I would agree with Mark.
It would be also good to state that neither of us is cross-trained, but are
one-trick dogs as far as NMR vs X-rays goes.
Still, I think that if you get any protein in good amounts, try to crystallize
it (there are even good facilities for that these days,
and funding
Dear all,
In a bit more than a year from now, we will be running the Gordon Research
Conference on Diffraction Methods in Structural Biology,
this time preceded for the first time by a two-day Gordon Research Seminar,
exclusively for young scientists and a few mentors.
I could not resist but comment at the end ... (sorry for cleaning up the thread
text)
I agree with Roberto that the system is actually not that bad when you think of
it. Or, it could be much worse.
In my experience, the editors of many journals - professional or academic - try
very hard, and
On 20 Nov 2013, at 21:56, Dhanasekaran Varudharasu wrote:
Dear Crystallographers,
I dialysed a 30 kDa protein
(Recombinant protein which was eluted by 20 mM Tris, 500 mM NaCl, 120 mM
imidazole) against water for overnight. But it gets precipitated
It is an interesting observation, Tim.
The fact that people do not read tutorials or manuals, is somewhat related to
the fact
that many questions asked in the ccp4bb could be answered by a more experienced
colleague,
a supervisor, a manual, a wiki, St Google the revealer, not to mention the
Dear all,
The biannual Gordon Research Conference in Structural Biology, accompanied by
the first Gordon Research Seminar, will take place in the last week of July at
Bates College, New England, a few hours drive from the IUCr meeting that
follows in the first week of August.
The theme for
Dear Hongshi -
I cant help but to first suggest that as this is the CCP4bb, the first thing
you should try is using CCP4mg, if you want to make pretty pictures.
If you just want to look at the map and work with it, you should use Coot.
If still for some reason you want to use Pymol, you should
Dear all,
We are getting closer and closer to the 2014 edition of my favorite Gordon
Research Conference
(https://www.grc.org/programs.aspx?year=2014program=diffrac ) on Diffraction
Methods in Structural Biology Faster, Smaller, Better: Novel Technologies for
Diffraction Experiments in
Dear all,
Unfortunately something went wrong in email archiving, and I recall receiving
more applications from specific people, than what are now in my mailbox. May I
kindly ask the people that did send an application, to re-send me their PDF
file by reply to this email?
Sorry again to
Dear all,
As I did give the full promotional message for why these are just outstanding
meetings to attend, I will only invite you to
look at the latest programs
GRC (http://www.grc.org/programs.aspx?id=11654)
GRS (http://www.grc.org/programs.aspx?year=2014program=grs_diff).
Dear all,
I am sorry to send one more post to the already overloaded bb, but please let
me remind you for the last time that the deadline for applications for the GRC
and the GRS is approaching, and is only three days from now.
http://www.grc.org/programs.aspx?id=11654
We are all looking
If you main point is dimer vs monomer, Guinier plots is in fact all you would
need, in my opinion according to what I have read so far...
A.
On 17 Jun 2012, at 13:01, David Briggs wrote:
Dear Xun,
Regarding your monomer vs dimer, theoretical vs observed crysol plots
- yes - they are
Just to add in the controversy, with a somewhat related issue:
Current crystallographic ethic presumes that a structure is deposited just
before
the submission of the paper. In a survey we did, we found that while
in one journal only 2% of structures are deposited after the paper submission
I am saying! 2% is good, 50% is bad.
(btw, the 'worse' is close to 70% - any guesses?)
A.
Or are you saying only 2% of structures are deposited in that journal ?
Jürgen
On Oct 18, 2012, at 3:24 PM, Anastassis Perrakis wrote:
Just to add in the controversy, with a somewhat related issue
talking semantics, kruos (Κρυος), means just cold, not icy cold.
