On 10/04/2017 20:14, Xiao Lei wrote:
Thanks Paul,
I tried, it failed with a message as below:
Coot>> set-symmetry-shift-search-size 2
BL Warning:: Python syntax error!
(or you attempted to use an invalid guile command..)
Python error:
invalid, syntax (, line1)
coot>>
You are mixing python
Dear all,
For my crystal, I have to merge 3-4 sets of diffraction data using HKL2000
program to meet requirements for data completeness, but the problem is the
Rmerge value was too high to go on every time.
Did anyone have met the same problem and how to solve it? or some tips for
solve this pro
Hi all,
Sorry for the very off topic message, but I recently upgraded my OS to Sierra
and all of a sudden MacPymol has stopped working for me. Clicking on the
program just gives the appearance of it about to start by showing the icon on
the dock, and then just blinks out, without ever starting
Gert,
There is nothing wrong with suggesting 45 softwares, as one of those may
do exactly what a person needs and save loads of time.
Besides, comparing protein structures locally need not involve any
superposition method. I would say comparing torsion angles/distances
between atoms is a mor
Hi Reza,
Maybe Dr. karplus's program ensemblator might be of some help.
https://github.com/Karplus-Lab-OSU/ensemblator
Naima G Sharaf
*
Postdoctoral Scholar-Division of Biology and Biological Engineering
California Institute of Technology
1200 E. California Blvd
Pasaden
Have a look at local distance difference
test.https://swissmodel.expasy.org/lddt/
It's superposition-free and compares local atomic environment only. You will be
able to see unusually different regions from the output.
I am not aware of a similar structure comparison method that would also take
I would also point out that a key part of the technique described in the
reference below is to vary the temperature. The Lenhoff group published a nice
study on protein phase behavior where they talk about liquid-liquid phase
separation amongst other things. Figure 1 of the paper (Dumetz et al,
I had success once by varying the drop volume ratios as described here:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2203341/
although we ended up getting data from a different crystal form.
~1 M LiSO4 is a surprising condition for cocrystallizing protein and DNA if
they aren't covalently or topol
Thanks Paul,
I tried, it failed with a message as below:
Coot>> set-symmetry-shift-search-size 2
BL Warning:: Python syntax error!
(or you attempted to use an invalid guile command..)
Python error:
invalid, syntax (, line1)
coot>>
On Mon, Apr 10, 2017 at 11:05 AM, Paul Emsley
wrote:
> On 10
On 10/04/17 18:39, Xiao Lei wrote:
Hi All,
I am using Coot 0.8.3 EL on Mac OS X 10.10. After I generate
symmetric molecule by Draw---> Cell & Symmetry. I found double click
a residue in symmetric molecules will give me a label sometime but not
always. I do not know if anyone has similar exp
Hi All,
I am using Coot 0.8.3 EL on Mac OS X 10.10. After I generate symmetric
molecule by Draw---> Cell & Symmetry. I found double click a residue in
symmetric molecules will give me a label sometime but not always. I do not
know if anyone has similar experience.
xquartz 2.7.11 (currently the newest version) running on MacOS 10.12.4
(upto date) has no problem either.
On Thu, Apr 6, 2017 at 3:26 PM, Didier Spittler
wrote:
> Hello Nikos,
>
> I use Zquartz 2.7.9 too and it works fine for me.
>
> Best,
>
> Didier
>
> 2017-04-06 11:52 GMT+02:00 Nikos Pinots
Dear All,
Please find enclosed details of a position with the Data Analysis Group at
Diamond Light Source:
http://www.diamond.ac.uk/Careers/Vacancies/All/040_17_CH.html
Job Title: Senior Software Scientist (informatics)
Job Reference: 040/17/CH
Post Type: Full time / Permanent
Salary informatio
To answer your question...
On 10/04/17 08:44, Mohamed Noor wrote:
Is it possible to directly build a ligand in real space (in Coot?) and then
generate a SMILES string for restraint generation.
I think that you are describing a 3D editor. It is not possible to do
this in Coot (Coot's molecul
4th ReNaFoBiS Integrated Structural Biology School. Oléron, June 16-23There are
still some limited places available for this school that will take place on the
Oléron island (France), from June 16 to June 23, 2017. The main objective of
this workshop is to offer a theoretical and practical tr
Rather then now start mentioning yet 45 other 3D superposition
softwares, I think a pointer to the Wikipedia should suffice:
https://en.wikipedia.org/wiki/Structural_alignment
The Russian Doll effect (if you align more residues the comparison stats
get worse) is best explained (my opinion) by th
Dear all
We are looking for a researcher to explore the druggability of
RNA-protein interactions with small molecule compounds. The successful
candidate will identify and characterize novel, disease-implicated
RNA-protein interactions, establishing and conducting assays to target
those interac
TM-align is used in the protein structure prediction community.
-Jack Tanner
Sent from Jack's iPhone
> On Apr 10, 2017, at 8:45 PM, Goldman, Adrian
> wrote:
>
> The right people to look at for this are found in the structure prediction
> community; a series of algorithms were developed to co
The right people to look at for this are found in the structure prediction
community; a series of algorithms were developed to compare different
predictions of the same structure. Look for papers from about CASP-3 (John
Mount) or pick up any recent CASP and look at how they compare the differen
Hey Mohamed,
I am not sure, if this is what you want, but you can import different PEG
molecules from coot's "File-> Get monomer". A list of different length PEGs
three letter codes can be found on page 1278 of this paper:
Naschberger et al., (2016) http://doi.org/10.1107/S205979831601723X.
I th
Dear all
Is it possible to directly build a ligand in real space (in Coot?) and then
generate a SMILES string for restraint generation. I have some unknown blobs in
my density where they look like PEG molecules but these do not really fit the
density (local CC of 0.7).
I am already using Polde
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