ication of sites that
are most suitable for mutation designed to enhance crystallizability.
Methylation is probably more invasive.
--
Tim Schulte
Ruhr-Universität Bochum
LS Biophysik
AG Proteinkristallographie
Universitätsstr. 150
44780 Bochum
Germany
Tel. +49-234-32-25754
ctoral Fellow,
> Department of Biophysics,
> Johns Hopkins University,
> Baltimore,
> MD21218
Maybe Dowser can do the job for you.
http://www.ks.uiuc.edu/Research/vmd/plugins/dowser/
--
Tim Schulte
Ruhr-Universität Bochum
LS Biophysik
AG Proteinkristallographie
Universitätsstr. 150
44780 Bochum
Germany
Tel. +49-234-32-25754
Hi,
You can easily test the crystals by adding a drop of "Ponceau S"
staining solution. If you have protein crystals they will get stained.
Best wishes,
Tim
yybbll wrote:
> Hi,
> A little danger this condition. I suggest you should firstly make sure
> they are protein crystals
s loop
alter 52-65/, ss='S' # assign residues 52-65 as sheet
alter 65-72/, ss='H' # assign residues 65-72 as helix
rebuild # regenerate the cartoon
Tim
--
Tim Schulte
Ruhr-Universität Bochum
LS Biophysik
AG Proteinkristallographie
Universitätsstr. 150
44780 Bochum
Germany
Tel. +49-234-32-25754
; Regards
> Rana
>
>
Hi,
you might want to try out Chimera.
http://www.cgl.ucsf.edu/chimera/
The program has a very nice function to fit maps onto each other. We
used Chimera to overlay two maps for our recent paper
http://pubs.acs.org/doi/abs/10.1021/bi802320q
Have a look on fi
Hi everybody,
Molprobity does not take into account contacts/clashes from
symmetry-related molecules, or does it?
Thanks in advance,
Tim
otein interactions calculation' server is very neat:
http://pic.mbu.iisc.ernet.in/
/Tim
On 10/03/15 11:25, Debasish Kumar Ghosh wrote:
Dear All,
Apologies for this little off-topic inquiry. I want to closely visualize the
interacting residues in an multimeric protein complex to understand the
to find a similar arrangement of histidine residues in contact with a
serine and a hydrophobic residue
figure 4A in
https://www.biorxiv.org/content/10.1101/2021.02.05.429362v1.full
hth,
tim
On 2022-11-23 11:16, Andrew Lovering wrote:
Dear CCP4 list,
I have just tried accessing the “old”
iated deposited maps/densities when interpreting deposited
structures.
Best wishes,
Tim
On 2025-03-04 00:27, Pavel Afonine wrote:
Greetings,
It's hard to disagree with this! Resolution, occupancies, and B
factors only indirectly suggest what's visible and what isn't — and
they can be
Dear Almudena,
SPOT_MAXIMUM-CENTROID is probably the keyword in XDS.INP that you want to
increase in your situation. The default is 3. Try e.g. 5, and increase slowly
to make sure that the suggested solution makes sense
Best regards,
Tim
On Friday, November 29, 2019 12:48:11 PM CET Almudena
start crystallisation trials at 70-90% of this concentration.
Best,
Tim
On Wednesday, January 8, 2020 5:16:31 PM CET Armando Albert wrote:
> Dear all,
> I was wondering how to guess the optimal protein concentration for the
> initial crystallisation trials. Is there any trick or assay other
Dear Jon,
in SHELX(L), you can name your atoms foo and bar, or jon and doe, if you like.
The scattering factor is derived from the number next to the name. The name is
just that, and identifier.
Best,
Tim
On Monday, February 3, 2020 9:20:03 PM CET 0c2488af9525-dmarc-
requ
s rejected, you may start to argue.
Best regards,
Tim
On Wednesday, February 5, 2020 1:48:32 PM CET Susan Lea wrote:
> ‘Role’ models are not what are needed - just a better representation of our
> community. This is lazy scheduling and in a community where there have
> always been influe
part N and part -N. In case you
deal with more than two conformations, take a look at SUMP (as Jon suggested).
