Dear James,
I hope I will not disturb this thread and you will further continue with the
theoretical aspects. But, what is the motivation for such a general question?
In my crystal structures, I usually have many bonds outside the 3-sigma
interval. Especially in the case of ligands. And not
Dear Gerard,
A great remark! Thank you for starting this thread separately. I think that you
are absolutely right in many of the points. However, it also raises several
questions. Here are my favourite ones:
1) If STARANISO generally suggests "the same" resolution as PAIREF, there are
fewer
Dear Matt,
There are great responses in this thread already. There are several points and
questions from my side:
1) I did not get clearly what exactly was done. Where did you start your paired
refinement? What were the statistics for your starting resolution?
2) Did it improve all the way to
Dear Florian,
I had a similar problem in the past. The uninterpretable electron density was
mainly because of weird refinement of anisotropic ADPs. The resolution was
about 1.2 AA. The refinement was somehow divergent. Is it also your case? You
can check the ellipsoidal ADPs in Coot. Moreover,
Dear Charlie Nichols,
when optimizing your SHELX runs, SHELIXIR may help you in some cases
(https://kmlinux.fjfi.cvut.cz/~kolenpe1/shelixir).
A couple of days ago, I created quick and dirty tutorial to SHELIXIR command
line: https://www.youtube.com/watch?v=dqi5_yLhWOc and also the same quality
Dear colleagues,
We have data from a twinned crystal (merohedral twinning with fraction of 0.71)
for which we want to see the anomalous map. Could you please guide me how to
calculate it using the i2? Running refinement with REFMAC5 with merohedral
twinning does not allow simultaneous
Dear Yang Meiting,
There are few things to know better about your structures first:
1) What is the resolution of the complex structure?
2) In what stage of structure refinement you are? Rwork/free would help.
3) Have you tried some automatic DNA building tools?
I am not surprised that you can see
Dear Shine.star1609,
Your structural observation may be really different from the original one.
There are several things to do now:
1. Check whether the same interpretation could be possible in the original
structure. Are there maps or the original diffraction data? You could also
MAIL.AC.UK; Petr Kolenko
Subject: Re: [ccp4bb] criteria to set resolution limit
Hello Petr,
I would like to understand more completely your assertion in the last email
regarding completeness: "I would not care about low data completeness in case
when PAIREF shows improvement of your model.&quo
Dear Farhan,
Your dataset does not seem to be that critically anisotropic to me. But of
course, try the STARANISO server and make your own decision.
To me, the dataset seems to be collected with a suboptimal data strategy.
Although I do not know your setup, I would make the crystal-to-detector
ENIX users.
3. Short tutorial (files will be provided).
4. Discussion.
Feel free to contact us with your data.
Best regards,
Petr Kolenko, Martin Maly, Kay Diederichs and Jan Dohnalek
To unsubscribe from the CCP4BB l
Dear David,
Although this is not exactly a topic of your question, an alternative approach
is to use the resolution screening and compare the results. I have implemented
this approach to my program SHELIXIR (because it uses SHELX C/D/E), which can
be found here:
u for your response,
Petr
From: Eleanor Dodson
Sent: Tuesday, July 7, 2020 7:08:44 AM
To: Petr Kolenko
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Twin law definition in REFMAC5
Is that twin law possible? Presumably the cell lengths for b and c are clos
Dear colleagues,
I have a crystal with space group P21212 and merohedral twinning according to
"-h, l, k" twin law. If I click "twin" in the interface, REFMAC5 recognizes a
different twin law and does not refine the structure properly. Is there a way
to tell REFMAC5 the proper twin law? I tried
Dear colleagues,
We, the developers of a program for paired refinement, have found a remarkable
feature that should be shared with the community. The fact that data beyond the
arbitrary cutoff may cause an improvement of electron density and make your
models better is generally accepted. We
For those of you who are in touch with these data, would deposition of unmerged
intensities in P1 in the whole detector range instead of complete dataset be
good enough to „correctly“ re-evaluete the structure? Or is there a doubt that
even this approach would not lead to optimal structure?
