Hi Francis
I guess it depends on how much residual high-affinity binder you have in the
mixture and what the difference in affinity is between Y and deriv-Y. Another
issue is of course whether Y and derY compete for the same binding site and
have the same stoichiometry. A well designed displacem
The fault is entirely with those who respond to phenix questions.
You can't blame the askers for guessing that CCP4BB will get a better
response.
I call this "The Republican Fallacy". This fallacy is predicated on
the assumption that it is easier to modify behavior than it is to
modify th
While I have as keen an interest in Russian history as the next
person, I personally feel that this thread has travelled far enough
from CCP4 and crystallography to warrant moving any further discussion
in this vein to another forum.
On Aug 25, 2010, at 3:57 PM, Ed Pozharski wrote:
I don'
But equation given in slide #4 is exactly least-square equation with
some modified maps. Just use Pareval's theorem, then for case of 2mFo-
Dfc you will have
sum_{reflection used) (2mFo-DF_{c current) -k F_{model})^2
F_model is equal to F_{c current} at the point of calculation. All
gradien
I don't see what George's attempt to point out that pure-phenix
questions should be asked in phenix bb (and the point itself may be
subject to different opinions) has to do with renaming Moscow streets
and subway stations (unless you thought that the proposition to rename
ccp4bb is serious).
You
I think Paul (Emsley) is better qualified to answer to this question.
However 1) coot uses 2mFo-DFc maps 2) you should be able to feed any
map you want to coot so it is nice place for experimenting this kind
of calculation 3) You may try to relax gemetry 4) Usually if the
model does not fit
Ethan,
I still don't understand. Real space refinement will minimize a fit
of model to density in whatever map you give it. It's up to you
which coefficients are used to calculate the map you are refining
against.
This is true.
However, I guess, the way it is implemented in Coot is a bit di
On Wednesday 25 August 2010 03:19:53 pm zhan...@umbc.edu wrote:
> I mean the density of 2mFo-DFc or Fc maps.
I still don't understand. Real space refinement will minimize a fit
of model to density in whatever map you give it. It's up to you
which coefficients are used to calculate the map you a
But there is no better way to accumulate wisdom than having children...And
certain types of wisdom are *only* accessible through having children! Then
again, I have always wondered why most of the authors of the western
classics were bachelors--weren't they missing a whole, major facet of life
expe
On Wednesday 25 August 2010 03:13:53 pm Hailiang Zhang wrote:
> Hi Garib:
>
> Actually I tried coot real space refine zone, but the model seems not
> sliding into the best density map (I also tried dragging it around, but
> still not working fine). Then I found some comments saying minimizing the
I mean the density of 2mFo-DFc or Fc maps.
> On Wednesday 25 August 2010 03:13:53 pm Hailiang Zhang wrote:
>> Hi Garib:
>>
>> Actually I tried coot real space refine zone, but the model seems not
>> sliding into the best density map (I also tried dragging it around, but
>> still not working fine).
Hi Garib:
Actually I tried coot real space refine zone, but the model seems not
sliding into the best density map (I also tried dragging it around, but
still not working fine). Then I found some comments saying minimizing the
difference between 2mFo-DFc and Fc may be better, thats why I am asking
>> On 25 Aug 2010, at 22:17, Pavel Afonine wrote:
>>
>>> On 8/25/10 2:11 PM, George M. Sheldrick wrote:
I would like to propose that we rename this list to the "Phenix (and
CCP4) Bulletin Board".
>>>
>>> Sounds too Russian: after collapse of USSR many street names in Moscow,
>>> as well
Hello,
I've been using an the on-line homology modeling program Jigsaw-3D, and would
like to run it on my own Linux box, but it requires CHARM, which I am
unvailable to get because I am currently looking for a faculty position... does
anyone know of an open source energy minimization program th
Why you do not use coot? It does exactly what you want.
regards
Garib
On 25 Aug 2010, at 22:33, Hailiang Zhang wrote:
Hi,
Can some utilities of CCP4 do the real-space refinement locally
with the
residue range explicitly specified?