The use of free variables is easier to explain right at the computer, so
please ask a colleague near you office, who is familiar with SHELXL for the
details.
Best,
Tim
On Thursday, Februa
Hi Phil,
yes, you are right. I mixed up the occupancy number with the part number.
I find these things easier in front of the res-file.
Thanks a lot for correcting this.
Best,
Tim
On Thursday, February 6, 2020 10:26:51 PM CET Phil Jeffrey wrote:
> That doesn't sound right re: PART
ake a look
at the crystallographic map itself in order to understand.
EM is totally different from crystallography, and why would one mix concepts
between the fields?
Best,
Tim
On Thursday, February 13, 2020 12:07:15 AM CET Marin van Heel wrote:
> Hi Tim,
> Good to hear from you! No longe
its job across ssh, hence you
only need the appropriate network connections.
XDS wouldn't run on Raspberry Pi, although it may not be difficult to port.
Best,
Tim
On Tuesday, February 18, 2020 8:48:17 PM CET Ana Carolina de Mattos Zeri
wrote:
> Dear all
> we have asked this of a few
ibution to
the diffraction data is in the low resolution data.
Best,
Tim
On Sunday, March 1, 2020 9:26:29 AM CET Dale Tronrud wrote:
> Dear Ethan,
>
>To move away from an abstract discussion of hydrogen atoms I'd like
> to describe a concrete example. In 2008 I d
n (>4).
Best,
Tim
On Friday, March 6, 2020 2:36:01 PM CET M T wrote:
> Dear BBers,
>
> I am trying to refine a structure using COOT and Refmac5 and I have some
> concerns about overrefinement and x-ray term weight in Refmac5, based on
> the fact that during refinement to let R facto
Dear all,
the arpnavigator can display the contour levels of a map ("map style plane").
Does anyone know how to change the orientation of the plane, i.e. the normal
of the cutting plane?
Best regards,
Tim
--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of
Dear Gerard,
you are wrong. 'he' in this context has as much information as 'someone' and
'person'. It does not refer to the sex of the person spoken about.
Best regards,
Tim
On Wednesday, March 11, 2020 4:44:47 PM CET Gerard DVD Kleywegt wrote:
> >>>
Dear Jurgen,
https://lmgtfy.com/?q=ccp4+twitter
do you need more?
Best,
Tim
On Wednesday, April 1, 2020 5:19:13 PM CEST Jurgen Bosch wrote:
> #theBB is too slow :-), Honestly, we probably should have an official CCP4BB
> Twitter account monitored by a few administrators to post relevant
Dear Bernhard,
your paper is actually not so much of a joke. Are you aware of K. Huemmer's
and E. Weckert's three-beam experiments? See e.g.
https://link.springer.com/chapter/10.1007/978-1-4615-5879-8_24
Best regards,
Tim
On Wednesday, April 1, 2020 4:00:19 AM CEST Bernhard Rupp w
ms in Coot would come very handy ;-)
Best,
Tim
On Fri, 24 Apr 2020 13:08:26 +0200
"Fred. Vellieux" wrote:
> Hi folks,
>
> Some of you may have had to do this already. Either in the lab or
> more recently perhaps from home.
>
> I have two structures that I wis
But maybe there are other ways that won't require gloves?
Best regards,
Tim
--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna
Phone: +43-1-4277-70202
GPG Key ID
useful for fume hoods,
but for most places, door handles and other curved surfaces are
probably much more the infecting parts, while they escape the UV light.
And vira are transported in water droplets, which are larger than 1um.
Best,
Tim
On Tue, 5 May 2020 17:19:56 -0700
James Holton wrote
I now.
Best regards,
Tim
On Thu, 7 May 2020 17:18:38 +
"Roversi, Pietro (Dr.)" wrote:
> Thank you Ethan for taking the the time to answer and explain.
> Yes I am sure I have asked a vague and imprecise question.
>
> Practically, I am going to point to xia2 for data pro
ately, the article itself is not there
Extinction is not the same as the dynamic effects that James mentioned,
but this seems the closest match.
Would anyone have a copy they can share with me?
Thanks a lot!
