might want to use it with the h... It does this in 0.3 second, so,
if it doesn't solve your problem, it certainly won't waste much of your
time.
MRS is open source, so you can install your in-house version (see
github). But we will keep the cmbi site up and running for a while...
Gert
refinement, or perhaps even the steps before you started
refining. One suggestion is to see what PDB_REDO can do for you.
Greetings
Gert
(Ps, feel free to send me your coordinates and I will give you my
opinion of-the-list).
Regards
Kahkashan
---
ither looking at TLS values or looking as residual B-factors.
Obviously, the BDB holds data only for deposited PDB files, but if
anybody contacts me outside the list we might be able to help.
Gert
To unsubscribe from the C
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
to protein folding remains
(very roughly, and this is practical experience for which no good theory
exists) about 1kCal/Mole.
Gert
On 11-7-2018 16:52, Eleanor Dodson wrote:
How do people decide on what is a salt bridge within a molecule and
how to count them for those Tables?
I have been
the
important reasons for having structures deposited in the PDB, it is not
at all related to crystallography in any way other than that both
techniques try to get the most precise and accurate coordinates of
(macro) molecules.
Gert
On 2-3-2018 12:44, Careina Edgooms wrote:
Dear all
What
ers of the list, if
you want)
Greetings
Gert
On 16-12-2017 23:01, chemocev marker wrote:
Hi
I am just calculating the Electrostatic Potential, and I wanted to
know your opinion which force field is better.What is criteria to
choose and not to choose the pKA...
best
Jiri
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 construct
a disclaimer needs to be written, then this is obviously best
done by the author of the software for which the disclaimer holds.
Greetings
Gert
Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het
handelsregister onder nummer 41055629.
The Radboud university medical center is
ovel
data/information/knowledge/insights is to publish it so the world can
benefit from it.
Gert
structures. <https://www.ncbi.nlm.nih.gov/pubmed/26249342>
*Touw*WG,*Joosten*RP,*Vriend*G.
Acta Crystallogr D Biol Crystallogr. 2015 Aug;71(Pt 8):1604-14. doi:
10.1107/S1399004715008263. Epub 2015 Jul 28.
Good luck,
Gert
On 10-10-2017 15:28, Yang Shi wrote:
Hi, Tristan Croll,
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
Dear Adriana,
-AMPPNP (Adenylyl-imidodiphosphate) or
-AMPPCP (β,γ-Methyleneadenosine 5′-triphosphate)
You can be buy them easily.
Best - Gert
Philipps University Marburg
LOEWE Center for Synthetic Microbiology &
Dep. of Chemistry
Dr. Gert B
the CATH people (Orengo
group), and Arthur Lest is the only one (still, I think) who has been
thinking extensively about the cutoff question.
Greetings
Gert
From: Reza Khayat
Sent: Sunday, April 9, 2017 6:07 PM
To: CCP4 bulletin board
Subject: Structure comparison
Hi,
I have refined several
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
Skype I am gvriend and my mail
address is vri...@cmbi.ru.nl.
Greetings
Gert
On 4/3/2017 11:17 AM, Adriana Sene wrote:
Dear members
I assigned the secondary structure to my pdb file by the DSSP
application from this webserver
http://www.cmbi.ru.nl/dssp.html
The application works and gives output
. DSSP has so its issues, but as everybody uses it,
these issues are known, and softwares for which they are critical deal
with those issues properly, normally.
Gert
On 03/24/2017 09:24 PM, Pavel Afonine wrote:
May be not exactly what you want, but should be close
rest including a CV and the names of three
referees as a single pdf document to: g...@bangelab.org.
With best regards,
Gert
-
Philipps-University-Marburg
LOEWE Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry
Dr. Gert Ba
...@yasara.org); he installed
it for us many years ago and he is THE specialist in this field
Greetings
Gert
On 12-11-2016 12:29, Brian Smith wrote:
Hi Xavier,
Any LG "Cinema 3D" capable TV should give you good passive stereo for the kind
of thing you need and definitely work with PyMol and
Lets stop this discussion before it divides this list of friends just as
much as the cause of this discussion divided the US.
