Given the average resolution of protein structures, reliability of ion site
identification is almost always in question.
Realistically, I think that only a combination of approaches and evaluation
of several factors (including other experimental methods) leads to good
answers (as I am trying to tea
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Dear Jacob,
the 'check-my-metal' server at http://csgid.org/csgid/metal_sites/
lists a couple of references which might be of interest.
As usual in crytallography one must understand the science in order to
understand the reliability of the models fr
Dear all,
It is well known that you can look at anomalous difference maps to see heavier
atoms - although I think not enough people do it. One technique that I think is
powerful, but under-used is to calculate element-specific maps by taking the
difference of anomalous difference data from ju
Dear CCP4 Users,
An update for the CCP4-6.4.0 series has just been released, consisting of the
following changes
◆ ARP/wARP (Mac, Linux)
1. Fix in the use of free R flag in the ARP/wARP CCP4i interface for solvent
building
2. Fix in the identification of non-crystallographic symmetry that in so
Thanks Eleanor,
I ended up using a glucose ligand lib file from a different protein that my
friend used and refinement Refmac5 worked out.
However I need to add the LINK Command in PDB so CCP4 recognizes that glucoses
connected.
Can I get help please?
Thank you,
Remie
> On Mar 5, 2014, at 10:4
Have you run refmac with the Review restraints option - that generates
LINKs if they seem necessary.
Or can you use the SUGAR links already set upin the library?
Eleanor
On 7 March 2014 11:51, Remie wrote:
> Thanks Eleanor,
> I ended up using a glucose ligand lib file from a different protein
There is another paper out there, which describes the use of long
wavelengths
to define anomalously scattering substructures. This method certainly
helps to
distinguish water molecules from something else, such as chloride for
instance.
http://journals.iucr.org/d/issues/2007/03/00/dz5094/index.ht
On 07/03/14 11:51, Remie wrote:
I ended up using a glucose ligand lib file from a different protein
that my friend used and refinement Refmac5 worked out.
The mind boggles :)... well, OK.
However I need to add the LINK Command in PDB so CCP4 recognizes that
glucoses connected.
In Coot,
Can anyone recommend a good docking program to look at protein-DNA interactions?
Hi,
Is the refmac5 indeed 5.8.006? The current ccp4 version 5.8.0049.
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Bee
Dear Jacob,
An example where special efforts were made to investigate biocatalysis and the
role of ions, harnessing both softer X-rays and ion substitutions and a WASP
analysis to be sure as possible of their identity, can be found here:-
http://www.ncbi.nlm.nih.gov/pubmed/20099851
The review ar
Dear all and dear Jacob
Please have also a look at another paper from Manfred where they show that
"both difference electron-density maps and anomalous difference
electron-density maps suggest that in crystals grown from a sodium sulfate
solution PPE binds Na+ in its metal-binding site." [Porci
Hi Boaz
It is 5.8.0069
And it prints the correct version for me on all platforms
Andrey
On 7 Mar 2014, at 13:13, Boaz Shaanan wrote:
Hi,
Is the refmac5 indeed 5.8.006? The current ccp4 version 5.8.0049.
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Ne
Hi Andrey,
Thanks a lot. I just wanted to make sure that I'm not downgrading refmac5
before implementing the update. It's fine now and I get 5.8.0069 just like you
do.
As was said so many times before on the BB, the update mechanism is wonderful.
Chapeau to you all.
Boaz
Boaz Sha
Dear colleagues,
ARP/wARP 7.4 Patch 2 is available for download on our FTP server, as well.
If you were installing ARP/wARP as a joint bundle with CCP4-6.4.0, you can
update ARP/wARP via automatic CCP4 update or download the patches from
http://www.ccp4.ac.uk/updates/
If you were installing A
>You indicate that oxygen anomalous scattering could be used; whilst this is
>applicable to chirality determination in small molecule organic
>crystallography the oxygen anomalous signal is very small and to my knowledge
>not used thus far in protein crystallography.
Perhaps I should have bee
Dear CCP4 Users
as ever with life, a couple of errors have made it into the update
a. ipmosflm.exe 7.1.0 is missing from the windows update
b. a small change in ccp4i/src/imosflm means that MOSFLM_EXEC is not being set
for csh users.
The suggested remedy is for windows users to hold off this u
A postdoctoral position is available at the Laboratory of Structural Biology
and Chemistry (www.icsn.cnrs-gif.fr/guittet) of the Institute of Chemistry of
Natural Compounds (ICSN) in Gif-sur-Yvette, France, 20km southwest of Paris.
The project aims at understanding the mechanisms of action of the
Dear Jacob,
Ah yes, I see.
Your wording is perfectly clear.
Sorry for my misunderstanding.
Best wishes,
John
Prof John R Helliwell DSc
On 7 Mar 2014, at 15:18, "Keller, Jacob" wrote:
>> You indicate that oxygen anomalous scattering could be used; whilst this is
>> applicable to chirality
Dear colleagues,
I am writing to inform you that the deadline for our workshop on *"Strategic
pipeline planning: from sample preparation to 3D structure determination
with bio SAXS and other biophysical techniques" *to be held at the National
Hellenic Research Foundation (NHRF) in Athens from Apri
Dear SDY,
It looks like ethylene glycol to me. Try EDO
(http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&operation=ccid&target=EDO)
Avinash
--
Avinash S. Punekar
Uppsala University
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