My
I apologize for the 1st April joke, but I could not resist. And it would not be
actual in three months. I guess that if the workshop were announced this way,
nobody would even care.
Dear colleagues,
We are pleased to announce the 8th South American Macromolecular
Crystallography School:
Dear colleagues,
I wonder if there were a bit less controversial possibility. No matter if that
was less efficient. Would there be an option of using human cell lines that do
not origin from killed children? As far as I know, the HEK cells do. Sometimes,
the science can be pretty cruel.
I am
Dear Manjula, #metoo :-D I think it is just a rare occasion that nobody has
posted anything (except you, of course). ;-) Best regards.
Petr
From: CCP4 bulletin board On Behalf Of Manjula Ramu
Sent: Tuesday, April 30, 2019 12:46 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unable to receive
This is easy to do in Pymol again. If you have atoms in selection "nameX", the
command is "select nameX, br. nameX". Very simple.
Best regards,
Petr
From: CCP4 bulletin board on behalf of Gianluca Santoni
Sent: Wednesday, April 3, 2019 5:13:59 PM
To:
Dear Stephen,
PyMOL can do it. You have to choose your atom and then use following command:
select your-name, (sele) expand 10; where (sele) is your selection - atom or a
group of atoms and 10 is the radius in AA.
Best regards,
Petr
From: CCP4 bulletin
Dear colleagues,
As all of you know, CIF will soon be the only acceptable file format in
macromolecular crystallography. CIF file has many advantages when compared to
traditionally used stone-aged formats like PHS, MTZ, or archaic PDB. One of the
advantages is the includability and mergability
Dear colleagues,
We all are very happy about the storage of raw crystallographic datasets. But,
is it really enough? No! Can we do better? Yes, of course!
The problem is that the crystal after the measurement is usually burned. It
does not make sense to store them any more. But, in order to
Dear colleagues,
We are working on a paper, where we want to discuss our crystal
structure. We have determined structure of non-active state first (much
easier). Than we tried to convert the protein into active state by
soaking (direct crystallization not possible). We have observed more
for your help!
Petr
Dne 08.02.2017 v 9:05 Petr Kolenko napsal(a):
Dear colleagues,
we have a dataset with potential enzyme:ligand complex at 2.2 AA
resolution. The ligand is very good substrate for the enzyme, we used
soaking. We do not see the ligand in the regular difference electron
density
Postdoctoral Associate
Baylor College of Medicine
--
Petr Kolenko
kole...@imc.cas.cz
http://kolda.webz.cz
proteins by the same part (maybe the same part but in
different conformations?)? Thank you in advance!!
yamei
--
Petr Kolenko
kole...@imc.cas.cz
http://kolda.webz.cz
(not in this case, but the previous one)
I do not have to solve this problem, but I do not want to have so
strange Validation Report from ADIT.
Many thanks for any idea.
Petr
PS: Not important, but refined with REFMAC5 at medium resolution.
--
Petr Kolenko
kole...@imc.cas.cz
http://kolda.webz.cz
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Petr
Kolenko
Sent: 22 June 2011 12:18
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Waters in ADIT
Dear colleagues,
I want to deposit one structure, but ADIT reports tens more waters that are
further than 3.5 AA away from macromolecule atoms. I inspected
of what's
going on ..probably a feature which would disappear with newer versions
anyway.
What's the version of Refmac you use, Petr?
Jan Dohnalek
On Thu, May 26, 2011 at 12:11 PM, Petr Kolenko kole...@imc.cas.cz wrote:
Dear colleagues,
I have two problems in two structure refinements using
should not add the TLS contribution to the output
coordinates when you use Refmac except in the last run before to deposit the
file into to PDB. Phenix removes it automatically.
