On 19-2-2015 1:38, Smith Lee wrote:
Dear All,
It often finds for the Ramachandran favored determined by Coot, MolProbity
regards as Ramachandran outliers. There are earlier posts regards Coot and
MolProbity has different database for the determination of the Ramachandran
plots. Then will you
On 03/06/2015 09:21 AM, Laurent Maveyraud wrote:
Dear all,
we are currently trying to pick up the trail of the PROMOTIF program
for which we can't find a link that works properly. Does anybody know
where I can find it ?
thanks for your help,
laurent
PROMOTIF seems to be an EBI product. Why
Ls,
I dont think these numbers are useful by themselves. It makes more sense
to look at differences in these numbers (between bound atoms in your
protein and in 'the rest of the PDB') as function of as many external
conditions as statistics allow. Then determine averages with SD, and
score
Dear Li Xue,
The questions you are asking are more the domain of protein structure
bioinformatics than X-ray crystallography. The CCP4 has a series of these
programs available, but their collection is limited. May I suggest that you
also look at http://swift.cmbi.ru.nl/gv/facilities/. There
On 25/02/15 18:08, Michael Murphy wrote:
Does anyone know of a way to adjust Ramachandran angles so that they
fall within the preferred range? Either in Coot or possibly some
online server? I have been trying to do it manually without much
success, I was wondering whether there might another
I saw several excellent remarks about Ramachandran plots come by, but
the main points still seem missing, I think.
Phi and psi are not fixed parameters with limited freedom like angles,
bond lengths or planarities. By keeping a certain bond lengths
restrained at, for example, 1.543+/-0.021
The following article was rejected by 'our' journal...
http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1097-0134/homepage/april_fools__day_special_papers.htm
http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291097-0134/homepage/april_fools__day_special_papers.htm
Greetings
Gert
This matrix-renormalizer comes from WHAT IF. Feel free to use it any way
you want:
SUBROUTINE GVSREN (RMAT)
C+++
C---
C
C RMAT IS
At around 4.0 A resolution one normally cannot talk about accuracy. The
density will at most locations not warrant any detailed interpretation.
If, at 4.0 A resolution, you move atoms around a bit, you will not see
significant changes in R/Rfree. So, you can do whatever you want, more
or less.
We addressed some of these electrostatics problems (Xray artefact like presence
of ions, crystal packing, etc) a long time ago. Feel free to look at:
Improving macromolecular electrostatics calculations.
Nielsen JE, Andersen KV, Honig B, Hooft RW, Klebe G, Vriend G, Wade RC.
Protein Eng. 1999
Being in software design myself, I want to look at it from the other
side. If I produce software I want to get from it:
1) Gratitude from the users, preferably expressed in the form of citations;
2) Nice collaborations that allow me to use my, novel software at the
edge of science;
3) The
The site swift.cmbi.ru.nl/gv/numbers/ is not official, unpublished, and
still poorly maintained. But just for the fun of it, I added a list of
modified cysteines. Be aware that the files are big, so better
download them and read them in the editor than opening them in the browser.
Gert
On
On 26/05/15 14:41, vijay srivastava wrote:
Dear All,
I want to superpose the nucleotide form one GTPase on to the
nucleotide of other GTPase in order to study
the interaction in the nucleotide binding pocket. I tried to superpose
but it is superposing on the basis of secondary structure as a
Dear Wenhe,
No 3D superpose tool will always align/map all Calphas. If in the one
protein the loop turns left, and in the other it turns right, then
mapping those loops is meaningless and thus not done by good software.
The other problem is that often two proteins that get compared do not
Lets stop this discussion before it divides this list of friends just as
much as the cause of this discussion divided the US.
Gert
Hia Xavier,
For about 10 years already we use a simple solution consisting of a
cheap computer with two graphics cards, a beamer from the game industry
that can project stereo, and simple liquid crystal shutter glasses. This
gives us projection on the wall (just a painted wall, nothing
Hai Matt,
If you are not interested in hard-core crystallography stuff like
interpreting electron-density maps or couplings to Coot or Refmac, then
I can certainly recommend that you look at Yasara. We use it for 15
years already for modelling and many different visualizations (and much
Many, many years ago I worked in Rossmann's lab. Some colleagues were
detwinning a structure. Whatever they tried, the twin ration went from
something near 50-50 to something near 95-5 without any improvement. I
wrote software that would look at reflection files in search of
systematic
Ls,
It is not possible to determine the secondary structure from the
position in the Ramachandran plot. For a residue to be helical, it must
have hydrogen bonds that correspond with a helix, and so need its
neighbours. If these conditions are met, a residue will by necessity
have backbone
Dear Adriana,
That server is ours, at the CMBI.