Best,
Tim
On Thu, 28 May 2020 15:43:00 +
Edward Snell wrote:
> This jogged m
7;off the shelf' is it was put, and such powders are not
amorphous (if you read bioarxiv) or 'simingly amorphous' (if you read
the peer-reviewed version)...
Scotch is not the same as adhesive tape, and pampers is not the same as
diapers (c.f. also Gerard Bricogne's post on this
Hi Clemens,
You can download a build for Debian (testing) from
https://homepage.univie.ac.at/tim.gruene/coot_deb/bullseye/binaries/stable/
it is not the latest, but a post-0.9-release version.
I'll update it from time to time with a more recent build.
Best,
Tim
On Thu, 4 Jun 2020 15:
Dear Kahkashan,
check out the Calculate->Modules... menu.
Best,
Tim
On Thu, 11 Jun 2020 17:56:11 +0530
Firdous Tarique wrote:
> Hi
>
> Just downloaded the new CCP4-7.1. Wondering where the extension bar
> in Coot 0.9 has gone. Please help me to find it. I think it is hid
Dear Kelvin,
the command 'ls $CBIN' lists the majority of CCP4 programs on your
system. This probably even works under Windows 10, since the powershell
acts like a linux/unix shell.
Best regards,
Tim
On Tue, 7 Jul 2020 16:00:18 +
Lau Kelvin wrote:
> Ah I see! Great I can ru
ance. DIALS can produce plots for the correlation between refined
parameters, which is very handy for electron diffraction data.
Best wishes,
Tim
On Thu, 16 Jul 2020
08:20:11 -0700 Jessica Bruhn
<450e5de75376-dmarc-requ...@jiscmail.ac.uk> wrote:
> As someone working with continuous rotat
the older instruments), and because I do not work with a parallel
beam, but focus the beam onto the detector surface. This is not a very
reproducible process. In those cases where I got high resolution data,
the cell is often quite stable, and the distance can vary by about 5%...
Best regards,
Tim
, the anomalous signal in ED is actually stronger than in X-ray
crystallography. As far as I know, this has not been pursued further.
Best wishes,
Tim
P.S.: This is a response to your email to Jessica Bruhns in the thread
'quote source inquiry'. This thread has reached an overflow, so
ynamic refinement. I also
understand that dynamic refinement is quite time consuming. Lukas is
working on this, though.
Best wishes,
Tim
On Mon, 20 Jul 2020 10:36:49 +
"Schreuder, Herman /DE" wrote:
> Hi Tim,
>
> thank you for your reply. The 1998 Schenk paper is
might give you a clue where the problem is.
Best regards,
Tim
On Thu, 30 Jul 2020 14:05:54 +0200
Rafal Dolot wrote:
> Dear all,
>
> Thank you for the response. I will try to explain it more precisely.
>
> The molecule of interest is a duplex with 9 nt length, but is paired
>
Dear David,
Kay Diederich's generate_XDS.INP
https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_XDS.INP
creates the full XDS.INP for you for a large number of frame formats.
It is not CCP4, but I think there are no restrictions for using it.
Best regards,
Tim
On Fri, 2
Hi Joana,
unless you are constrained to a molprobity tool, you could use the CCP4
program ANGLES to list the omega angle for each residue. See
$CEXAM/unix/runnable/angles.exam
for an example.
Best,
Tim
On Fri, 4 Sep 2020 11:28:47 +0200
Joana Pereira wrote:
> Dear all,
>
> Does an
ed to.
That's how I interpret Paul's statement
"[...] many people learnt (I discovered, rather late in the day) [...]"
Has anyone of the disappointed users asked how to do it properly? Maybe
it is just as easy.
Cheers,
Tim
On Wed, 9 Sep 2020 17:22:27 +0200
Georg Zocher wrote:
>
,
Tim
On Wed, 9 Sep 2020 20:27:55
+ "Schulz, Eike-Christian" wrote:
> Hi Tim,
>
> I don't think that metaphor is quite correct. To me it seems that no
> matter what button you pushed you got coffee. In my opinion intuitive
> software is a blessing and sh
version of the meeting will be made available the following week.
Thank You,
Tim Sweeney
MiTeGen
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB
Dear Doo Nam Kim,
the indexing procedure is independent of the starting angle of the
first frame.
