On Sun, May 23, 2010 at 12:57 PM, David Briggs wrote:
> I like to generate some models using the "Phyre" server
>
> ( http://www.sbg.bio.ic.ac.uk/~phyre/ )
>
> Feed the best .pdbs into Mr Bump.
>
> Go and get coffee. Come back and find a solution with post-refmac
> R/Rfree in the mid-30s.
>
> IMHO
On Tue, May 11, 2010 at 8:07 PM, intekhab alam wrote:
> I solved one structure of a viral RNA polymerase in complex with some
> ligands at 2.6 A resolution. The ploymerase structure has 3 monomers in the
> asymmetric unit and in all the 3 monomers i found |Fo|-|Fc| as well as
> 2Fo|-|Fc| map for
On Sat, Apr 24, 2010 at 5:25 PM, James Stroud wrote:
> I want to programmatically generate the symmetry mates for a molecule and
> write out the files containing the symmetry related molecules. I'm resisting
> the urge to reinvent the wheel.
>
> What is the best way to do this? I'd prefer to do i
On Fri, Apr 23, 2010 at 4:12 AM, Tim Gruene wrote:
> we are using the latex phenix version (1.6.1) on PCs with Debain Stable or
> Testing. After starting a refinement job, the following error message shows
> up:
>
Tim: please report these errors to either b...@phenix-online.org, or the
phenixbb.
On Tue, Apr 20, 2010 at 7:35 AM, 商元 wrote:
> I've seen a website where there are some dynamic pictures to show the
> effects of the absence of various diffraction data to the electronic
> density, such as the changing process of the electron density as the
> deletion of low-resolution data. But I
On Thu, Apr 8, 2010 at 3:26 PM, Daniel Bonsor wrote:
> Following my previous question, there was something wrong with the staring
> model for molecular replacement. Now that is sorted, I have 8 complexes in
> the ASU. After a few rounds of refinement with NCS and isotropic Bfactors,
> both the Rf
On Wed, Mar 31, 2010 at 5:57 PM, Muhammed bashir Khan <
muhammad.bashir.k...@univie.ac.at> wrote:
> I am working with protein which are supposed to be bound with Magnesium
> and Cobalt metals.I have now its crystals which are diffracting quite
> nicely.I want to know the Magnesium and Cobalt bindi
On Wed, Mar 31, 2010 at 8:47 AM, Dirk Kostrewa
wrote:
> this is very interesting! From the list of changes, it appears that in
> version 1.6.1, you use a similar idea to implement hydrogen bonds via DSSP
> during refinement that I used to stabilize the 4.3 A refinement of Pol II in
> complex with
On Wed, Feb 10, 2010 at 12:16 PM, Raja Dey wrote:
> I need someone expert in PYMOL. I am getting a trouble to prepare a
> figure to display electron density for some water molecules. I can see clear
> density in COOT at sigma level 2.5. But, I could not see the density in
> PYMOL even at sigm
On Mon, Feb 8, 2010 at 1:51 PM, William G. Scott wrote:
> This is available to install as a binary from here:
>
> http://molprobity.biochem.duke.edu/get_molprobity.php
>
>
> Although probe and MolProbity3 are said to be "free and open source
> software distributed under a BSD-style license", I ca
On Thu, Jan 14, 2010 at 7:02 AM, Schubert, Carsten [PRDUS] <
cschu...@its.jnj.com> wrote:
> you could use ksDSSP, which is an OpenSource implementation of DSSP.
> Requires some compiling though and I am not sure if OSX is supported.
> You also need to compile the PDB record I/O libraries.
>
It ru
On Tue, Jan 5, 2010 at 9:24 AM, Raja Dey wrote:
> Assuming all the above data are right, which of the following way would
> give the best model for C?
>
> 1. Building homology model of C with A as template.
>
> 2.Building homology model of B with A as template and then use B as
> template t
On Tue, Dec 15, 2009 at 9:40 AM, Eleanor Dodson wrote:
> Yes, the PDB required format is H 32 - but the xHM symbol is: 'R 3 2 :H'
>
> I guess the PHENIX group are trying to pressurise the wwwPDB to change..
>
You'd have to ask Ralf. Besides, it isn't just PHENIX/CCTBX that uses this
notation:
h
On Thu, Dec 10, 2009 at 5:59 PM, Jacob Keller wrote:
> I assume this is the denouement of the Ajees et al debacle a while back?
