Dear Alice,
Instead of printing on paper, why not 3D-print it?
Cheers,
Clement
-Original Message-
From: Alice Clark
Sent: Friday, March 10, 2017 1:18 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] making a paper model
Dear All,
How can I get a 2D net diagram from a 3D PDB structure,
Have you tried changing the file extension to .ccp4 instead of .map?
Cheers,
Clement
From: Appu kumar
Sent: Wednesday, March 01, 2017 7:54 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] ANODE anomalous map in pymol
Hi,
I Already did that in COOT, but PYMOL does not read it in map format.
the affinity much stronger than in CA’s?
Jacob Pearson Keller
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Clement
Angkawidjaja
Sent: Friday, November 11, 2016 12:11 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Nitrate versus Carbonate
Dear JPK
What I
Dear JPK
What I know is we do not have much nitrate in the blood unlike
carbonate/bicarbonate.
Nitrite, a nitrate byproduct can cause problems but it has a different
structure and probably does not interfere with bicarbonate binding to relevant
proteins.
Cheers,
Clement
From: Keller, Jacob
Dear Wenhe,
Have you looked at the Additional Log File from Superpose?
Cheers,
Clement
-Original Message-
From: WENHE ZHONG
Sent: Sunday, October 30, 2016 12:47 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Superpose program in CCP4
Dear all,
I always use the SUPERPOSE tool in
Dear Rojan,
Get the mmCIF, then use CIF2MTZ from CCP4.
Cheers,
Clement
On 10/25/13 3:07 PM, Rojan Shrestha wrote:
Hello,
Is EDS (electron density server) dead? In the absence of EDS, how can
be mtz file directly downloaded?
Regards,
Rojan
Dear Dee,
Some proteins with chaperone-like activity (perhaps your B?) can only
bind to partially folded proteins.
Probably A folds to a molten globule structure after 1-2 days. You can
check by spectroscopic techniques (ANS or Trp fluorescence, CD).
Hope that helps.
Cheers,
Clement
On
Hi Deepak,
Assuming that you have done the necessary things to measure the pKr of
that particular Asp, I would say that the increase is advantageous for
your enzyme. Enzyme catalysis often involves very subtle changes on the
ionization state of the active site. But you need to be very careful
conc. disrupted the tetrameric assembly and enabled crystallization of the
protein as a monomer.
Curious to know if there has been any similar precedence before.
Cheers,
Shiva
Clement Angkawidjaja, PhD.
G30 Assistant Professor
Hi Seema,
Small addition to the already abundant suggestions, if you have high solvent
content or significant portion of non-observable density, you normally get
higher R-free.
Clement
Clement Angkawidjaja, PhD.
G30 Assistant Professor
But you have to do solvent flattening (density modification), which people
often (unintentionally?) skip for structures solved with molecular replacement.
Please correct me if I am wrong.
Clement
On May 24, 2011, at 6:01 PM, herman.schreu...@sanofi-aventis.com wrote:
This is not my
and look for extra molecule(s), which may have
been overlooked. If these extra molecule(s) are disordered, this will
off course lead to high Rfree values.
Best,
Herman
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Clement Angkawidjaja
Sent
?
Thanks.
Andreas
--
Andreas F#65533;ster, Research Associate
Paul Freemont Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk
Clement Angkawidjaja, Ph.D
Specially appointed assistant professor
-410-955-3655
http://web.mac.com/bosch_lab/
On Nov 14, 2010, at 8:32 PM, Clement Angkawidjaja wrote:
DALI server (http://ekhidna.biocenter.helsinki.fi/dali_server/). Choose the
pairwise alignment function. It is all automatic and will give you the
lowest rmsd. Note, however
I strongly agree with Eric Larson’s suggestion on trying to see the diffraction
of your crystal. The most straightforward solution. Other suggestions may work
too, but there are chances they will still give you false positives.
If you need bigger crystals, try to slow down the nucleation (use
need to specify the
residues you want to use for calculation for the lsq fit function.
Regards,
Clement Angkawidjaja, PhD
Specially Appointed CMP Assistant Professor
Graduate School of Engineering
Osaka University
2-1 Yamadaoka GSE Commoon East 8F
Suita-shi, Osaka 565-0871, Japan
Tel/Fax +81-6
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