Are you possibly looking for the OSCILLATION_WIDTH=, i.e. the degree
per frame during data collection?
Best regards,
Tim
On Thu, 8 Oct 2020 09:28:07 +0100
Doo Nam Kim <4e720d49e642-dmarc-r
), it does not take very long.
Wenn you plot the LLgain, listed at the end of the refmac log-file, and
its curve flattens out, your Rfree reflections should be independent
and not model-biased anymore.
Best regards,
Tim
On Wed, 4 Nov 2020 13:18:06 +
Nika Žibrat wrote:
> Hello,
>
>
Dear Paulina,
you can find plenty of names of experts on electron powder
diffraction at this announcement of the ePDF workshop,
https://www.uni-ulm.de/einrichtungen/hrem/epdf/epdf/, organised by
Tatiana Gorelik.
They can probably answer your question
Best regards,
Tim
On Thu, 12 Nov 2020 08
he past 20
years. I am surprise Mitegen found a market for their 'resuable' bases.
Best,
Tim
On Sun, 15 Nov 2020 15:45:01 -0500
Patrick Loll wrote:
> Hi everyone,
>
> I’ve become very fond of the Mitegen reusable bases for mounting
> crystals, since the reusable aspect savse
the registration at the
workshop URL
https://www.uni-ulm.de/en/einrichtungen/hrem/christmas-elec-crystall/christmas-elec-crystall/
The workshop program will soon be available.
Best regards,
TG on behalf of Tatiana Gorelik, Mauro Gemmi, Lukas Palatinus, and
Stephanie Kodjikian
--
--
Tim Gruene
k might be related:
https://github.com/microsoft/WSL/issues/4694
Cheers,
Tim
On Mon, 7 Dec 2020 13:50:23 +0100
Johannes Cramer wrote:
> Dear board,
>
> has anyone gotten ccp4 (specifically shelx and arpwarp) installed and
> working under wsl2 (windows subsystem for linux)?
> arp
Dear Gottfried,
you can compile from source, http://www.ccp4.ac.uk/download/#os=src
and/or spend 150-200Euro for a new computer.
Best,
Tim
On Thu, 10 Dec 2020 12:07:17 +0100
"Palm, Gottfried" wrote:
> Dear all,
>
> I am running into a "known issue"
works greatly.
Best,
Tim
On Mon, 4 Jan 2021 11:10:34 +0100 Andreas Förster
wrote:
> Dear Graeme, all,
>
> to make it easier for Rigaku Oxford Diffraction's CrysAlisPro to
> process EIGER and EIGER2 data collected at the synchrotron, Herbert
> Bernstein created a Windows in
I remember correctly, pointless also offers reindexing.
Cheers, Tim
On 08/26/2011 05:55 PM, Gregory Bowman wrote:
> Hi all,
>
>
> We have several primitive monoclinic datasets for the same protein with
> various ligands, with essentially the same unit cell parameters. We would
s part of the validation process.
Tim
> shortly after) your coordinates (and SF's!) are in the PDB database, your
> structure will be available through the EDS website to whoever is interested.
>
> Cheers,
>
> Boaz
>
> /Boaz Shaanan, Ph.D.
> Dept. of Life Scie
ligand is disordered or not.
Cheers,
Tim
On 09/13/2011 09:01 PM, Francis E Reyes wrote:
> Hi all
>
> Suppose you have a high resolution xtal structure (from usual x-ray
> diffraction) and you wanted to verify the location of a ligand. You can
> purchase a heavy atom isotope ver
are going at, refinement might ruin the
good model if you use inappropriate settings, causing Rfree to go up.
Cheers, Tim
On 09/14/2011 04:34 PM, Md Shaik wrote:
> Dear ccp4,
>
> I am refining one structure at low resolution (3.5 A). I solved the
> structure in space group P622
allisation trials
at 7mg/ml.
Tim
On 09/21/2011 05:57 AM, Obayed Ullah wrote:
> Hi all
>
> I am working with a human protein (not membrane protein) which is forming gel
> at higher concentration. I am not able to concentrate the protein even more
> than 7 mg/ml. It become like jelly
aliased to `pushd $CCP4>/dev/null'
I suppose you mean 'ccp4i' instead in order to start the CCP4 interface.