Cold in Greece is not nearly icy. Unlike the Netherlands ... it only gets cold
when its really icy ;-)
Tassos
On 15 Nov 2012, at 19:45, Ethan Merritt wrote:
From Greek kruos, icy cold
I think the real challenge (and one that makes for an excellent
macromolecular crystallographer) is how well one can interpret a map with
poor phases.
Let me disagree ... An excellent macromolecular crystallographer, is one that
given some crystals can derive the best strategy to collect
Post-doctoral positions are available in the Netherlands Cancer Institute in
the groups of Anastassis (Tassos) Perrakis and Titia Sixma (http://xtal.nki.nl).
The Netherlands Cancer Institute (http://www.nki.nl) is a center of excellence
with a high standard of biological research and an
I am of the opinion that the truth lies somewhere in between ...
Here are my two cents based on personal experience ...
For example, I am happy myself using a MacBook Pro, which is sufficient for all
my activities, and has all software and data that I need.
Thus, I am myself on the 'new'
Indeed there are many web tools predicting solubility.
My personal bias is that your brain is the best tool for ideas on how to design
expression constructs.
(since one question in a multi-domain protein, is which bit is interesting ...!)
Many brains are better than one (talk to your colleagues
We did work with a full blown OSX Server in 2004 - indeed many issues on NFS
were Ok, but NIS was a problem - or we could not figure it out.
We used it as server for developers, running X-grid, SVN, WebObjects servers
for a couple of EC networks, but never deployed it fully
as a
We have suffered from that a lot at the NKI a few years back.
What worked for us was a combination of strategies, that were all mentioned
before but I will repeat:
1. Buy T1 phage-resistant strains, and also use an old incubator (and luckily
an old building
that was available at the time) to
On 9 Mar 2013, at 12:11, Jon Agirre wrote:
Espript will do. http://espript.ibcp.fr
Well, if you want a topology diagram, espipt will not do. Brilliant as it may
be, it will annotate the topology linearly on top of a set of aligned sequences
(and more!).
As for a topology diagram, I
to the
description. Seems to be just what I've been looking for. Thanks, Partha!
Anastassis Perrakis wrote:
On 9 Mar 2013, at 12:11, Jon Agirre wrote:
Espript will do. http://espript.ibcp.fr
Well, if you want a topology diagram, espipt will not do. Brilliant as it may
be, it will annotate
And indeed this experiment was done properly ... in a suit and tie!
http://www.embl-hamburg.de/aboutus/general_information/HH_about/history/HH-holmes.jpg
A.
PS The journal is indeed a bit obscure ...
On 13 Mar 2013, at 20:22, DUMAS Philippe (UDS) wrote:
Jean Witz (now deceased) once told
It might be worth to consider the question more in detail.
Do you want to study thermodynamics of the interaction, or a KD would do? If
the former, you need ITC. If the latter, and you want to study things at the
level of KD only, maybe investing on a plate reader, thermophoresis, or some
Dear all,
Let me start by apologizing for finally making this email longer than I
intended - I did not have the time to make it shorter.
I must say I am humbled by the amount of positive energy and constructive
thinking that Bill has. That must explain also how he manages to keep up a
Hi -
You can use Xia2
or, you can use Pointless (Find or Match Laue group) to combine the two
datasets after Mosflm in one MTZ with common correct origin etc,
and then use SCALA to scale them together.
For more info:
I would be tempted to say that you don't need to combine; with 1.7 A
data, refinement should do it with no trouble.
And, yes, of course ARP/wARP (7.0) would be the best way to do it ;-)
If you want to combine though, I use the molrep phases to get all
heavy atoms
in an anomalous fourier map,
Hi Tracy -
Thats actually a warning message (sorry to use the word error
there ...) and it should not stop the program from running.
I believe, you dont have to take any action.
If the procedure however stops indeed, please send us detailed log
files and more complete output to try and
Since I was reading it this afternoon again, I cant help but suggest
to all refinement newbies and more experienced 'refiners' my favorite
read:
Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2156-68.
Epub 2004 Nov 26.
