Hi all
I am interested to make a cartoon image file from a old PDB. This PDB
contains the coordinates of the only C-alpha atoms.
Is there is any program to create cartoon image from this PDB?
please, can any one suggest me?
Thanks in advance
With Best Regards
Jhon Thomas
Matthew,
I have not had any problem with our Cryojet XL (90 - 300 Kelvin), it is
very stable at sub-zero temperatures, I checked it over a longer period
using a highly sensitive electronic device. Also, you can buy the
Cryojet HT that can be operated from 90 – 490 Kelvin!
The heaters will be
We used to use FTS-cooler for stable
temperatures in Laue-experiments on
protein crystals in capillaries.
Check out BioCARS at the APS for this device.
http://cars9.uchicago.edu/biocars/pages/timeresolved.html
It has a big opening for constant air flow
and temperature along the capillary and
it c
a couple of points from long BC about approx. 0 C cooling...for what its worth!
i) don't forget that high concentrations of salts can have a significant effect
on the freezing point ( remember freezing point depression?). We used to
collect data at -15C from crystals grown in 2.4M Ammonium Sul
Hi,
I suppose any program that makes cartoons can handle a C_alpha-only-file. I
just tried rasmol and molscript without problems. pymol probably also works,
or ccp4mg.
Have you had any problems, or are you just not familiar with programs that
make cartoons?
Cheers, Tim
-Original Message-
Dear All,
we are dealing with a difficult case of a 'partially ordered' protein
crystal.
Here it would be very useful to view the reciprocal space
as a 3D map. Is anyone aware of a program that would convert
standard oscillation data (one-degree frames, mar225)
into such a map? What we need is
Dear all, before heading for holidays make sure to apply for your
September/October beamtime at BM14. Deadline for submission of online
proposals is next Wednesday the 18th
Link: http://www.esrf.fr/exp_facilities/BM14/applyforbeamtime/eproposal.html
See below for full details
Don't hesitate to
Just a thought, Mary - going back to your original question about MPD. I
extracted the crystallization conditions from REMARK 280 of 3939 PDB entries a
couple of years ago. The average concentration of the MPD used was high -
38.6%, while PEGs tended to be used at lower concs, e.g. PEG400 25.7
Dear Mary,
the problem encountered with cryoprotectans is the change in the solution
surrounding your crystal as they may not be present in your crystallisation
conditions or you need to increase their concentration to make them act as
cryoprotectant.
So I don't thik is the cryoprotectant itsel
Good day all,
I have a metal center in my enzyme active site, in a
roughly square pyramidal coordination. I know from
EXAFS and other work how this coordination sphere
should look, but following REFMAC the cofactor here
does not end up realistically coordinated/oriented.
Although it is in the de
Hi James,
I've seen something similar with another metal site. It may be that the
X-rays have photoreduced the metal and you may have a different
coordination from that seen from the EXAFS data (recorded at much lower
dose). A good example is Yano et al. PNAS 102, 12047-12052, X-ray damage
to the
Instructions for reading CCP4-format maps into pymol can be found in the
pymol wiki. Point your browser to
http://www.pymolwiki.org/index.php/Display_CCP4_Maps.
--
Roger S. Rowlett
Professor
Colgate University Presidential
Details here:
http://www.york.ac.uk/univ/mis/cfm/vacancies/vac_detail.cfm?vacno=BR07299&mode=standard
Software Engineer in Protein Crystallography Graphical Model Building in
"Coot"
Structural Biology Laboratory, Department of Chemistry
Vacancy reference: BR07299
You will work with Dr Kevin Co
Hi, Sam,
Have you tried to put the map on 1sigma at the control panel and then the
mesh to 1 sigma after loading the map in Pymol?
It is not enough load the map.
--
Emmanuel Prata de Souza
The Management of Synchrotron Image Data:
Changes to the imgCIF dictionary and software, interaction with NeXus
Sponsored by DOE under grant ER64212-1027708-0011962, NSF under grant
DBI-0610407 and NIH under grant 1R13RR023192-01A1
You are cordially invited to a CBF/imgCIF workshop in two lunch
Hi all, I was hoping to receive some guidance on the following subject.
I'm refining a structure using REFMAC that shows all the symptoms of
radiation damage. Namely partially broken disulphide bonds and
decarboxylated Asp/Glu residues. I have an idea of how to handle the
partially broken
At the risk of sounding too commercial, here are some suggestions:
1. See if you can either place your crystallization tray in a cold room or
crystallize it there. Mount your crystal in a capillary here so that at
whatever lower temperature you use, the distillation of solvent will be
reduced.
Hi Mary,
There is another expt. you might look into after trying out the different
cryoprotectants, small vs. large crystals, capillary mounts, etc. as suggested.
Dr. Robert Thorne's group (from Mitegen & Cornell U.)) has been doing some
studies on flash freezing procedures and effect o
Hi everyone
Whenever, I try to run pymol I get following errors
Traceback (most recent call last):
File "", line 1, in ?
ImportError: No module named pymol
TypeError: expected string or Unicode object, found
PyMOL-Error: can't find 'pymol.exec_str()'
Can any body suggest how to fix this error
Two postdoctoral positions are available in the Department of
Microbiology and Molecular Genetics at UMDNJ - New Jersey Medical
School starting Fall 2007 in a newly-opened laboratory to study the
structural mechanisms regulating bacterial signal transduction. In
addition to a recent Ph.D.
You can also try to use the micromount loops (look like ink-pen nibs) sold by
Mitegen. They are a
much easier alternative to capillary mounts; they are easy to handle and work
well for room
temperature data collection.
Good luck.
Raji
-Included Message--
>At the risk of sound
Thank you to all who replied to my original post. Here is the result.
Original query:
Sorry for the off-topic question.Does anyone know a way to just
buy the spin columns from the Qiagen (or similar) PCR clean up / Gel
extraction / miniprep kits, without buying the entire kit? Our lab is
delu
Perhaps someone would barter with you for your reagents?
On Wednesday 11 July 2007 18:28, Eric Dollins wrote:
> Thank you to all who replied to my original post. Here is the result.
>
> Original query:
> Sorry for the off-topic question.Does anyone know a way to just
> buy the spin columns fro
23 matches
Mail list logo