Kind regards,
David
On 05/27/2011 10:57 AM, Petr Kolenko wrote:
Dear colleagues,
regarding Q2:
I do not use TLS
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab: +1-410-614-4894
Fax: +1-410-955-3655
http://web.mac.com/bosch_lab/
On May 26, 2011, at 6:11, Petr Kolenko kole...@imc.cas.cz wrote:
Dear colleagues,
I have two
results.
Many thanks for any response.
Petr
--
Petr Kolenko
petr.kole...@biochemtech.uni-halle.de
http://kolda.webz.cz
for P222 and for P6 integration.
HTH,
Fred.
Petr Kolenko wrote:
Dear colleagues,
I appreciate any help, or any suggestion with my difficult data. Many
thanks at least for consideration.
I work with datasets at 3.6AA of resolution. Integrated with XDS,
scaled with SCALA. After
:17 AM, Petr Kolenko wrote:
Dear colleagues,
I appreciate any help, or any suggestion with my difficult data. Many
thanks at least for consideration.
I work with datasets at 3.6AA of resolution. Integrated with XDS,
scaled with SCALA. After integration and scaling in P1, POINTLESS
suggested
have tried more than half of your suggestions before, but I
still learned a lot from you. I think that this community is so far the best
what internet offers. ;) Many thanks again.
Petr
--
Petr Kolenko
petr.kole...@biochemtech.uni-halle.de
http://kolda.webz.cz
2010/11/23 Petr Kolenko kole
, please?
Btw, we have several structures in the PDB from this experimental setup.
This is the first problem I have met.
Many thanks for any response.
Petr
--
Petr Kolenko
petr.kole...@biochemtech.uni-halle.de
http://kolda.webz.cz
for low-resolution
structure, or should I spent a long time to fix them all?
Many thanks.
Petr
Petr Kolenko
kole...@imc.cas.cz
---
Institute of Biochemistry/Biotechnology
Martin-Luther-Universität Halle-Wittenberg
Kurt-Mothes-Str. 3
06120 Halle (Saale
, e.g. Has
anyone of you observed something similar for intein-chitin chromatography?
Is there any serious structural damage to the target protein during the
purification?
--
Petr Kolenko
kole...@imc.cas.cz
http://kolda.webz.cz
Yes, I know.
I am already working on some other modifications, or analogues. The
questions was only to know some experience from different labs. Thanks.
Petr
2010/7/5 Vellieux Frederic frederic.velli...@ibs.fr
Petr Kolenko wrote:
Dear all,
I am working on crystallization of a protein
create a new directory in your directory with XDS.INP with
symbolic link to the images to have the path like
../my-data/crystal1_001.img because long path may not work in XDS.
It may not solve your problem, but I would try this at first.
Best wishes. ;)
Petr
Petr Kolenko
kole...@imc.cas.cz
http
, please? Thanks for all of them.
Best Regards,
Petr
Petr Kolenko
[EMAIL PROTECTED]
Unfortunately, it also failed:
Failed to find spacegroup in SYMINFO!
MTZTONA4: Fatal error in ccp4spg_register_by_symops
Does anybody know how to fix it?
Petr
? Either Solve or CCP4?
On Tue, Jul 8, 2008 at 10:15 AM, Petr Kolenko [EMAIL PROTECTED] wrote:
Unfortunately, it also failed:
Failed to find spacegroup in SYMINFO!
MTZTONA4: Fatal error in ccp4spg_register_by_symops
Does anybody know how to fix it?
Petr
Petr Kolenko
[EMAIL PROTECTED]
Martyn Winn wrote:
Dobre den,
If all else fails, use a text editor! I use emacs for this ...
Most of the file will look like garbage, but the header at the end of
the file can be edited. Be very very careful not to change the number of
characters just do
Hi Fred,
we use this version and we did not have any problem.
http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/coot-0.4-pre-2-revision-618-binary-Linux-i386-redhat-8.0.tar.gz
We usually use redhat-8.0 binary versions. Best wishes!
Petr Kolenko
Vellieux wrote:
hi
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