t; George
>
> PS There are lots of solution NMR structures as well supporting the
> physiological crystal structures
>
>
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nat
> Echols
> Sent: Friday, February 10, 2012 10:35 PM
&
On Fri, Feb 10, 2012 at 12:29 PM, James Stroud wrote:
> How could they not be snapshots of conformations adopted in solution?
Packing billions of copies of an irregularly-shaped protein into a
compact lattice and freezing it to 100K isn't necessarily
representative of "solution", especially when
On Wed, Feb 1, 2012 at 11:17 AM, Dianfan Li wrote:
> I am working on a kinase and would like to get an ATP analogue into
> the crystals. When soaked with AMP-PCP, the kinase crystals crack in
> about 15 min at 4 C.
This isn't too surprising; most kinases undergo global conformational
changes (dom
On Tue, Jan 24, 2012 at 10:24 AM, Ian Tickle wrote:
> reassuring air of finality! Maybe a Python expert will answer this
> but I've often wondered, what happens if as some editors do
> (particularly if as I do you have to use different editors at
> different times depending on where you are worki
On Tue, Jan 24, 2012 at 1:38 AM, Adam Ralph wrote:
> CUDA is a set of extensions for C which will allow you to access hardware
> accelerators (certain NVidia cards in this case). CUDA has been around for
> a
> while and there are CUDA libraries for FFT and BLAS.
> I have not used cuFFT mysel
On Fri, Jan 20, 2012 at 9:37 AM, Jim Fairman wrote:
> New Fourier transform algorithm supposedly improves the speed of Fourier
> transforms get up to "a tenfold increase in speed" depending upon
> circumstances. Hopefully this will get incorporated into our refinement
> programs.
Perhaps if sour
2012/1/6 Pete Meyer :
> However, at 3.2 Angstroms I'd recommend against using atomic B-factors -
> the "rule of thumb" for this is 2.8 Angstroms for atomic B-factors (or
> at least it was back in the day). It might help to use an overall
> B-factor combined with one (or a few) TLS groups.
This ma
On Wed, Nov 23, 2011 at 7:57 AM, Ian Tickle wrote:
> On 23 November 2011 07:54, Careina Edgooms wrote:
>> I have a question about a 2F0-Fc difference map that I calculated with
>> Refmac.
>
> On 23 November 2011 15:40, Nat Echols wrote:
>> The negative density arou
On Tue, Nov 22, 2011 at 11:54 PM, Careina Edgooms
wrote:
> I have a question about a 2F0-Fc difference map that I calculated with
> Refmac. In some instances it gives me negative (red) density around part of
> a side chain and no positive density in sight. Furthermore the entire
> residue fits wel
On Tue, Nov 8, 2011 at 4:22 PM, Francois Berenger wrote:
> In the past I have been quite badly surprised by
> the no-acceleration I gained when using OpenMP
> with some of my programs... :(
Amdahl's law is cruel:
http://en.wikipedia.org/wiki/Amdahl's_law
This is the same reason why GPU accelera
On Sat, Nov 5, 2011 at 3:02 PM, Caitlyn Claire Yeykal
wrote:
> Hi -- has anyone had crystals that are colored in regular (unpolarized)
> light? Mine are yellow, and I'm not aware of anything in the buffer
> conditions that might cause this. I read online that glutaraldehyde can
> turn protein cr
On Thu, Oct 27, 2011 at 1:47 PM, Adrian Goldman
wrote:
> 1) this is not a matter of science, but science (internal) policy, and so
> the majority actually SHOULD count.
>
It's worth keeping in mind that there was once strong opposition to the
current rules on PDB deposition - the best example I c
On Tue, Oct 25, 2011 at 3:20 PM, Pete Meyer wrote:
> This is probably an idea that has already been tried (or discarded as
> unsuitable for reasons that don't occur to me at the moment) - but why not
> start with good crystals (such as lysozyme) and deliberately make them
> worse? Exactly how wo
On Mon, Oct 17, 2011 at 10:09 AM, Napoleão Valadares wrote:
>I have tried A LOT of Molecular Replacement using Phaser and Phenix
> AutoMR. I'm using a 80% identity coiled coil helix as search model. The
> programs give me solutions with "reasonable" maps, but it is never possible
> to refine t
On Fri, Oct 14, 2011 at 1:20 PM, Quyen Hoang wrote:
> Sorry, I don't quite understand your reasoning for how the structure is
> rendered useless if one refined it with all data.
>
"Useless" was too strong a word (it's Friday, sorry). I guess simulated
annealing can address the model-bias issue,
On Fri, Oct 14, 2011 at 12:52 PM, Ed Pozharski wrote:
> The second question is practical. Let's say I want to deposit the
> results of the refinement against the full dataset as my final model.
> Should I not report the Rfree and instead insert a remark explaining the
> situation? If I report th
On Tue, Oct 11, 2011 at 10:34 AM, Ed Pozharski wrote:
> CNS defaults to excluding them. As for phenix, I am not entirely sure -
> it seems that phenix.refine does too (fill_missing_f_obs= False), but if
> you use the GUI then the fill in option is turned on.
In practice, it will be turned on fo
2011/9/29 Xiaopeng Hu
> I just notified that there is a big difference between the Ramachandran
> plot analysis results produced by Coot and Morprobity (or Phenix). For the
> structure I am working now, Phenix(Morprobity) gives out Ramachandran
> outliers 0.2%, favored 95.2%, whileas Coot gives o
On Wed, Sep 28, 2011 at 5:26 PM, Jacqueline Vitali
wrote:
> (2) Second option is an IMAC 4 GB 2.5 GHz with AMD Radeon HD 6750M 512 MB
> GDDRS.