> Does this mean all authors on all of those papers were complicit? Otherwise,
> how would one author alone perpetrate this kind of thing? He pretends to go
> to the syn
On Tue, Nov 17, 2009 at 10:49 AM, Pavel Afonine wrote:
> one of many possible options to do this:
>
> If you have the latest PHENIX installed ( http://www.phenix-online.org/
> download/nightly_builds.cgi), then you can use "Reflection file editor"
> from the main GUI to do what you want.
>
With
On Mon, Nov 9, 2009 at 10:44 AM, RONG hui Rong wrote:
> Could somebody tell me some server online that can do jobs like
> Autobuild Wizard in PHENIX (generating iterative-build composite OMIT map
> for molecular replacement model and removing existing model bias) or some
> methods that can
On Thu, Oct 22, 2009 at 11:41 AM, vanessa delfosse <
vanessa.delfo...@gmail.com> wrote:
> I'm looking for people using Phenix to refine RNA or DNA structures. I work
> on RNA structures since some months and I observed quite large differences
> between CNS and Phenix, especially concerning rms dev
On Wed, Oct 21, 2009 at 6:20 AM, Katja Schleider wrote:
> I solved my first crystalstructure and now want to publish it. But how do I
> know the structure is ready for publication and deposition in the pdb. We
> can explain our theory with the structure but which factors I have to regard
> to publ
On Fri, Oct 2, 2009 at 3:31 AM, Adam Ralph wrote:
> The python scripts CCTBX are not part of the CCP4 core but can
> be obtained from the associated phaser tar file. CCTBX can also be
> obtained from cctbx.sourceforge.net. This stuff is almost certainly
> free to academics, I do not know about
On Thu, Oct 1, 2009 at 2:11 PM, Raja Dey wrote:
> Dear Friends,
> Sorry for the off topic question. How I can force PYMOL
> to display a portion of the molecule as beta sheet? PYMOL is displaying this
> part as a loop by default, but I like to see this as beta sheet. Is there
>
On Thu, Sep 3, 2009 at 1:33 AM, Eleanor Dodson wrote:
> Lattice translation is effectively one form of twinning, you can visualise
> it as a set of crystals where that lattice are aligned in 2 dimensions but
> there is slippage along the third. So each "reflection" is in fact the sum
> of two or
On Mon, Aug 24, 2009 at 12:30 PM, Joseph Ho
wrote:
> Did you also install Phenix in your machine? Phenix contains another
> version of phaser and will alias "phaser" to the phaser in Phenix.
No, it will be called phenix.phaser. The Phenix environment scripts
($PHENIX/phenix_env*) do not alias
On Tue, Jul 28, 2009 at 8:05 AM, Salgado, Paula wrote:
> I'm planning to upgrade my laptop and would like to run most
> crystallography programs. I was wondering if people could comment on their
> current prefered options. I would prefer not to go for a Mac, so any other
> alternative suggestions
On Thu, Jul 23, 2009 at 9:42 AM, Jacob Keller wrote:
> Dear Crystallographers,
>
> I have not done the statistics, but I have noticed that a large portion of
> the inquiries directed to the BB are twinning-related. While I recognize
> that many of these issues have case-specific details, it may b
On Mon, Jun 15, 2009 at 3:21 PM, Arnon Lavie wrote:
> we collected SAD data sets to 3.0 A on our protein, once as a Se-Met
> protein and once soaked with a mercury compound. Data statistics indicate an
> anomalous signal in both data sets. However, the maps are not great. Is it
> possible to comb
On Thu, May 21, 2009 at 11:04 PM, Tim Gruene wrote:
> this usually means that you have a second version of phaser installed, e.g.