About the python:
What is the output of the command
stat /opt/CCP4/Python-2.6.7/bin/python
Maybe you do not have executable permission.
Tim
On 09/23/2011 12:29 AM, Jo
which you recognise as alpha-helix or beta-strand and
simply ask your model building program of choice to "place a helix here"
which you can incorporate into your model or at least use as a guideline
for correcting yours.
Tim
On 09/22/2011 10:18 PM, Pete Meyer wrote:
> I've n
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hello Franck,
maybe you could tell us what you are actually struggling with? Do the
programs not recognise the space group? Does IDXREF.LP report any problems?
Tim
On 09/27/2011 03:38 PM, Franck wrote:
> Dear all,
> i'm strugglin
.
Cheers,
Tim
On 09/30/2011 09:01 AM, Yuri Pompeu wrote:
> Hello everyone,
> I am refining a structure to 2.4A with 2-fold NCS and twinned.
> Maps look ok and Rfree is 0.27however as I start checking my validations I
> notice that after refinemnt
> my geomtry gets sign
n there is no need to either ;-). I
> use both Ubuntu and Mac with OO.
>
> Adam
>
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.11 (GNU/Linu
;t win 'em all.
Cheers,
Tim
Design Parameters to Control Synthetic Gene Expression in Escherichia coli
Welch et al, PlosONE 2009
Medizinische Hochschule Hannover
Zelluläre Chemie, OE 4330
Zentrum Biochemie
Carl-Neubergstr. 1
30625 Hannover
-Original Message-
From: CCP4 bulletin
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On 10/06/2011 06:54 AM, Ashley Buckle wrote:
> [...]
> Sent from my iPhone
How appropriate ;-)
> [...]
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID =
ect.
This should be easier than fiddling around with ellipses and rectangles
since rectangles are usually parallel to the detector edges, but your
beamstop shadow is not.
Cheers, Tim
On 10/09/2011 04:24 AM, Francis E Reyes wrote:
> I already started with an ellipse... should I extend with a r
- N) refls, then
> filling in F_estimate for those N refls by back-transforming the map?
> Sort of like phase extension, except generating new Fs rather than new phases?
Some people call this the "free-lunch-algorithm" ;-)
Tim
> Ethan
> [...]
- --
- --
Dr Tim Gruene
Ins
order to find out the
B-factors of some coordinates in the PDB file, you can open the file
with any text editor of your choice and look at its entries.
Best wishes,
Tim
On 10/12/2011 01:53 PM, 王瑞 wrote:
> Dear Everybody,
>
> I am sorry for a little off-topic. Could anyone tell
. Berry wrote:
> Tim Gruene wrote:
>> -BEGIN PGP SIGNED MESSAGE-
>> Hash: SHA1
>>
>>
>> On 10/11/2011 09:58 PM, Ethan Merritt wrote:
>>> On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote:
>>>> In the limit yes. however limit
onate 1000Euro to the 1000 clubs with the most votes, and
I would appreciate your support.
Mens sana in corpore sano,
Tim
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.10 (GNU/
during refinement which will destabilise the refinement.
Tim
On 10/13/2011 01:14 PM, 王瑞 wrote:
> hello everyone:
>
> Excuse me, could anyone give me some suggestions? Afetr several cycles
> of refmac, it give me such a result:
>I
ome obsolete I would
appreciate some clarification on the required number of flagged
reflection, but until then I will keep on flagging 500-1000 reflections,
rather than 5%.
Tim
On 10/15/2011 10:48 AM, Nicholas M Glykos wrote:
>>> For structures with a small number of reflections, the statistical
around line 231 in $CBIN/include/ccp4.setup
My python binary is /usr/bin/python, and I have used buccaneer without
errors.
Tim
On 10/17/2011 09:30 PM, Frank von Delft wrote:
> Hi, we got around to switching to ccp4 version 6.2.0, but now buccaneer
> fails from the GUI. Below is what shows up
list counting from 0 rather
than 1 and swap the two items, because C was developed since Fortran did
not match the requirements to develop an OS like UNIX.
