super! Glad to have been a help. Do point us to it when you feel that is
appropriate.
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer w
After a big network upgrade and installing the latest version (the one that
eliminated the need for JSmoljQuery), everything seems to be working fine.
I have tried various protonation and deprotonations on all of my test cases
and they all seem to produce no further issues.
Thank you very much! Th
could be you have an older version -- that is, that I did not update that
JavaScript. What version are you using? I just ran this successfully with
JSmol/HTML5 and in the Java app. Looks right to me.
load =2ace;select atomno=62;print {selected}.label();assign atom
({atomno=62}) "Mi";select atomno=
I have just installed the latest JSmol and the problem remains, though I
think I have found a plausible reason for the problem. When the command
"assign atom ({selection}) "Pl"/"Mi"" is issued, all of the atom numbers
shift by a certain amount, and this also changes their atom names.
My current te
so that is one of the fixes in the recent release. Let me know if you have
any more problems, Vinushka.
On Wed, Jul 24, 2013 at 6:43 AM, Robert Hanson wrote:
> OK, I can reproduce that now. I'll look into it.
>
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
N
OK, I can reproduce that now. I'll look into it.
--
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Isolate bottlenecks and diagnose ro
The PDB file I am loading, 3tim from RCSB, contains HIS,GLU,ASP and LYS
residues. The HIS residues are recorded on the 3tim PDB file as follows:
ATOM250 N HIS A 35 17.176 46.945 15.774 1.00
35.08 N
ATOM251 CA HIS A 35 18.324 47.821 15.822 1.00
22.12
You're going to have to help me find that. I'm just not seeing it. Please
describe exactly what you do.
On Fri, Jul 19, 2013 at 12:06 PM, Vinushka Schalk
wrote:
> The functions you gave work wonderfully and the protonation/deprotonation
> works appropriately now, at least on a functional level.
The functions you gave work wonderfully and the protonation/deprotonation
works appropriately now, at least on a functional level. However, I am
still encountering a problem where after the protonation/deprotonation the
atom's name changes from "NZ" to something like "N175" (where 175 is the
atom n
That should have read:
I think the problem is that your formal charges are not being set up for
proteins. If you do not have multiple bonds, then there is no way for Jmol
to set the correct formal charges. If you use
set pdbaddhydrogens
load xxx.pdb
then Jmol will assign multiple bonding correct
I think the problem is that your formal charges are not being set up for
proteins. If you do not have multiple bonds, then there is no way for Jmol
to set the correct formal charges. If you use
set pdbaddhydrogens
load xxx.pdb
I took a look at OpenBabel, converting 1blu with adding hydrogens at p
Ah, I see. definitely odd. I'm sure the hydrogen addition to proteins needs
some work -- this was not designed with proteins in mind. I can look into
that. Please send hans...@stolaf.edu the pdb file that comes from
OpenBabel.
Have you tried
set pdbAddHydrogens
load xxx.pdb
? There's no pH depe
>> Hi,
>>
>> I'm a web developer who has been using JSmol since January for various
>> graphical functionality on a molecular simulations website (visualizing
>> point-mutations, building custom ligand molecules, etc.) I am currently
>> trying to develop a visualizer for changing protonation states
On Wed, Jul 17, 2013 at 5:50 AM, Vinushka Schalk wrote:
> Hi,
>
> I'm a web developer who has been using JSmol since January for various
> graphical functionality on a molecular simulations website (visualizing
> point-mutations, building custom ligand molecules, etc.) I am currently
> trying to d
Hi,
I'm a web developer who has been using JSmol since January for various
graphical functionality on a molecular simulations website (visualizing
point-mutations, building custom ligand molecules, etc.) I am currently
trying to develop a visualizer for changing protonation states in a
protein: JS
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