To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] chloride or water
I reiterate that assigning a chloride is not “wild speculation” or “just making
something up” in light of what we know about the situation.
I see your point about not knowing that it’s a chloride, but I think you would
agree
.)
Sent: Thursday, January 22, 2015 10:26 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] chloride or water
After reading this exchange, I think at the core of the dispute is the question
what a structure
model really is supposed to represent (a), and how to annotate/describe it (b).
ad
On Wed, Jan 21, 2015 at 10:17 AM, Keller, Jacob kell...@janelia.hhmi.org
wrote:
I see your point about not knowing that it’s a chloride, but I think you
would agree that it is certainly more likely a chloride than map-noise, and
perhaps more likely than water as well. Would you agree that
and wrong data, especially
considering that not all users are experts on interpreting electron density
maps or protein structures.
Zhijie
From: Keller, Jacob
Sent: Wednesday, January 21, 2015 1:17 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] chloride or water
I reiterate that assigning
: Zhijie Li
Sent: Wednesday, January 21, 2015 2:12 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] chloride or water
Hi Jacob,
I would agree with Nat. I think with the 3A data and the local environment,
putting a Cl there is only justified by the need of supressing a peak in the
difference map
@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] chloride or water
On Wed, Jan 21, 2015 at 9:05 AM, Keller, Jacob
kell...@janelia.hhmi.orgmailto:kell...@janelia.hhmi.org wrote:
Not sure why there is this level of suspicion about the poor halide when waters
generally get assigned so haphazardly. I would say
No, I think I don't know is the most honest and scientifically robust answer.
It will impress at least with its solemn humility, but in this case, you *do*
know something, and that information makes the most likely answer that there is
indeed something in that blob, and that something is
On Wed, Jan 21, 2015 at 12:16 AM, Engin Özkan eoz...@uchicago.edu wrote:
Carbon in chloride's coordination sphere? To me, it looks like you have
serious vdW violations, and neither water nor chloride could go there.
Halides can interact with carbon too - discussed in Dauter Dauter (2001)
-
,
Jacob
Sent: Wednesday, January 21, 2015 10:27 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] chloride or water
Check other Cl- in the pdb to see whether the bond lengths and VdW are an issue
(wouldn't H2O have the same VdW issues?). I am thinking (this happened to me
once by mistake) that maybe
best and is plausible, I say go for Cl-.
Hopefully your reviewers will at least agree with each other!
JPK
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nat Echols
Sent: Wednesday, January 21, 2015 11:35 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] chloride or water
On Wed, Jan 21, 2015 at 9:05 AM, Keller, Jacob kell...@janelia.hhmi.org
wrote:
Not sure why there is this level of suspicion about the poor halide when
waters generally get assigned so haphazardly. I would say that there are
probably more “wrong” waters in the PDB than wrong chlorides, but
For those who insist on annotating every density blob, UNX atoms are the
PDB's officially supported method for doing so (unless this has changed
recently), or UNK/UNL for unknown amino acids and ligands. These are not
without their own problems but they at least make both the presence of an
If you do that then what chemical type you are going to put into that
rightmost column of ATOM record of PDB file? Note, that must be a valid
chemical element symbol so that you can use such PDB file to calculate
R-factors, maps and whatnot (Obviously, X would not work!).
Why, Cl- of course!
If you do that then what chemical type you are going to put into that
rightmost column of ATOM record of PDB file? Note, that must be a valid
chemical element symbol so that you can use such PDB file to calculate
R-factors, maps and whatnot (Obviously, X would not work!).
Why, Cl- of
On Wed, Jan 21, 2015 at 12:24 PM, Keller, Jacob kell...@janelia.hhmi.org
wrote:
I think this will probably never happen, but maybe there could be a
confidence value associated with each atom in structures a posteriori,
although it might be difficult to find the right automatable criteria
On 01/21/15 15:04, Pavel Afonine wrote:
(And why not make every water into UNX for good measure as well?)
Why not indeed, except that I would not call it water but Dummy Atom
with an element type of your choice.
there was a time long ago when budding crystallographers were taught to
Hi Rohit,
What about your Rfree? what about your protein geometry?
I will try to figure out this residual density at the realy latest step
of the refinement.
Because of your resolution, no anomalous signal available and Van der
Waals problems
it could be difficult for a referee believe in a
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Carlos
CONTRERAS-MARTEL
Sent: Wednesday, January 21, 2015 9:03 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] chloride or water
Hi Rohit,
What about your Rfree? what about your protein geometry?
I will try to figure out this residual density at the realy
is not as
pretty as that of cations.
HTH,
Robbie
--
Van: rohit kumar rohit...@gmail.com
Verzonden: 20-1-2015 08:05
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: [ccp4bb] chloride or water
Dear all,
I am solving a data of 3.0 Å resolution. In the active site we
@JISCMAIL.AC.UK
Subject: [ccp4bb] chloride or water
Dear all,
I am solving a data of 3.0 Å resolution. In the active site we found an
unidentified blob. The crystallization condition is (PEG 3350-25%,
Naformate-200mM, MES (100mM)-6.5pH, and Nacl-200mM).
Can anyone suggest what it could be? If I suppose
, unless the environment strongly suggests
an anion binding site (as what Robbie said) my personal view is that it is more
proper to put a water there.
Zhijie
From: rohit kumar
Sent: Tuesday, January 20, 2015 1:59 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] chloride or water
Dear all,
I
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