> from the phenix package. To find out, go to a terminal from which you would
> start ccp4i and type 'which phaser'. My guess is that the answer to that
> command does
On Thu, Apr 23, 2009 at 2:54 PM, Francis E Reyes wrote:
> It seems I have a case where I have 5595 reflections but my protein is
> about 102 residues. With a mean atom / residue * 4 parameters for each atom
> I get about 7833 parameters. So it seems that I have a observation :
> parameter ratio
On Fri, Apr 10, 2009 at 12:29 AM, Claudia Scotti
wrote:
> I'm trying to model the 20 residues-long single transmemebrane domain of a
> protein and it is recognised, as expected, to be an alpha-helix by several
> programs. Homology modelling fails for lack of sequence similarity and
> modelling by
>
> I used phenix to assign the free reflections putting in the twin
> operators. Doing simulated annealing in phenix, I get a rather large
> difference in R/Rfree of ~7%. Well, I guess I need to do some tweaking of
> the parameters in phenix (running the latest phenix and cci_apps). When I
> tha
On Wed, Feb 18, 2009 at 3:32 PM, Francis E Reyes wrote:
>
> Single isomorphous replacement with anomalous scattering uses two datasets
> that are isomorphous while using the anomalous signal in one (here
> scattering and dispersion are synonymous?). How does SIRAS use the anomalous
> scattering si
This is Bill Scott's machine, but it's no longer in service:
http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Sources.list_for_10.5_and_10.4_intel_only
You should be able to find the proper URLs somewhere on his website.
On Wed, Feb 11, 2009 at 12:45 PM, Raja Dey wrote:
> Dear All,
Here's another very similar case:
http://www.ncbi.nlm.nih.gov/pubmed/12270703
On Thu, Feb 5, 2009 at 11:48 AM, William G. Scott <
wgsc...@chemistry.ucsc.edu> wrote:
> Some things improve with age. Here is one of my favorite stories:
>
>
>
> http://tinyurl.com/oldtrna
>
>
> The crystal structure o
On Thu, Jan 29, 2009 at 1:25 PM, Anastassis Perrakis wrote:
> Dear all,
> I was wondering what is the state of the art for this old dark art ... are
> there any good servers / programs that allow to easily upload your own
> sequence alignments or create a 'transparent' alignment (I want to see th
On Wed, Jan 7, 2009 at 1:54 PM, Jacob Keller
wrote:
> I am sure that most here have dealt with the issue, when making
superpositions of conformationally-different structures,> of which regions
to align as references and which to call "mobile." Conformational changes
can range from very local (e.g.
>
> There are also options for virtualization of Windoze and Linux via the
> software Parallels although I have yet to test this out.
Parallels is okay; I only use it for testing GUI code on Linux. It doesn't
support multiple processors, which probably isn't necessary for most people.
The graph
On Thu, Dec 11, 2008 at 8:09 AM, Santarsiero, Bernard D. wrote:
> In parallel with the discussion around this off-CCP4-topic, are they any
> good examples of the opposite case, where the protein is a monomer in
> solution (as evident from light scattering, MW determination through
> centrifugation
On Thu, Nov 13, 2008 at 9:47 AM, iulek <[EMAIL PROTECTED]> wrote:
>
> But..., no one commented about c-myc tags. As I expected, there is no
> experience with this one yet - ?
>
I have a more general question that's come up in discussion with former
colleagues: what's the largest tag that has bee
Andrzej, I had the same thought earlier this year. There are several
problems:
1) There is no good non-proprietary, truly cross-platform solutions yet.
CUDA is very specific to NVidia's hardware, obviously. Apple claims to be
adding generic support for GPU acceleration in their next OS release
>
> I find that depth-cue/fog is a sufficient cue for me to determine the
> "3-dimensionality" of what I am viewing on my 2-dimensional monitor,
> and I find that most 3D systems tend to give me a headache long before
> I would get one without them.
>
Even when the depth-cue/fog isn't enough, simp
>
> I am working with a protein that turns a yellowish-brown color when it is
> concentrated to around 2 mg/ml or higher in a small volume (a few hundred
> uL). I was wondering if the protein bound a metal or other prosthetic
> group that would give it this color? The protein's color somewhat
> r
On Mon, Jun 23, 2008 at 4:09 AM, Exec <[EMAIL PROTECTED]> wrote:
> Dear All,
>
> I have econo column from Biorad and AKTA FPLC system. how shall i connect
> the econo column to AKTA FPLC system i.e what are the different
> connections / tubings to be used since akta system the tubing are all
> sma
I just graduated, but I didn't look very hard for experimental
crystallography positions, so I can't comment on job ads. Still, I live in
Berkeley, which gives me plenty of perspective on the state of the field.
Two thoughts:
1. Many universities would prefer not to hire many tenured professors i
42 matches
Mail list logo