Introduction to macromolecular refinement.
Tronrud DE.
Hi -
Its not clear to me if the 2.3 A dataset is from a different crystal,
if it has the same space group as the 2.7 A dataset and if it is
isomorphous, and how the 'jump' from the 2.7 A dataset to the 2.3 A
dataset has been done. I can think of quite a few ways to do that
transition,
Kay - disagreeing once was enough ... so:
I share your thoughts about the wiki !
However, the dynamics of Wikipedia are an interesting issue and
relate to 'vandalism'.
Being a small contributor to the Greek Wiki, which has far less
subscribers than the English one,
I can see that the
Hi -
On 28 Jul 2007, at 13:59, Karthikeyan S. wrote:
Dear CCP4BB members,
I am using the loop building module of new arp/warp 7.0 version in
RHEL. I
am sure during installation everthing went well. But when I try to
run the
program the following error occured. I think the problem is
On Aug 9, 2007, at 15:02, Tommi Kajander wrote:
so, a) WHAT IS GAMMA??
gamma is possibly the letter of the greek alphabet that has had most
abuse from scientists.
http://en.wikipedia.org/wiki/Gamma_%28disambiguation%29
seriously now, I have seen that as well, but never increasing to such
On 10 Aug 2007, at 18:59, Pavel Afonine wrote:
Hi Mike,
the best is to do both in a loop:
for cycle in cycles:
- do real space refinement;
- do reciprocal space refinement
Well - thats what we all do - right ?
The real space refinement can be done either with the tools from
Chapman at
On 10 Aug 2007, at 20:12, Pavel Afonine wrote:
Anastassis Perrakis wrote:
On 10 Aug 2007, at 18:59, Pavel Afonine wrote:
Hi Mike,
the best is to do both in a loop:
for cycle in cycles:
- do real space refinement;
- do reciprocal space refinement
Well - thats what we all do - right
On Aug 16, 2007, at 15:22, Randy J. Read wrote:
Raw images are probably even harder to simulate convincingly.
If i was to fabricate a structure, I would get first 'Fobs', then
expand, then get the images
(I am sure one can hack 'strategy' or 'predict' or even 'mosflm' to
tell you in
On Aug 17, 2007, at 8:36, George M. Sheldrick wrote:
Dominika is entirely correct, the F and (especially) sigma(F) values
are clearly inconsistent with my naive suggestion that columns could
have been swapped accidentally in an mtz file.
Since the sigma(f) issue has been raised, let me
... all these are correct indeed - but ESI-TOF is also a nice
solution, especially coupled to an LC system.
My understanding was that MALDI-TOF is better for smaller fragments,
accuracy can be about 10 Dalton ...
for more info there is a useful short review of the use of ms
techniques for
Hi -
A quick note -
We (with Chris Ulens) have seen recently in one case that in a case
MATRIX AUTO would give 'excessive' RMSD, close to 0.030.
Checking the cell based on the projection of RMSDs to the cell axes,
a utility kindly provided by WHATCHECK,
it was suggested that the cell
Hi -
ARP/wARP only likes standard space groups, like P21212,
P22121 is not-standard ... oh well ...
(Eleanor is complaining about it for about 13 years ... but never
mind that she is right)
Just re-index your sg to be P21212 (refl. utilities, reindex, in ccp4i).
Choose 'Entering reflection
Dear all -
I am wondering if there are out there people that for one reason or
the other still use ccp4 5.0.
Could anyone that can only use ccp4 5.0 send me a personal email ?
Don't bother explaining why - just a line will do and would be helpful !
The question is related to ARP/wARP
Just to add that the R-free and R-sleep are nothing else than what is
'officially' known as 'test' set and 'validation' set.
In statistical pattern recognition for example, one would use a
'training' set to establish the 'model'; the power of the model
(in this case the 'model' can be for
Let me make three short notes:
1. If the protein does not bind in a 'normal' buffer try first under
denaturing conditions to see if everything is expressed correctly
(a repeat of Artem's suggestion basically!). Protocols for that are
in all materials manuals.
