We addressed some of these electrostatics problems (Xray artefact like presence
of ions, crystal packing, etc) a long time ago. Feel free to look at:
Improving macromolecular electrostatics calculations.
Nielsen JE, Andersen KV, Honig B, Hooft RW, Klebe G, Vriend G, Wade RC.
Protein Eng. 1999
Dear users.I'm comparing surface charge of a structure with its homologous (85%
seq ID), and noted that APBS suggest completely opposite charge distribution
(exactly what I expected, since despite its similarity molecules have opposite
biochemical profile)
But since molecules are quite
Why not ?
Look at the partner protein is there a similar charge reversal present?
The function is preserved (interaction of both proteins) in different species
but the charges have swapped over time in evolution while the backbone scaffold
(fold) of the protein was maintained.
Just as an
Dear Boaz (and others)
it immensly improves readability of your emails if you can ask your email client
to also include a plain text version of your email on top of the html-version
;-)
Cheers,
Tim
On Tue, Jul 05, 2011 at 05:55:28PM +, Boaz Shaanan wrote:
html dir=ltr
head
meta
Leave it to the crystallographers to be the last on the Planet with
text-only email readers Just before the ccp4bb will migrate to
google+ :)
Flip
Op 7/6/2011 10:27, Tim Gruene schreef:
Dear Boaz (and others)
it immensly improves readability of your emails if you can ask your email
@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] APBS
Dear Boaz (and others)
it immensly improves readability of your emails if you can ask your email client
to also include a plain text version of your email on top of the html-version
;-)
Cheers,
Tim
On Tue, Jul 05, 2011 at 05:55:28PM +, Boaz Shaanan wrote
[summer break flame]
I'm sure there are a lot more computer admins than crystallographers who
prefer high-tech over fancyness - aka outlook usually marking my signed(!)
emails as spam ;-)
And, yes, I know that both thunderbird/enigmail and kmail combine both very
elegantly, but with mutt I can
Tim Gruene t...@shelx.uni-ac.gwdg.de writes:
[summer break flame]
I'm sure there are a lot more computer admins than crystallographers who
prefer high-tech over fancyness - aka outlook usually marking my signed(!)
emails as spam ;-)
And, yes, I know that both thunderbird/enigmail and kmail
Dear CCP4BB,
I apologize for the off topic question.
I have determined the 3D structure of a membrane protein transporter and want
to make a figure showing the surface charge. So, I ran PDB2PQR and specified pH
5.4. I understand the next step is to run APBS. I know there are different
, July 05, 2011 8:24 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] APBS
Dear CCP4BB,
I apologize for the off topic question.
I have determined the 3D structure of a membrane protein transporter and want to make a figure showing the surface charge. So, I ran PDB2PQR and specified pH 5.4. I
Hi Sebastiano,
Can you send me the problematic PDB (offlist) and we'll take a look?
Thanks,
Dave
On Jun 25, 2007, at 8:50 AM, Sebastiano Pasqualato wrote:
Hi all,
despite using the latest version of pdb2pqr ( http://
agave.wustl.edu/pdb2pqr/server.html) and having downloaded the
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