interactions and
> placing a compound with confidence is questionable anyway.
>
>
> Cheers
>
>
> M
>
>
> From: CCP4 bulletin board on behalf of John
> Berrisford
> Sent: 22 July 2019 22:23:47
> To: ccp4bb
> Subject: Re:
d chemical interactions and placing
a compound with confidence is questionable anyway.
Cheers
M
From: CCP4 bulletin board on behalf of John Berrisford
Sent: 22 July 2019 22:23:47
To: ccp4bb
Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
Dear
lf of Patrick Loll mailto:pjl...@gmail.com>>
Sent: Friday, July 19, 2019 1:17 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
The idea of contacting the editor (and/or auth
@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
Hi John
These are great, but the things that make me suspicious are the values of
overall R(merge); these are tucked away in the full reports, rather than
highlighted with all the other structural metrics in the
--
Von: CCP4 bulletin board im Auftrag von David Schuller
Organisation: Cornell University
Antworten an:
Datum: Montag, 22. Juli 2019 um 14:45
An:
Betreff: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
On 7/22/19 3:40 AM, Bärbel Blaum wrote:
"As I said, the lead autho
On 7/22/19 3:40 AM, Bärbel Blaum wrote:
"As I said, the lead author may not actually be the crystallographer here"
Bärbel
No need to wonder, that info should be in the PDB file header. The
author of the coordinates is not necessarily the same as the author of
the primary reference.
--
===
>725 W. Lombard Street N571
>Baltimore
>MD 21201
>
>
>
>From: CCP4 bulletin board on behalf of Patrick Loll
>
>Sent: Friday, July 19, 2019 1:17 PM
>To: CCP4BB@JISCMAIL.AC.UK
>Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6M
> Sent: 19 July 2019 18:43
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
>
> Would it be possible to add a public annotations section to the PDB, to allow
> us to potentially flag/warn whoever downloads that particular struct
@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
Would it be possible to add a public annotations section to the PDB, to
allow us to potentially flag/warn whoever downloads that particular
structure, there could be something wrong with it, such as wrong space
group, no/poor
477 94 72--
Von: CCP4 bulletin board im Auftrag von "Keller, Jacob"
Antworten an: "Keller, Jacob"
Datum: Freitag, 19. Juli 2019 um 23:09
An:
Betreff: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
I don’t think anyone mentioned contacting the author
he protein chain right, and should then look if there would still be
> >> density available to fit the ligand.
> >>
> >> Best,
> >>
> >> Herman
> >>
> >> VON: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] IM AUFTRAG VON
> >>
4 bulletin board on behalf of Robbie Joosten
Sent: Friday, July 19, 2019 1:24 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
Even though PDB-REDO cannot salvage this model without extensive rebuilding
which is what Tristan showed, it is fun to l
Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
If it is as it appears, it is disappointing to see this in JACS. I would expect
better. Unfortunately, reviewers don't always get a lot of information to judge
quality of structures (which has been discussed extensively on
properly refining B-factors is really important!
Cheers,
Robbie
*From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf
Of *Bärbel Blaum
*Sent:* Friday, July 19, 2019 17:24
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
Hi R
-Mail: baerbel.bl...@intherabio.com
Phone: +41 43 477 94 72--
Von: CCP4 bulletin board im Auftrag von "Manfred S.
Weiss"
Antworten an: "Manfred S. Weiss"
Datum: Freitag, 19. Juli 2019 um 16:03
An:
Betreff: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
Begin forwarded message:
From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>>
Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
Date: July 19, 2019 at 1:32:53 PM EDT
To: Patrick Loll mailto:pjl...@gmail.com>>
Hi Pat,
I, too have fallen into this
: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
The idea of contacting the editor (and/or author) is an excellent one, and
indeed the correct thing to do scientifically. However, I’m disillusioned: I’ve
been down this path before with a high-profile vanity journal, and while the
editors paid
Mail: baerbel.bl...@intherabio.com
> Phone: +41 43 477 94 72--
>
>
>
> Von: CCP4 bulletin board im Auftrag von "Manfred S.
> Weiss"
> Antworten an: "Manfred S. Weiss"
> Datum: Freitag, 19. Juli 2019 um 16:03
> An:
> Betreff: Re: [ccp4bb] Quest
Best,
>>
>> Herman
>>
>> VON: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] IM AUFTRAG VON
>> Rhys Grinter
>> GESENDET: Freitag, 19. Juli 2019 15:22
>> AN: CCP4BB@JISCMAIL.AC.UK
>> BETREFF: [EXTERNAL] [ccp4bb] Questionable Ligand Density: 6MO0,
,
Herman
VON: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] IM AUFTRAG VON
Rhys Grinter
GESENDET: Freitag, 19. Juli 2019 15:22
AN: CCP4BB@JISCMAIL.AC.UK
BETREFF: [EXTERNAL] [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1,
6MO2
EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk
Hi All,
I
: baerbel.bl...@intherabio.com
Phone: +41 43 477 94 72--
Von: CCP4 bulletin board im Auftrag von "Manfred S.
Weiss"
Antworten an: "Manfred S. Weiss"
Datum: Freitag, 19. Juli 2019 um 16:03
An:
Betreff: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
Hi Rhys,
all three structures are at modest resolution and they don't seem to
be properly refined. At least they are all below average. I wonder
how this paper made it past the referees.
I haven't checked the paper, but there are ways and means how to
deal with weakly bound ligands in the best p
to:CCP4BB@JISCMAIL.AC.UK
> <mailto:CCP4BB@JISCMAIL.AC.UK>] Im Auftrag von Rhys Grinter
> Gesendet: Freitag, 19. Juli 2019 15:22
> An: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
> Betreff: [EXTERNAL] [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
>
> EX
available to fit the ligand.
Best,
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Rhys
Grinter
Gesendet: Freitag, 19. Juli 2019 15:22
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
EXTERNAL : Real sender is owner
Hi All,
I was chatting with a colleague during a recent synchrotron visit and
they'd recently come across some ligand/drug bound structures associated
with a paper recently published in a high impact factor journal.
They had pulled the associated SFs from the PDB and found that the electron
densi
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