By the way, I have registered phenix bb. Just didn't reali
Hey Garib,
LOL... no of course, I was just saying that I'm a bit allergic to
re-naming well established things, and some other people may be too -:)
Why don't we rename you Mr. Refmac -:) ?
Pavel.
On 8/25/10 2:25 PM, Garib Murshudov wrote:
Are you suggesting ccp4 is collapsing and people a
Are you suggesting ccp4 is collapsing and people are coming back to
the original source?
Garib
On 25 Aug 2010, at 22:17, Pavel Afonine wrote:
On 8/25/10 2:11 PM, George M. Sheldrick wrote:
I would like to propose that we rename this list to the "Phenix (and
CCP4) Bulletin Board".
Sounds
Hi,
Can some utilities of CCP4 do the real-space refinement locally with the
residue range explicitly specified?
By the way, I have registered phenix bb. Just didn't realize this before,
sorry again.
Best Regards, Hailiang
On Wed, Aug 25, 2010 at 2:11 PM, George M. Sheldrick <
gshe...@shelx.uni-ac.gwdg.de> wrote:
> I would like to propose that we rename this list to the "Phenix (and
> CCP4) Bulletin Board". What have people got against sending purely
> Phenix questions to the Phenix list?
>
Actually, people who don
Just realized there is a seperate phenix bb. Sorry guy...
> I would like to propose that we rename this list to the "Phenix (and
> CCP4) Bulletin Board". What have people got against sending purely
> Phenix questions to the Phenix list?
>
> George
>
> PS. Since there is no SHELX list, if you have
On 8/25/10 2:11 PM, George M. Sheldrick wrote:
I would like to propose that we rename this list to the "Phenix (and
CCP4) Bulletin Board".
Sounds too Russian: after collapse of USSR many street names in Moscow,
as well as metro station names, were renamed back to their "original"
names they h
I would like to propose that we rename this list to the "Phenix (and
CCP4) Bulletin Board". What have people got against sending purely
Phenix questions to the Phenix list?
George
PS. Since there is no SHELX list, if you have a specifically SHELX
question you should just email me directly, as i
Hi Hailiang,
phenix.refine does local real-space refinement indeed. Here are the
details about the algorithm:
http://cci.lbl.gov/~afonine/rsr.pdf
Slide #10 shows how to use it. Although it works fine in its present
shape, there are still some things that need to be improved and some
limita
Hi there:
As I understand, phenix.refine do real-space refinement locally (by
DiffMap), but from the documentation, I didn't find the keywords to
specify the residue range to be refined. Thanks for any help!
Best Regards, Hailiang
Mark, you might want to try PDBsum (http://www.ebi.ac.uk/pdbsum/), it will
generate a LIGPLOT output for a given PDB code entered, which can be
downloaded as high resolution .pdf or .ps
Best,
Javier
On Wed, Aug 25, 2010 at 2:49 PM, Tim Gruene wrote:
> Hello Mark,
>
> if you would describe the er
Hello Mark,
if you would describe the error message you get from the UNIX version of
LIGPLOT, someone on the list might be able to help you while you have to wait
for and apple installer version or the (commercial) alternatives.
Looking at the pictures about ligplot I found on the web and conside
Hi Mark,
MOE from ChempComp does something similar, but I think it is not for free.
Regards
Christian
Am Mittwoch 25 August 2010 19:51:08 schrieben Sie:
> Dear All,
>
> Having just installed LIGPLOT under Windows, I find it rather convoluted to
> run. It has to be run via de command line wi
Dear Roger,
We have had success using the non-detergent sulphobetaines (NDSBs) to improve
solubility of protein samples. For a couple of projects they have proved
crucial for concentrating the protein to a reasonable level for crystallization
(e.g. PMID: 18765907). Be careful since there is a b
Dear All,
Having just installed LIGPLOT under Windows, I find it rather convoluted to
run. It has to be run via de command line window, and I try to avoid Windows as
much as I can anyway.
I also tried to install the Unix version on MacOSX, but was not able to get it
running properly, probably a
Dear Rakesh,
at least for pymol you have to convert the mtz-file into a ccp4-map. The program
'fft' does this from the ccp4i. Give the output file the name extension .ccp4,
than it's recognised by the default filter in pymol.