150 kD in E.coli is very very
In ARP/wARP 7.0 there is a loop building program that will build only
Rama-sensible conformations.
Its mostly structure driven and not density driven, but:
I never dared to try it at 4.5 A though.
A.
On 18 Oct 2007, at 20:55, seglynn wrote:
Dear CCP4ers,
I am attempting to build a short
Hi -
I would agree with the twining possibility - I4122 is guilty until
proven innocent ;-)
As for the SHARP idea, I don't think that SAD phasing again would
help. At 3.2 A resolution,
and if radiation damage permits, good old MAD (phased by SHARP
naturally ...) will most likely give you
Dear J.Kryst -
I am basically very puzzled to see that a 3.1 A structure has R and
Rfree of 15.3 and 23.8 % respectively !
Is that the diffraction limit of the crystal or is it a home dataset
collected with rather short exposures?
Is the Wilson B very low by any chance ?
As for the gab,
The R and Rfree after refining domain 1 are 39% and 44%. The
density is good for the existing model but disconnected in the
missing part of the structure in which I can hardly place any residue.
2) Is there any other method to improve the density of the
missing structure? I tried
against your data
- try simulated annealing
Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Tue, 23 Oct 2007, Anastassis Perrakis wrote:
Dear J.Kryst -
I am basically very puzzled to see that a 3.1 A structure has R
and Rfree
Just my two cents with a bit of a delay ...
1. I have tried the 'cheap' solution and simply lost not so much
money since it was damped to the junk yard at the end. We now have an
'expensive' solution (Crystal Farm) but - guess what - it works. Our
cheap solution was the BioTom robot, from
Dear Andrew,
Thank you for that posting; I would like to simply agree with the
Bobscript manual and your suggested practice.
I think the 'carve' commands should not be there; if you wonder why,
take a ligand, put it wherever you want in space,
set the map sigma to -0.5, display a map with
On Nov 4, 2007, at 14:23, Eric Dollins wrote:
Are you expressing a eukaryotic protein? If so, you might want to
check for rare codons. There are a number of websites where you can
put in your coding sequence and check. I recently had this issue and
it turned out to be incomplete/stalled
If I may make a general note:
I would suggest to everybody not to install anything as the 'root'
user, unless these are system utilities.
Most if not all packages can be installed under a user account, or
under another dedicated account (eg Software)
and be made available to others. This
On Nov 22, 2007, at 14:43, Kay Diederichs wrote:
Pierre Barraud schrieb:
Dear all,
I am working on a data set which is severely anisotropic, with
diffraction limits of 2.6 A along the a* and b* direction but only
3.3 A along the c* direction. I attached a screen shot of the
Anisotropic
In one case, for example, cleaving the N-terminal His-tag improved
the solubility of the protein dramatically. Interestingly,
expression levels of the protein without the His-tag were much
lower than with it!
That is also quite common ;-) Look at the second and third codons:
optimizing
On Dec 5, 2007, at 14:05, Jianghai Zhu wrote:
Hi all,
I updated refmac5.3 to refmac5.4 and found out that the reported
RMSDs are quite different from these two versions even the refining
protocols are the same.
refmac5.3
rmsBOND rmsANGLE rmsCHIRAL
0.006 0.694
I have already changed occupancies as Eleanor mentioned, and got
approximate values. But my hope is to try to get much precise ones if
possible.
I never expected to preach the 'Kleywegt Gospel' in the ccp4bb,
but in this case what you need is more accurate answers, not more
precise ones
(or
, Anastassis Perrakis wrote:
I have already changed occupancies as Eleanor mentioned, and got
approximate values. But my hope is to try to get much precise
ones if
possible.
