Hi Natalia,
One rule of thumb in crystallography: anything is possible!
We have seen many cases of individual proteins (or their complexes with small
molecules, proteins or nucleic acids) where we ended up with structures
starting from low resolution initial crystals. So before taking a decisio
Hello,
I got crystals of protein-nucleic acid complex, rod-shape, reproducible,
don’t visibly get damaged upon freezing; however they gave diffraction only
to about 12 A. I tried several crystals. My question is whether such
crystals worth optimization. Clearly a 4A diffracting crystal could
pot
I misstated something earlier, and I would like to correct the record:
Magic Eye books instruct you on using wall-eyed stereo (with excellent
instructions, highly recommended!). Currently (with computer monitors) I
find cross-eyed much easier (and I think more people should try it).
Thanks,
Nat
Hi Nat,
could you be referring to side-by-side stereo in this (computer monitor)
use case?
http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node97.html
W.
On Fri, Mar 2, 2018 at 2:41 PM, nathanielclar5 .
wrote:
> To learn how to cross eyes, just hold you index fingers strait up, ~12-18
> inches
To learn how to cross eyes, just hold you index fingers strait up, ~12-18
inches from your eyes, and cross your eyes until the two fingers overlap to
form a third finger in the middle. Then practice holding your eyes there.
You can also practice with ceiling tiles, floor tiles, anything that
repea
You already have stereo built in, just turn on 'cross eyed stereo' and
learn to cross your eyes! It's brighter than any 3d monitor, requires no
hardware, and no, it won't hurt your eyes (even for hours at a time)
Nat
On Fri, Mar 2, 2018 at 11:01 AM, Jim Fairman wrote:
> Daniel,
>
> To best
Daniel,
To best of my knowledge, options for 3d stereo on Mac are limited to
Zalman:
https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Zalman_Stereo
If you're willing to go to Linux or Windows, you can do an Nvidia Quadro
Card with a 120 or 144Hz monitor with a 3D Vision glasses kit.
I'm looking for some computer hardware advice.
I have a MacBook Pro with a "Retina" screen and
an Intel HD Graphics 4000 1536 MB graphics card,
running OS X 10.11.16 ("El Capitan"), and I would
like to view structures in 3-D in Coot.
Which computer monitors and which 3-D glasses brands
would allow
Hi all,
We have two positions available at the Structural Genomics Consortium (SGC) in
Oxford, a post-doc and a technician position, to work with Liz Carpenter's
group on human integral membrane protein structural biology.
The post-doc position will involve running and optimizing our pipeline fo
Dear Niegel,
May be Shijun had to cancel his registration to the PhenixBB as I had to do
since 2015 due to "too many bounces" whatever the email address I used,
professional, yahoo or gmail ?... Has this been fixed at some point ?
All the best,Philippe
Philippe BENAS, Ph.D.
Laboratoire de Cris
Hi Sayli -
PrePPI may be helpful if you're interested in interactions among human proteins.
http://honig.c2b2.columbia.edu/preppi/
Cheers,
Jared
Dear Careina,
Your message is a bit confusing... Which kind of validation are you
referring to? Do you want to check the geometrical quality of the
backbone and side-chain rotamers, or do you want to evaluate how likely
it is that the fold proposed by homology actually represents the fold of
Hi Careina,
This is a little confusing. A homology model *is* a set of coordinates
(usually provided as a PDB file by most servers/packages I know of). The
MolProbity site at http://molprobity.biochem.duke.edu/ allows you to
upload your own PDB file, and in my experience is quite forgiving
re
Dear Sayli,
I have used cluspro in past:
https://cluspro.bu.edu/publications.php
Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C, Beglov D, Vajda
S. The ClusPro web server for protein-protein docking. *Nature Protocols.*2017
Feb;12(2):255-278
Best,
Dipak
On Fri, Mar 2, 2018 at 3:28
Dear Careina,
If you do not have coordinates, what do you have then? A sequence alignment? In
that case you can look at the %identity and %homology to see how well the known
structure fits the unknown structure.
If you do have coordinates in some other format generated by some modeling
softwar
On 02/03/2018 11:44, Careina Edgooms wrote:
What programs are best used for validate homology models? I know of molprobity but if there are no
coordinates I cannot use it. Is there a way to use such programs with homology models?
Also I wish to use pdbepisa for to charaterise dimer interface
Dear all
What programs are best used for validate homology models? I know of molprobity
but if there are no coordinates I cannot use it. Is there a way to use such
programs with homology models?
Also I wish to use pdbepisa for to charaterise dimer interface but again for
homology model this cann
Dear Sayli
Here are some options from Table 10.1 of this book chapter
https://link.springer.com/chapter/10.1007/978-94-024-1069-3_10
cons-PPISP
Uses sequence profiles and solvent accessibility for residues and their
neighbours
http://pipe.scs.fsu.edu/ppisp.html
18 matches
Mail list logo