Tim
On Wed, Aug 25, 2010 at 11:56:17AM -0400, Rakesh Joshi wrote:
> Hi
Hi all,
I am having problems opening an electron density map on chimera as well as in
pymol( tried mtz and xplor formats). Chimera gives a "error in line 2
ANOMalous=false" message or "bad MRC grid size" message,where as pymol just
gives
a "error reading map" message.
Any help will be apprec
The Structural Biology Laboratory at UT Southwestern Medical Center
currently has an opening at the Research Assistant Professor level for
a highly motivated individual who enjoys working in a collaborative,
multi-disciplinary setting. A Ph.D. in biochemistry, chemistry,
physics or a relate
Have you tried to use glycerol or ethylene glycol as the precipitant? What
happens when you go to 50% or higher concentrations?
_
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Roger
Rowlett
Sent: Wednesday, August 25, 2010 9:19 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject
Dear Roger,
Since you already have initial crystallisation conditions and crystals you could
try dialysis buttons to further reduce the glycerol content (and hence get
bigger crystals). They are available e.g. from Hampton, the minimum volume is 5
mul and I find they require a little skill to set
Hi Roger,
I crystallized a protein that started in solution with 250 mM NaCl, 50%
glycerol, and 50 mM Arg+Glu. I initially used traditional microbatch under
paraffin oil to get crystallization hits (where protein and screen are 1:1;
glycerol ends up at 25%). Then, I found that setting up sittin
Dear All,
We have an opening for a postdoctoral position within the EMBL
interdisciplinary postdocs initiative (EIPOD). The project on 'Combined
computational methods for macromolecules' aims at interpretation of
macromolecular crystallography data at a resolution from 4 to 10 A,
making use o
I would try the following approach, some of
which you may have done already:
Broad pH screen, by 0.5 pH units to see if you are in the pH
sweet spot.
Finer PEG-4000 screen at the pH identified in the pH
screen--the precipitate in the we
Does anyone have practical experience
crystallizing low solubility proteins from solutions containing
significant (10-20%) glycerol? We can get small crystals by mixing
4:1 ratios of protein to well solution, but the drops do not
concentrate back to the well solu
Hi Rui,
I would try the additive screen.
http://hamptonresearch.com/product_detail.aspx?cid=1&sid=36&pid=27
Best Regards,
Georg
rui schrieb:
Hi, All,
I'm trying to crystallize a soluble protein and got something like
granular, they are rounded shaped and not so regular and also don't
have
Hi Kornelius,
A possible solution at this resolution would be to use Arcimboldo which
localizes model fragments such as small helices with Phaser and then does
density modification with SHELXE. See:
Nature Methods 6:651-3. "Crystallographic ab initio protein structure
solution below atomic resolu
Hi, Did you use detergent? It seems look like detergent crystals.
2010-08-25
yybbll
发件人： rui
发送时间： 2010-08-25 20:37:18
收件人： CCP4BB
抄送：
主题： [ccp4bb] turn granular to crystal
Hi, All,
I'm trying to crystallize a soluble protein and got something like granular,
they are rounded sha
Dear all,
I'm trying using Jligand for generating a new ligand describition. Have to
say I'm using it for the first time, but so far it look very nice.
I trying to optimize a new lib file for a modified NAD molecule.
I'm using a nad_ebi.cif file of NAD supplied by Garib a while ago which
works fi
Hello Kornelius,
In 2 or 3 cases I successfully used a homology model for molecular
replacement using a model generated from the PHYRE server
http://www.sbg.bio.ic.ac.uk/~phyre/.
I know it is not the same as ROSETTA but if there is some sequence homology
you might be lucky...
Best regards
Eike
Hello,
I know at least the following papers on this topic:
---
"High resolution protein structure prediction and the crystallographic
phase problem"
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2504711/
"Prospects for de novo phasing with de novo protein models"
http://www.ncbi.nlm.nih.gov/pmc/
Dear all,
I was wondering if anybody has used the ROSETTA software to generate a MR model
that could subsequently being used successfully for a MR solution case.
The sequence of the protein we work with is relatively small, ~ 85 residues.
Crystallization is not very reproducible. Resolution is
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