Gert
even have equally many residues so that there will always be some
unaligned/unmapped Calphas left at the end. Look for some articles by
Arthur M Lesk on this topic, he has explained protein superposition
(problems) very clearly.
Gert
Ps, if you want proteins superposed and get different output
ook at www.yasara.org
Greetings
Gert
On 27-10-2016 17:20, Matthew Graf wrote:
Hello All,
I am looking for suggestions on a good, but not too costly, 3D
monitor for visualizing pdb structures and looking at outputs of
modelling programs. I am not personally a structural biologist, but am
on the hu
7;t work: wrong spacegroup.
Gert
a protein helix...).
Unfortunately you will have to go through the hassle of installing WHAT
IF, and learning how to operate it also isn't trivial.
It is free, though.
Gert
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
tell them to first get their old products back up and running and that
they can resubmit their new software next year.
So, I agree with Robbie, but also with the many people who said that
'we, ourselves' are the problem, not the system or the journals.
Greetings
Gert
Aug;12(8):657-62
and
Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a)
calculations.
Nielsen JE, Vriend G.
Proteins. 2001 Jun 1;43(4):403-12.
Greetings
Gert
On 05/10/2015 12:37 PM, Andre Godoy wrote:
Dear users.
I'm comparing surface charge of a structure wit
doubles or near-doubles till you have less then
300 structures. Proteins that are >95% sequence identical normally are 'the
same anyway'.
Gert
Forwarded Message
Subject:[ccp4bb] Structural classification
Date: Fri, 24 Apr 2015 13:36:42 +0100
From: D
authors probably went through great pains
for you getting these coordinates close to where they should be).
Gert
Dear Mishba,
Just check density vs model by simply open 'Coot',
Go to: 'File' -> 'Fetch PDB & Map using EDS'
Type the pdb entry into the field - enjoy the densities.
Best and god save the EDS,
Gert
-
LO
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
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
and
score on Z and RMS Z.
Also, look at our recent BDB article in PEDS (Vol 27, Iss 11 457-462),
because not every B-factor in the PDB is what you would expect it to be.
Gert
On 26/03/15 12:32, herman.schreu...@sanofi.com wrote:
Dear Bulletin Board,
A referee wants for the “Table
ottom server on that page.
Greetings
Gert
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 nature of interactions. Is there any good software to
give this information with good clarity
. Why don't you first try asking the
EBI? (It is a dead link at the EBI web site, but the EBI is an
international service institute so I would think they would respond
quickly if made aware of this problem.
Gert
Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het
handelsregi
all new PDB files and store the
results in easy-to-parse files, one per PDB file.
Greetings
Gert
On 03/04/2015 11:20 AM, Li Xue wrote:
Hi,
I am new to ccp4. I am writing to check the possibility to use ccp4 as a
platform to develop my software.
I was wondering whether I could get the following
re we will come-up with novel validation methods.
Gert
Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het
handelsregister onder nummer 41055629.
The Radboud university medical center is listed in the Commercial Register of
the Chamber of Commerce under file number 41055629.
d psi to pull
residues into the Ramachandran plot's preferred regions.
Greetings
Gert
Ps, feel free to send me your coordinates (I promise to keep them
secret) and I will see if the latest WHAT_CHECK provides some hints for
what you can try to do.
coordinates guaranteed, of course).
Gert
Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het
handelsregister onder nummer 41055629.
The Radboud university medical center is listed in the Commercial Register of
the Chamber of Commerce under file number 41055629.
- Analysis of Metabolic Networks
Dr. Gert Bange
Hans-Meerwein-Strasse, C7
35043 Marburg, Germany
office: +49-6421-28-23361
fax: +49-6421-28-24430
web: www.synmikro.com/bange
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