Tim
On 10/18/2011 10:58 AM, Miguel Ortiz Lombardía wrote:
> Hi community,
>
> I have been waiting for someone more knowledgeable
from to see what python is doing ('man python').
Tim
On 10/18/2011 11:34 AM, Frank von Delft wrote:
> Mine reads:
> /usr/local/ccp4/6.2.0/ccp4-6.2.0/share/python:/usr/local/ccpnmr/ccpnmr1.0/python
>
>
> That should work, right? Where else can I look, for the fai
the newly created chain ID (Calculate->Change Chain ID...)
Tim
On 10/19/2011 01:20 PM, Leonid Sazanov wrote:
> Hi,
> If I have two somewhat different overlayed models, is it possible in
> COOT to replace part of one model by another?
> Similarly to O command: merge_atoms residue_end>
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hi Jacob,
to semi-answer your question: coot runs under windows, as far as I know,
but it may not be in the gui.
Tim
On 10/19/2011 08:41 PM, Jacob Keller wrote:
> Well, I see that it fixes/edits waters, but it seems to add them too,
> accord
-BEGIN PGP SIGNED MESSAGE-
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Dear Claude,
why do you expect stereo to work with a laptop? Usually it requires
special equipment, e.g. a shutter system or polarizing screen and
goggles, like the Zalman 3D monitors.
Maybe you want to let us know more about your setup.
Tim
On 10
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Grand - with every python script one has to distribute a specific python
version. More food for my prejudice against python ;-)
Tim
On 10/26/2011 12:15 AM, Paul Emsley wrote:
> FYI, from version 0.7, I will not distribute binaries without pyt
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Good luck - I registered with Bruker one or two years ago and have not
heard a reply since ...
Tim
On 10/26/2011 09:32 AM, Pedro M. Matias wrote:
> You need to register at their site first, I suppose. Have you tried to
> ask them for the so
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear list,
I just re-registered at
http://www.brukersupport.com/Login.aspx?ReturnUrl=%2fdefault.aspx, and
supported by a notifying email to Martin Adam
(martin.a...@bruker-axs.de) the registration succeeded within a couple
of minutes.
Tim
On 10/26
ng data at room temperature?
Hope this list contains some new ideas.
Best wishes,
Tim
On 10/26/2011 06:46 PM, Leonard Thomas wrote:
> Hi All,
>
> I have run into a very sensitive crystals system when it comes to cryo
> protecting them. I have run through the usual suspects and t
-BEGIN PGP SIGNED MESSAGE-
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Dear Jiyuan Ke,
the SSBOND
(http://www.ccp4.ac.uk/html/refmac5/files/coordinates.html#pdb_ssbond)
does allow symmetry related molecules, so it seems that is the header
entry you are looking for.
Tim
On 10/27/2011 03:56 PM, Ke, Jiyuan wrote:
> D
for a well refined structure), your resolution might not be 1.24A,
i.e., you may have integrated noise (check I/sigI over resolution shells).
Tim
P.S.: I wonder what power somebody might have to _force_ you use a
specific software version...
On 10/28/2011 03:48 AM, Kenneth A. Satyshur wrote:
&g
solves your question:
You should always use the same file as input, i.e., should never have
used anything but the original mtz from scala...?
Tim
> [...]
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE
ata if the SHEL card is left at its default (10 0.1).
Cheers,
Tim
P.S.: "obvious" can be just a dangerous word as "trivial"...
On 10/27/2011 09:31 PM, Ian Tickle wrote:
> Hi, currently Refmac writes the wrong info for the low resolution
> cutoff, for example:
>
>
rk to delete them all?
Tim
On 10/28/2011 03:48 AM, Kenneth A. Satyshur wrote:
> Has anyone had problems with Refmac 5.6? I tried refining our stucture at
> 1.24 A,
> aniso with H in riding position and it just exploded! I get error in
> distances such as
>
>
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Sorry, "should NOT appear in the list of deviations", of course!
- Original Message
Subject: Re: [ccp4bb] refmac 5.6 ccp4 6.2.0
Date: Fri, 28 Oct 2011 17:39:06 +0200
From: Tim Gruene
Reply-To: Tim Gruene
To: CCP4BB@JISC
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Zhang Qi,
I like this url: http://www.lmgtfy.com/?q=topology+diagram+protein
which quickly takes you to e.g. pdbsum.
