Hi All,
This is a job posting on behalf of a friend at Biogen, Cambridge, MA, US:
We have a postdoctoral position open to study Wnt signaling and its role in
neurodegeneration. A number of studies have shown the importance of the Wnt
signaling pathway in the survival and maintenance of dopaminerg
Hi all,
Can someone kindly explain what is that "match pairs related by inversion
of indices" option doing for handling anomalous data? If I have collected
the inverse beam data, does it mean I have to use this option to match the
I+ and I- pairs in merging? But why does it lead to seriously incom
This is a forwarded message. For inquires please contact Bill Weis (
bill.w...@stanford.edu).
Dear Colleagues:
We are delighted to announce that the* 6th International Conference on
Structural Analysis of Supramolecular Assemblies by Hybrid Methods *will be
held from *March 14-18, 2012 in Lake
1. Yes, just "Save Molecule" (individually) after align
2. > show stick, &HETATM around 4
( is your pdb name, 4 = 4 angstrom)
On Wed, May 4, 2011 at 3:26 PM, jlliu liu wrote:
> Hi All,
>
> I have two questions for Pymol.
>
> 1. Can you write out the PDB file after structural align
sorry, this is the right link for the mac-pymol movie:
people.chem.umass.edu/jhardy/BMS2006Files/pymol%20morphing/PymolMorphingMovie.pdf
On Mon, Mar 7, 2011 at 2:07 PM, Matthew Chu wrote:
> Hey Mark,
>
> In Window PC, I used ImageReady, which comes with Photoshop.
> see
Hey Mark,
In Window PC, I used ImageReady, which comes with Photoshop.
see this:
http://sage.ucsc.edu/~wgscott/xtal/movie/making_movie.html
Alternatively, using Mac version of Pymol, you can easily make a movie and
save it in quick time format
see this:
www.chem.umass.edu/.../*BMS2006*Files/.../P
Is it possible that the phosphates are just disordered rather than being
cleaved? It's always the case for inactive kinase-ATP or AMPPNP complexes
that the phosphates are not stabilized by Mg2+ or the residues in the
binding pocket and hence they become disordered and are not seen in the
electron d
ISRDB Cryoprotectant database for protein crystals is a good resource, not
only for the cryoprotection methods but the freezing methods used from
literature.
http://idb.exst.jaxa.jp/db_data/protein/200304E02478000.html
It is under maintenance at the moment though...
HTH,
Matt
On Thu, Sep 9, 201
Yea, Parveen has actually asked about this here a year ago and I found this
discussion quite useful indeed:
www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg11717.html
and I think we all get tons of these crystals especially in conditions with
PEGs.
There are lots of things you can try and have been
Hi Rui, for some reasons, I also always encounter problems when building new
ligand by CCP4 Sketcher. You can try PRODRUG (
http://davapc1.bioch.dundee.ac.uk/prodrg/index.html) to build your new
ligand and get the cif from the server, it always works for me.
HTH,
Matt
2009/11/27 rui
> Hi,
>
> I
Hi Koustav,
I had the same question before and here is the answer from Eugene Krissinel,
the developer of PISA:
"Yes PISA has a database of compounds, which contains certain interaction
parameters. If a compound is not found in the database, then PISA does not
know how it interacts with other mol
Hi Madhavi,
try the prodrg server:
http://davapc1.bioch.dundee.ac.uk/prodrg/index.html
2009/6/26 Nalam, Madhavi
> Hello:
> I am using CCP4 version 6.1.1 now.
>
> I refine protein-small molecule complexes (the small molecules are new
> and hence I have to input the cif file).
> In the previous
Hi Marek,
I had a similar problem before, which the active site was partially occupied
by a PEG molecule and my ligand couldn't get into the site. Sequential
soaking-out can solve my problem; basically you need to slowly remove the
PEGs from the crystal (in order to balance the osmotic shock): Ste
be in the imminent 7.1 release.
>
> A.
>
>
>
> On Jan 8, 2009, at 12:59, Matthew Chu wrote:
>
> Thanks Damian, but I have been using my library file for refmac refinement
> and it works fine. And I can't find the line "Unrecognized atom type", but
> presumably,
that is passed on to refmac.
>
> When using the auto_solvent.sh script, please omit the '[' and ']'
> characters. Type e.g.: auto_solvent.sh datafile L1.mtz protein L1.pdb fp
> F_New sigfp SIGF_New extralibrary refmac5_templ.03957_lib.cif
>
> I hope this will hel
Dear all,
I tried to use ARP/wARP 7.0.1 GUI for solvent building, however it couldn't
recognize my ligand library file (.cif), which works fine in refmac
refinement.
Apparently, the error message is:
===> Error: New ligand has been encountered. Stopping now
Refmac_5.2.0019: New ligand has been
N-terminal sequencing / MS for intact mass analysis are the only ways that I
can think of.
Matt
2008/7/1 Klaus Futterer <[EMAIL PROTECTED]>:
> We have a 150 kDa protein that reproducibly crystallises at one of the
> Hampton Screen conditions. However, we know from SDS gel analysis that the
>
Hi Nadir,
No I didn't and I am not concerning CHROMATOFOCUSING, and you are right, I
have been thinking of using both pH and salt gradients to refine the
separation. Thanks!
Matt
2008/6/25 Nadir T. Mrabet <[EMAIL PROTECTED]>:
> John,
>
> You can adjust your ionic strength not only with NaCl/KC
Thank you for all your advices.
I usually employ salt gradient in MonoQ for my proteins, but I just wonder
if we can use pH gradient in the same column and see if it can improve the
separation.
I know the condition that my protein binds to Mono Q, so I will try to
titrate toward its pI to reduce
t;
>
> The proprietary buffers are a bit expensive, but as you found out, they're
> a bit complicated to make. I don't know if you'd ruin your Mono Q with a pH
> gradient. If in doubt, buy one of the dedicated Mono P column.
>
> Hope that helps.
>
>
> Andreas
Dear All,
Sorry for off-topic question. Does anyone have any experience in purifying
protein using pH gradient in Mono Q column?
I have been googling for a whole day, only one paper was found to mention
performing pH gradient in Mono Q, but in a mixture of amine buffering
species, which is a bit
lf occupancy'.
> And which one is working for you.
>
> Thanks,
> bb
>
>
> *Matthew Chu <[EMAIL PROTECTED]>* wrote:
>
> Thank you for all the advices, I am now able to refine the ligand in half
> occupancy!
>
> Matt
>
>
>
> 2008/6/10 Guilla
Thank you for all the advices, I am now able to refine the ligand in half
occupancy!
Matt
2008/6/10 Guillaume Marassio <[EMAIL PROTECTED]>:
> I'am not sure it is your problem but you can try with A and B before the
> residue number.
> Hope it will be helpfull.
> Guillau
Dear All,
Can anyone teach me how to refine a ligand in a protein structure with half
occupancy in refmac?
I have tried to combine the coordinates of the two different conformations
of that particular ligand in one pdb, after modeling in Coot individually,
and then changed the occupancy to 0.5 for
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