Description: A postdoctoral position is available immediately to study the
structure and function of microbial sensory rhodopsins, including
channelrhodopsins. The position requires a recent Ph.D. in one of the natural
sciences relevant to structural biochemistry. Applicants must be highly
mot
Hi Matt,
WHAT_CHECK writes out a file called check.db that contains per-residue scores
for several quality metrics. It is fairly easy to parse.
Cheers,
Robbie
Date: Thu, 8 Dec 2011 23:08:45 -0500
From: mattw...@gmail.com
Subject: [ccp4bb] How to assess geometry in a model?
To: CCP4BB@JISCMAIL
Hi Folks
I'm looking for a way to score each atom (or residue) in a model based on
it's geometry. I know these scores exists because various software
packages speak of outliers, even including a sigma value in some cases.
So I'm looking for a simple way to get a complete list (not just outliers)
Check your Rfree flag. Phenix and refmac may use different flag. Have a look
into log file. If percentage of Rfree reflections is 95% then flags need to be
swapped.
Garib
On 9 Dec 2011, at 02:50, Mark J van Raaij wrote:
> are you sure that you are using the original input intensities for the R
My money is on the the wrong test set (as Jonathan Elegheert suggested).
I have seen this several times with newbies, when the test set is
created by phenix. It does it the "xplor-way". When it comes to the free
set, refmac defaults to 0, phenix tries to be intelligent (i.e. if 1/0
it uses 1, if mo
Hi Petr,
The automatic weighting scheme in the recent Refmac version that comes with
6.2.0 is fine but there is a limit to what it can do if something is seriously
wrong with the model/data/whatever. It has just worked well for me in all
respects (Rw/Rf gap, maps quality, FOM, ligands,
all-the
In a non-computational capacity would also suggest perhaps resequencing
your clone. Occasionally the published sequences are off, the specific base
is polymorphous or there is also the possibility that you introduced a
mutation somewhere. That would be the cheap and easy way to definitively
answer
That's a good question ! Here is my take on it:
We are talking of say 5% PEG 2K weight per weight. So 5% PEG 2K and 5% PEG 20K
contains ~ the same weight of polymer per liter of solution, and therefore the
~ same molarity of the ethylene oxide motif. Hence neglecting the effect of the
ends of t
Dear Tim,
I agree with you completely. The question then becomes why does the automatic
weighting scheme in refmac allow R and R-free to run away from each other by 8%
in a 1.1 A resolution structure?
Petr
On Dec 8, 2011, at 6:50 PM, Tim Gruene wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Ha
In addition to the remarks of Mark and Tim, could you make sure that you are
refining in Refmac with the correct flag for the Rfree set (value = 0)? In
Phenix, this is the opposite: the value is 1 for test reflections and 0 for
work reflections. So going from a PHENIX environment to Refmac, you
Hello folks,
After a discussion with a colleague a question aroused regarding
precipitants in crystallisation conditions. I must confess that I do not
know if it is a really naive question or just a stupid one (guess the
second option thought...), anyhow there we go:
Imagine you have crystallisat
Hello all,
Since no one offered a good utility for Ed Pozharski's idea to easily cut a
region of a density map, I made a permanent web location for my utility called
mapreg:
http://mapreg.bravais.net/
Enjoy.
James
On Dec 8, 2011, at 8:39 AM, Ed Pozharski wrote:However, I'd see no harm in posting just a small cutout of the map in the region ofinterest. It's not a difficult task (fft/mapmask or perhaps some usfmagic), but is there some user-friendly approach to cutting out a smallmap volume? There's probably
are you sure that you are using the original input intensities for the REFMAC
map calculation (and the refinement run) and not the output ones of the
(previous) run?
if you are not, you may have model bias, and Rfree can be fooled, especially
with NCS (if you have it).
- or perhaps anisotropic
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Christopher,
if your R/Rfree from Refmac5 really are 10% vs. 18%, you might simply be
looking at an electron density map with strong model bias, i.e. the map
shows the features of the model and not of the data. Although at 1.1A
resolution this se
Christopher,
if you send me the input PDB and data files (off-list, of course) I will
have a close look and then explain what exactly happens and why. I also
promise to post the summary on this mailing list (without revealing the
identity of your structure, of course).
If you send me the command y
Dear All,
Question: Has anybody ever refined the same structure using PHENIX and
then tried REFMAC to see what happens?
I did and I stumbled on something funny. I'm refining a structure at
1.1A resolution which was solved with Iodine phasing using PHENIX
AutoSolve. Got a great map and the structu
Dear Kumar
Could you please provide some information on your refinement protocol/progress
and quality of your partial model thus far. Also, what is the quality and
completeness of your data, in particular in the lowest resolution to 10 angs
range. In this way one might be able to provide more
For the second time today I have to apologize. In no way I wanted to discourage
anyone and especially people new to crystallography from posting questions to
this BB. Especially good thoughtful questions.
Sincerely,
Petr
On Dec 8, 2011, at 5:24 PM, Petr Leiman wrote:
> wrote:
>> I am not sur
There is indeed the phenix.cut_out_density tool (by Tom Terwilliger)
which does a nice job of reducing the size of the output mtz-file (it
shifts the cutout region to the origin and reduces the unit cell).