Tim
On 11/03/2011 01:48 PM, lysudiezhang1985 wrote:
> Dear all
>
> Does anyone know what tools can get a topolog
isual" people) than
looking at figures and statistics.
The phs-files can be loaded into coot after loading the .hat-files also
created by shelxe (if coot crashes when you load the hat-file, edit it
and remove everything below the first occurrence of the word "END").
Tim
On 11/11/2011 1
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Hi Paul,
I just checked and did notice that coot (version 0.6.2) does not crash
anymore in the presence of two 'END' cards in the .hat-file.
I am sorry for mis-blaming coot.
Cheers,
Tim
On 11/14/2011 04:39 PM, Paul Emsley wrote:
> O
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Hi Ed,
you can probably set hklout to /dev/null in order to not produce the
output mtz-file, but this would not prevent refmac5 from doing the
calculations.
Tim
On 11/17/2011 06:44 AM, Ed Pozharski wrote:
> Is there some way to make refmac *not*
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Dear all, dear Phil,
how can a dataset be merged if the space group is unknown? Does
pointless require the Friedel pairs present in the file, too?
Tim
On 11/17/2011 08:34 AM, Graeme Winter wrote:
> Dear Ping,
>
> You need the unmerged
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Dear Eleanor,
Sorry, but I don't see how your comment answers any of my two questions.
Tim
On 11/17/2011 12:10 PM, Eleanor Dodson wrote:
> Aaagh - you merge the POINT group!
> Not the spacegroup...
>
>
> Eleanor
>
>
ether this will prevent the last error to occur, but
since you can run other graphical programs there is a fair chance.
Cheers,
Tim
On 11/19/2011 05:53 PM, Rajesh kumar wrote:
>
> Dear All,
>
> I have connected to unix server of the lab through ssh/xming/x11. I can run
> open
means that this solution and the one from MR are
equivalent (because of the freedom of choice for the origin some space
groups allow you).
Tim
On 11/20/2011 06:42 AM, Napoleão Valadares wrote:
> Hello,
> I'm observing a very strange phenomena (at least to me, I'm a beginner).
>
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Dear Wei,
you could use coot "Calculate->Model/Fit/Refine->Simple Mutate" also for
nucleic acids.
It may be worth running geometry idealisation in coot or refmac5 before
using the model in MR.
Tim
On 11/19/2011 09:44 PM, Wei Shi
the possible existence of
X11-clients, but I would think that most suggestions to you assumed that
your client computer was also a linux-machine.
Cheers,
Tim
On 11/22/2011 02:27 PM, Rajesh kumar wrote:
>
> I don't know if I need that installed on my windows computer terminal.On the
&g
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Dear Jacob,
Coot prints this information to the terminal, so you can start coot and
'tee' its output into a file.
Tim
On 11/28/2011 11:53 PM, Jacob Keller wrote:
> Let me refine my question (sorry for my lack of clarity): is there a
&
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Hello Saugata,
if you want coot to refine the bond length, you have to rename the
residue to some name coot does not yet understand and create a cif-file
which includes the restraints of the residue, the ligand, and the bond
between the two.
Tim
On
oning your protein with that N-terminal part chopped
off - there is a fair chance that the product is more stable and hence
diffracts much better than 3.2A.
Regards,
Tim
On 12/08/2011 07:47 AM, atul kumar wrote:
> Dear all
>
> I have crytals which diffract up to 3.2 A at synchrotron, I a
seems quite unlikely, but that's what might explain this
great gap between R and Rfree.
Tim
On 12/08/2011 06:36 PM, Christopher Browning wrote:
> Dear All,
>
> Question: Has anybody ever refined the same structure using PHENIX and
> then tried REFMAC to see what happens?
>
&g
- - surely several more.
When a well tested program does something unexpected, it is usually the
user and not the program which misbehaves...
The optimisation of the weighting scheme is based on the geometry of the
model and not one the gap between R and Rfree.
Cheers, Tim
On 12/08/2011 08:43 PM, Petr
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