I never expected to preach the 'Kleywegt Gospel' in the ccp4bb,
but in this case what you need is more accurate answers
I would only like to iterate a small comment I posted before:
Should the cell parameters be inaccurate, optimization of weights by
cross-validation (getting the best Rfree) will result in 'higher' RMSD.
It is easy to think about it: if in a cell is measured to be 1%
larger than in reality,
Dear all -
Under the BIOXHIT home page,
http://www.bioxhit.org
you can navigate to Section 1 or HTP Crystallization,
or simply follow the link below:
http://icarus.embl-hamburg.de/bioxhit/bioXHITSection1.jsp
It has quite a lot of data on what people use, available facilities,
and testing
More recently, I've looked at all of the crystallization robot
vendors.
For single lab users, all of the systems work well. Systems like
the Hydra
or Mosquito are less automatic, but provide the basic functions for
crystallization trial setup. For more of a user facility with a large
number
On Jan 21, 2008, at 14:08, Ian Tickle wrote:
I meant to post this response to Pietro's reply to the BB:
I agree that bugs in software are an ever-present source of annoyance,
but the only software in general use that I'm aware of that can't cope
with the conventional ITC-A settings is Arp/Warp
. So please be nice... ;)
phx.
Anastassis Perrakis wrote:
Dear all -
Sorry to intervene on a 'book keeping' issue, but indeed over the
last
few months an increasing number of people (Jerry is not the
first, so
Jerry please do not take it personally) attach pictures etc. I think
in a bb
Dear all,
May I ask you, if you had cases at low resolution (lets say at least
below 2.5 to be generous) that ARP/wARP produced a useful result for
you, to send me (... not to the list) a very short email, also
mentioning a publication that refers to that result?
Thanks in advance,
Look for an example at:
http://www.phenix-online.org/pipermail/phenixbb/2007-August/000432.html
Interestingly thats the result from the google search for
'phenix TLS groups'
http://www.google.com/search?client=safarirls=enq=phenix+TLS
+groupsie=UTF-8oe=UTF-8
A.
refinement.refine.adp {
Hi -
I don't think there is something necessarily wrong with the values
you report.
A few questions to see *if* something is wrong are:
- as you wrote to Tim you have NCS: do you use NCS restraints ?
- what is the resolution / B factor of the data ?
- have the data been checked for twining
Bottom line: thin shells are not a perfect solution, but if NCS is
present, choosing the free set randomly is *never* a better choice,
and almost always significantly worse.
hmmm ... I wonder if that is true. For low order NCS (two- three-
fold, even five-fold) I don't believe that thin
On Feb 29, 2008, at 10:29, Johan Turkenburg wrote:
Hi,
You need to firstly check that you did the map calculation
correctly, see comments below:
Sun Tang wrote:
Dear All,
In my structures, I want to assign Mn or Ca ions for some
densities. But when I did not have anomalous density in
Dear all,
We would like to announce that we are organizing two courses on:
Biophysical Characterisation of Macromolecules (20-23 May)
HTP Crystallization and Information Management (18-20 June)
Both will take place at the NKI at Amsterdam, at our brand new lab
space (we have not even moved
Hi -
I would tend to argue as follows:
An I/sigI of 3, and Rmerge of 33.6% are most definitely acceptable
values with a redundancy of 4.8. Thus, despite the 74% completeness,
that data are most definitely useful and should be included in
refinement.
A good question now is why is the
Hi -
I am sure that its not a fink problem really, but why not try the
CCP4 distribution?
http://www.ccp4.ac.uk/download/
A.
On Mar 22, 2008, at 5:34, Kurt Padilla wrote:
Hello,
When I click on 'Apply' in the Directories Project Directory
window, I get the following error:
ERROR
was successful. I don't remember the details, but
the installation did not produce an executable .app file and typing
ccp4i into Terminal didn't launch the program either.
