Hi Ronnie,
you will need to create a dictionary of the link in Jligand or Acedrg (ccp4i2)
if we talk about ccp4 programs, and provide this as a LIBIN input in Refmac5.
In coot you will need to delete ND2 atom of Asn residue (if your dictionary
contains link Lys NZ - Asn CG) and in menu calculate/
Hi
I am wondering if there is a simple program that would convert a pdb file into
a matrix that
shows the smallest distance between all pairs of amino-acid side chains?
Thanks,
Misha
To unsubscribe from the CCP4BB lis
Hi Guto,
I would be very cautious with the InnerShell merging statistics as yours.
Rmeas in this shell is higher than Rmeas overall,
which probably means you have a lot of overloads,
(or problems with backstop shadow, which is not so likely
on Diamond nowdays).
And generally InnerShell Rmerge ov
Dear Nishant,
For successful MR a choice of domain boundaries and loop trimming is
crucial.
Last couple of years I do not even try to run molrep/phaser before
running MrBump and Morda, which do a good job with model preparation.
Only when these pipelines give leads, but not quite the results I use
Hi,
I have seen cases where in a correct space group
'R-work and R-free values 0.25 and 0.32 respectively'
at 2 A resolution sound like not too bad values.
In some of such cases when data from a different crystal
in the same space group was available R-factors were much lower
when the structure w
Hi,
I have already uninstalled the latest update (23), on Snow Leopard
the new COOT was crushing
on attempt to mutate residue in graphical interface.
Regards,
Misha
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of wtempel
[wtem...@gmail.com
:mat...@itqb.unl.pt>> wrote:
>
> Thanks, there must be something wrong with the update.
>
> Às 18:13 de 01/02/2016, Isupov, Michail escreveu:
>> As a temporary fix I have uninstalled the latest update
>> and jligand works again.
>> Cheers,
>> Misha
Hi Graeme,
in a data set with just below 800,000 independent reflections I use 1 % for
freeR which
is still impressive 8,000. xia2 would have assigned 40,000 for freeR
at 5 %. I think this is way too much.
Often we collect many data sets of the same project to find the better data.
We do use de
Hi Todd,
disulfides (both intra and intermolecular) are quite common in extremophile
cytosolic proteins. I routinely come across these.
Many of these disulfides are retained when the proteins are overexpressed in
E.coli regardless of the
strong reducing environment.
Usually these disulfides are r
Hi Florian,
When your pseudo-translation (native Patterson peak) is close to (0.5,0.5,0.5)
even in p22121 you will have have most of reflections with
h+k+l=2n+1
measured as weak. In your lower resolution datasets 2.6 and 3.0 A non-weak
reflections can be lost in noise and your group assignment
12121.
Best,
Misha
From: Chris Fage [cdf...@gmail.com]
Sent: 12 July 2014 00:33
To: Isupov, Michail
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Proper detwinning?
Nat and Misha,
Thank you for the suggestions.
Xtriage does indeed detect twinning in P
I would recommend to run ZANUDA in the default mode from ccp4i or on CCP4 web
server.
ZANUDA has resolved several similar cases for me.
Misha
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Chris Fage
[cdf...@gmail.com]
Sent: 10 July 2014
Dear Steve,
Presence of several Patterson peaks at impossible (as far as crystal packing is
concerned) distances
and an NCS two-fold normal to the crystallographic one suggests it could
be an order-disorder (OD) structure, like the one we had in Exeter.
An order-disorder twin crystal of L-2-ha
Dear Hua,
Your problem sounds like a 'false origin' one, where due to the
pseudotranslation the molecular replacement
choses the wrong origin out of the two possible ones. Your space group is
probably P212121.
The best approach is to run Andrey Lebedev's program ZANUDA on YSBL server.
http://ww
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