valency of nitrogen.
Jligand puts three hydrogens on nitrogen N1 when the ligand is regularized.
Should there be two hydrogens or three?
--
Thanks,
Abhinav
__
Abhinav Kumar, Ph.
Dear All,
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Department of Biological Sciences and Bioengineering at the Indian
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Hi everyone,
Does anyone know how to rearrange chains when looking at a structure in PyMol
(maybe it has to be done in coot, don’t know).
I have the ligand first now in PyMol and would like to see the sequence of the
protein first, then ligand.
It is worth mentioning that I did reorder the ch
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Dear all,
Apologies for the non-CCP4 related post, but does anyone know where the HOLE
program for mapping the conduction pathways of ion channels may be obtained
from these days? Preferably in a form that may be run on Mac or Linux systems.
It no longer appears to be available from the Sansom
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