Kurt
On Tue, Mar 25, 2008 at 10:35 AM, Anastassis Perrakis
[EMAIL PROTECTED] wrote:
Hi -
I am sure that its
James must be too fast - he better be to follow the 93,000 (or is it
more?) csh lines of code in Elves in the speed I recall he does.
So, most likely he lost less time writing it than us reading it: its
a cunning plot, he is wasting our time not his.
A.
On 1 Apr 2008, at 21:54, So Iwata
We have had good experience with the awfully simple minded approach
of using two pET vectors with different antibiotic resistance.
Its the easiest thing to do, and it often works ...
Apologies for the shameless plugin, since there are many good papers
on the subject, but you can read some
Hello all,
I have still a question about LSQKAB
Why LSQKAB gives a rmsd (or a rms xyz I don't mind) non null for
glycine side chains ?
Disclaimer: The following is just humor with the best intentions to
entertain the bb audience and not aiming to annoy anybody, but hoping
that some
I would suggest to look at the papers of Thomas Schneider that deal
with that subject.
http://www.ncbi.nlm.nih.gov/pubmed/10818348?ordinalpos=1itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum
Objective comparison of protein structures: error-scaled difference
distance
Remember that phi-psi angels are excellent for validation purposes,
but only when they are unrestrained, so if you restrain them you
lose this option.
The above is a very important point!
Having now said that, restraining alpha-helices hydrogen bonding, and
beta-sheet cross-strand
in arp/warp classic the script does not call refmac5 (the first thing
in your path) but $CBIN/refmac5 (refmac from the CBIN place)
I suspect that you still kept refmac 5.2 in the official CBIN
directory and put refmac5 in another location but earlier in your
path, so its picked up first
Dear all,
Has anyone succeeded to connect an old StereoGraphics emitter (eg
revision M) with an RS232 outlet to a more modern 3-pin DIN graphics
board such as the Nvidia FX series? If so, could you please send me
the wiring diagram for the cable ?
Thanks in advance, Tassos
Tassos
Dear Jorge,
I was unable to reproduce the error you report with 7.0.1.
I selected an MTZ file, then chose 'use' FreeR flag and I run the job.
I get:
#CCP4I VERSION CCP4Interface 1.4.4.2
#CCP4I SCRIPT LOG arp_solvent
#CCP4I DATE 29 Apr 2008 10:56:28
#CCP4I USER Tassos
...
mtz labels taken: FP
On May 6, 2008, at 18:57, Jerry McCully wrote:
Hi, All:
Thanks a lot for the prompt reply from all of you.
Probably I have another problem.
My complex was mediated by two separated interfaces between
the receptor and two subunits of the ligand.
I tried HEX
... your protein is the dream of any NMR spectroscopist. Small and
ultra-soluble.
Maybe just do the structure by NMR? It should be totally
straightforward for any NMR lab.
A.
On May 13, 2008, at 18:16, Jennifer Han-Chun Tsai wrote:
Hi,
This topic is not related to CCP4. I am having
Dear Raja,
The problem appears to be that you are not the owner of the CCP4, but
root is;
this can happen even if you are the only user. From your email it
looks CCP4 belongs to root.
There are three solutions:
1.
cd $CCP4
cd ..
sudo chown -R yourname.yourgroup
2.
for ARP/wARP
On 21 May 2008, at 7:00, yang li wrote:
Hi,
I have a structure with 3 different resolutions, 2.3A, 2.4A,
2.5A, the qualities seem normal, not good but also not too bad.
The B factors along a,b,c axis have notable difference, for example
B(a)=80, B(b)=30, B(c)=20. We used molecular
Hi-
I am afraid that the real issue might be that the real question is:
'How do I tell the referee of my paper that 1500 reflections are
enough?'
Something along the lines of a statement like:
It is generally accepted by the X-ray crystallography community that
1000-1500 are far enough
On 17 Jun 2008, at 19:56, Roger Rowlett wrote:
Sampath Natarajan wrote:
Dear All,
I am refining a structure with 2.5A resolution by
refmac5. I could find the solution by MR using molrep. After
fitting the model, I refined the structure again with 0.3
weighting term, but the
Just to add on that: I converted to OSX in 2001 when it first appeared.