On the link-versus-attachment issue, certainly the link is preferred,
but the aforementioned
On Thu, 2011-12-08 at 12:17 +0530, atul kumar wrote:
> I can't build anything in this region,this could be because of
> disordered structure or because of low resolution.
Both, and also the presence of disordered fragment may be the reason the
resolution is low, thus the already mentioned suggesti
Hmm- I wonder if B-factor unsharpening (applying a large POSITIVE B-factor to
the data)
would have the same effect?
Francis E Reyes wrote:
On the other hand, shooting a lower resolution crystal may get you the
conformation of the disordered domain.
Surprising at first thought, but was true in
On the other hand, shooting a lower resolution crystal may get you the
conformation of the disordered domain.
Surprising at first thought, but was true in p97/VCP from the Brunger Lab.
F
On Dec 7, 2011, at 11:47 PM, atul kumar wrote:
> Dear all
>
> I have crytals which diffract up
wrote:
> I am not sure that sending links is the way to go. Our company blocks many
> websites that it considers not of professionel interest and were employees
> may spend too much time.
What a brilliant idea! If only this could be implemented in academia. Our Ph.D.
students would stop aski
Hi Stacy,
If you give the CCP4 program crank a try, I can give you advice, if
needed. It can work with SAD data.
Best wishes,
Raj
On Thu, 8 Dec 2011, stacy William wrote:
Dear All...I am new user for Phenix. I am right now working with SAD data. I
had run Ausol in GUI interface with my SAD
I am not sure that sending links is the way to go. Our company blocks many
websites that it considers not of professionel interest and were employees may
spend too much time. More often than not I find that I cannot open the link
provided to the bullitin board. E.g. I just checked the yousendit
posting these attachments as links rather than attachments in CCP4bb messages
is the way to go I think.
many institutions offer this service (ours does), and there are also free and
for-pay online ways to do this (for example www.yousendit.com, but there are
many others).
Then it is also not a p
Colleagues,
One recurring question on this bb is "I got this blob of density - is it
my ligand or what in the name of pink unicorns this is?" Often, a
screen snapshot is posted, which is very helpful. But it may be better
if those helping out could rotate density around in 3D. Understandably,
p
On Thu, 2011-12-08 at 17:49 +0800, Dr. STEPHEN SIN-YIN, CHUI wrote:
> I tried to look at all density regions bit by bit, but the density for
> the protein atoms always interfere with my vision. Is it possible to
> mask out
> the density of protein atoms,
Isn't that what difference density map is
On Thu, 8 Dec 2011 09:19:57 +, Mads Gabrielsen wrote:
I believe Charlie Bond's ALINE
(http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/) will let
you
make a nicely coloured sequence alignement, and then write out a
Pymol
script which will colour the surface by conservation.
Mads
--
Dear All,
I have a protein crystal co-crystallized with a rigid molecule (solved by
small-molecule X-ray method). The color of that crystal is orange (native is
colorless) after 2d cocrystallization experiment. Then I collected synchrotron
data with a resolution at 1.25 Ang. I can solve it by MR.
I believe Charlie Bond's ALINE
(http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/) will let you
make a nicely coloured sequence alignement, and then write out a Pymol
script which will colour the surface by conservation.
Mads
--
Mads Gabrielsen, PhD
Institute of Infection, Immunology and I
Coot is beyond competition (is there any nowadays?), but it cannot do what Yuri
Pompeu asked about.
Petr
On Dec 8, 2011, at 10:10 AM, Francois Berenger wrote:
> On 12/08/2011 05:11 PM, Petr Leiman wrote:
>> Dear Bostjan,
>>
>> There is Chimera for almost anything you can think of.
>
> Not co
On 12/08/2011 05:11 PM, Petr Leiman wrote:
Dear Bostjan,
There is Chimera for almost anything you can think of.
Not coot, you are sure?
Because (i) Chimera is not part of CCP4 and (ii) usually
coot does everything on this mailing list. :)
> Search for "Structure-Based Sequence Alignment" on
8-Dec-2011 10:40am
Dear Bostjan
Consurf is also interfaced to Proteopedia, http://www.proteopedia.org, i.e.
for all structures that have at least several sequences, one can automatically
see an evolutionarily colored 3D Jmol image of the structures by just pushing
the ConSurf button.
See, e.g
Dear colleagues,
We would like to announce the availability of mmView - the web-based
application which allows to comfortably explore the structural data of
biomacromolecules stored in the mmCIF (macromolecular Crystallographic
Information File) format. The mmView software system is primarily
inte
Just to add on others' tips: Consurf is interfaced to Chimera.
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
Do I feel stupid! My previous message about Chimera should have been addresses
to Yuri Pompeu, but not to Bostjan Kobe.
Sincerely,
Petr
On Dec 8, 2011, at 6:26 AM, Yuri Pompeu wrote:
> I once saw a figure showing the protein as surface, but instead of having it
> coloured by atom type
> or p
Dear Bostjan,
There is Chimera for almost anything you can think of. Search for
"Structure-Based Sequence Alignment" on this page:
http://www.cgl.ucsf.edu/chimera/features.html
Petr
On Dec 8, 2011, at 6:39 AM, Bostjan Kobe wrote:
> Consurf will do this for you.
>
> Bostjan
>
> ---
> Bostja
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