I realize that you are a bit confused about things. Feel free to address
me personally (and I am mailing this to the whole list because this
offer holds for all the 3D structure related servers reachable via
swift.cmbi.ru.nl/gv/facilities). In
Arthur Lesk (at Penn state Univ, I think)m is the only one I know who
has worked on this topic. I suggest you ask him. The topic you elude to
is commonly known as the Russian Doll Effect.
If you want to discuss the topic, feel free to Skype me.
Greetings
Gert Vriend
On 10-4-2017 1:37, Reza
The fact that the PDB holds hundreds of FABs and a handful whole ABs
suggests to me that the latter are hard to get crystals for. So, all the
more reason for us bioinformaticians that you, experimentalists try it :-)
Gert
On 22-6-2017 20:39, Cheng Zhang wrote:
Hi all,
I have a naive
Look at http://swift.cmbi.ru.nl/servers/html/index.html under "structure
validation" you will find a server that predicts which peptide planes
most likely need to be flipped. This server is the implementation of:
Detection of trans-cis flips and peptide-plane flips in protein
structures.
In 1996 we wrote a short note on WHAT_CHECK. The fact that protein
structures contain errors caught the community by surprise at that time.
A few weeks later Nature published another note, now by some prominent
crystallographers who stated that WHAT_CHECK produced many false
positive error
That is a simple question with a long and tedious answer.
The question is like: "I have this protein crystal, can you suggest some
ways to solve the structure"?
The best is to leave this to an expert in the field (I am not a real
expert in this field, but I can give you some pointers of the
A related question. If you have a crystal structure and found a novel
ligand binding site that can be used to regulate protein activity,
could you patent such "binding site"? If not, how to make the best use
of such findings?
I would say that the best one can do with important novel
I would try your local bioinformatician (or a remote one if there isn't
any one local).
With the sequence in the mail, I could have given it a shot...
Gert
On 12/6/2017 3:14 PM, zheng zhou wrote:
Dear CCP4 community,
Sorry for the off-topic question. I am trying to design constructs for
Batch mode generation of residue-based diagrams of proteins
Fabien CampagneEmmanuel BettlerGert VriendHarel Weinstein
/Bioinformatics/, Volume 19, Issue 14, 22 September 2003, Pages
1854–1855,https://doi.org/10.1093/bioinformatics/btg236
Published:
22 September 2003
On 4-8-2018 10:38, Joana
TLS groups are a good way to reduce the R-factor without doing very
stupid things. They give a better fit of coordinates to the data, so,
when done well, you get a better description of reality without
(hopefully) over-fitting. Most times, I think, TLS groups are defined by
the experimentalist
On 17-8-2018 18:27, Firdous Tarique wrote:
Hello everyone.
I have a basic question. When a validation report of a coordinate is
generated we often come across a term known as "Too-Close Contacts".
Essentially evey PDB file has at least a few of those.
First of all can somebody please
Dear Eleanor,
Salt bridges are a compromise between entropy and enthalpy. If, say, an
Asp and an Arg side chain are a bit restricted in their freedom and the
charges are close, enthalpy wins, and if they are very exposed, and not
close at all, entropy wins. The enthalpic gain upon protein
Careina,
Feel free to contact me about these things without using the CCP4BB list.
I am sending this to the list with as purpose that others might in the
future refer people with questions about homology modelling to me. After
all, although the possibility to build homology models is one of
The MRS server at the CMBI (http://mrs.cmbi.umcn.nl/) is very quick. It
is not a dedicated ligand searcher, but it finds 23 files with
tetraethylene glycol. It is just a Google-like text-search engine, but
much smarter than grep; for example "tetraetylene glycol" suggests that
you might want
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