Before I was Irix/Linux and -alas- the relatively happy owner of a
SONY VAIO with Windows XP.
For 8 years I remained impressed. But, 10.5 has been a massive
disappointment after being spoiled for so long,
with stable
That being said, in-line SEC-DLS-SLS etc is a much more powerful
technique, but is less straight-forward, has a larger footprint and as
has been mentioned, less-inexpensive.
Having an online SLS (or MALLS as people call it as well these days,
multi angle laser light scattering ) is indeed
Hi -
I would try SHARP; or to be exact be tempted to think less and use
autoSHARP with the description of all datasets and only give it the Se
sites for the seMet crystal. The same thing can also be done easily in
Solve. In both cases I would start with unmerged data and let these
If resolution is around 2.0 or better, ARP/wARP is particularly
powerful for such cases when model bias needs to be reduced.
For more info:
http://www.ncbi.nlm.nih.gov/pubmed/18094467?ordinalpos=1itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum
On 20 Aug 2008, at 8:11, Wim Burmeister wrote:
James Pauff a écrit :
Hello all,
I have a refined structure at 2.6 angstroms that at about 73%
completeness at this resolution. The I/sigma is about 2.0 at 2.6
angstroms, and the omit density for my ligands is great contoured
at 3.0sigma.
On 20 Aug 2008, at 18:24, James Pauff wrote:
Hello all, thank you for the responses. Just to clear up a couple
of things...
1) My dataset was acquired on a synchrotron and scaled/truncated
there. To my knowledge they used the same procedure as for other
structures that we have obtained
Dear all,
I am sure that being readers of the bulletin board you have run once
or twice across the ARP/wARP software suite - if for no other reason
reading the bug reports and the shameless promotions from my side,
recommending people to use it!
Well, there is still plenty of work to be
Since InFusion now got mentioned, I cant resist, but give my naive non-
expert overview for cloning from the experience in my lab:
1. Typical sub-cloning: Add restriction sites in your primers, make
sure you have a few additional 5' bases overhang else the enzymes will
not cut, digest then
Hi -
If you could compromise to do it outside coot you could also:
a. Use ARP/wARP Ligand Build and treat the peptide as a ligand (if
its not too big)
b. Use ARP/wARP Loops if its a missing loop (a part of a bigger
chain).
Both should also work well at 2.1 A.
Tassos
On Sep 3, 2008, at
Dear all,
After the rather unexpected positive responses on CCD over the last
few days, according to our web log and the emails we got, please note
that we got motivated to:
1. Establish a Help button that explains what the program is and is
not for, gives some general instructions
2.
Its something I have been thinking about, at the level of reading
about CUDA ;-)
I did not go even as far as 'hello world' or buying a card yet!
Awfully old fashioned.
From what I understand, GP-GPU is useful for specific problems, under
the general idea of 'stream processing'
That means
On Sep 30, 2008, at 9:56, Anshul Awasthi wrote:
Hi all the crystallographers,
I am trying to solve a structure of a protein with some inhibitor. I
want to
know how I can put in my inhibitor in the density map of the data i
got. I
can see some density in the active site where the inhibitor
Hi -
I would not use mlphare for anything marginal (to be honest not at all).
Both SHARP (use eternal pdb file in top page of the gui) and the new
Phaser (look at the doc for scripts for this case) can do what you want.
Tassos
On Nov 4, 2008, at 11:55, Thomas Edwards wrote:
Dear BB,
I
disappointed users may be more likely to respond and their
testimony might reflect out-of-date versions,
Indeed! According to the emails I get, ARP/wARP never works!
Crystal Farm - (1 response, made/distributed by Bruker AXS)
Response was unfavourable. Noted reliability and service issues.
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