>
> --How does Coot work with this graphics card?
>
I don't have exactly this, but something very similar (6770M), and it works
very well for me so far, b
On Tue, Sep 27, 2011 at 11:16 AM, Yuri Pompeu wrote:
> I have a 2.3A data set that could be scaled in C 2 2 21 and P 1 21 1
> Intensity statistics tests indicate twinning (pseudo-merohedral h,-k,-h-l
> in P 1 21 1)
> I find a good MR solution and when I try to refine it with the twin law I
> get
On Mon, Sep 26, 2011 at 1:53 AM, Dirk Kostrewa
wrote:
> when I played with H-bond restraints for secondary structures for the
> refinement of a 4.3 A structure (only a few weeks before they were
> introduced in phenix), I've made the following observation: at low
> resolution without H-bond restra
On Thu, Sep 22, 2011 at 4:18 PM, Pete Meyer wrote:
> In short, the effective observation to parameter ratio improves by ~4%.
> This seems like a relatively small improvement, especially if the trade-off
> is that Ramachandran statistics can't be used for validation anymore. It
> also seems like
On Mon, Sep 19, 2011 at 6:39 AM, Dirk Kostrewa
wrote:
> Great! Maybe, they should add an extra term for correlation of Fcalc to
> Fobs (or LLG or R) to their game. I wonder, if structures could be solved ab
> inition by players, then :-).
>
Actually, Kam Zhang's group did something exactly like t
On Sun, Aug 28, 2011 at 7:23 PM, Jacob Keller <
j-kell...@fsm.northwestern.edu> wrote:
> are there any additional problems or known issues running ccp4 or
> other xtal software on windows 7 (beyond those of Vista, etc.?)
Phenix, ARP/wARP, and HKL2000 do not run on Windows. I'm pretty sure none
On Thu, Aug 11, 2011 at 9:40 AM, Diana Tomchick <
diana.tomch...@utsouthwestern.edu> wrote:
> A quick glance at the header of the PDB file shows that there is one
> glaring discrepancy between it and the table in the paper that hasn't been
> mentioned yet in this forum. The data completeness (for
2011/8/11 Antony Oliver
> Surely in this ''modern age" data could be uploaded to "review server"
> whereby a reviewer could be given privileged access - to be able to see the
> model and maps, via something like AstexViewer, to gauge the quality and
> reliability of modelling - without actually g
On Tue, Jul 26, 2011 at 10:46 AM, Bernhard Rupp (Hofkristallrat a.D.) <
hofkristall...@gmail.com> wrote:
> Is there a simple way (or already an existing list) to extract/parse from
> the heterodictionaries or monomer libraries which 3-letter symbols are
> actually modified standard amino acids (as
On Tue, Jul 12, 2011 at 6:08 PM, Jiamu Du wrote:
> I am now working on a low resolution phase determination (around 3.3 A with
> Se anomalous signal around 3.8 A).
> I can find the Se site and get the phase, but the density map is not so
> good.
> Some part of the protein (about 1/3) has a homolo
On Mon, Jun 20, 2011 at 4:09 PM, Jayashankar wrote:
> Should I be happy if i get my crystals with one of the condition with a
> commercial kit
> containing citric acid and 40%MPD+ protein in(hepes+MgCl2)+ADP+VO3
>
Citric acid will chelate magnesium - this may not disrupt the
crystallization of th
On Thu, Jun 16, 2011 at 2:11 PM, Xun Lu wrote:
> I have a 3.2A dataset for a protein-DNA complex. The protein is a
> homodimer, and the DNA is almost palindromic (except one base pair in the
> middle and two or three base pairs at both two ends). It is my first time
> solving structures, an
On Tue, Jun 14, 2011 at 2:51 PM, wtempel wrote:
> Dear colleagues,
> following a discussion in our lab, I have volunteered to dig out
> articles from the literature about erroneous assignments of non-water
> entities such as metal ions, halides in protein models. For example I
> have the faint re
On Mon, Jun 13, 2011 at 9:48 AM, Dhanasekaran Varudharasu <
dhana...@gmail.com> wrote:
> We have solved one protein structure with barium as
> a heavy atom using SAD technique. But in the final refinement one barium
> site shows split. But the distance between the two posit
On Wed, Jun 8, 2011 at 4:44 PM, Madhu shankar Madhu shankar <
mad07...@student.otago.ac.nz> wrote:
>I am a beginer in crystallography. I have carried out molecular
> replacement in 'phenix' and now want to refine the structure in ccp4. Could
> anyone tell me what the proper Rfree_flag valu
On Wed, Jun 1, 2011 at 4:45 PM, Pavel Afonine wrote:
> to get feeling about how maps may look like at different resolutions do the
> following learning exercise: download a structure from PDB and compute Fcalc
> maps at different resolutions:
>
> phenix.fmodel model.pdb high_res=1
> phenix.fmodel
On Mon, May 23, 2011 at 1:17 PM, wrote:
> Thanks Nat! I am not doing real space refinement. Actually I am only using
> the maps for manual model building/adjustments. In this case, if some
> Rfree reflections have strong scattering intensities, removing them may
> lead to featureless density maps
On Mon, May 23, 2011 at 1:02 PM, Hailiang Zhang wrote:
> I have a preliminary question. I understand Rfree reflection sets are
> never used during automatic refinement, but, when generating the real
> space density maps, do we have to exclude Rfree columns? Any references
> will also be greatly a
On Thu, Mar 31, 2011 at 10:14 AM, Jacob Keller <
j-kell...@fsm.northwestern.edu> wrote:
> Also,
> setting occupancy = zero is not fudging but rather respectfully
> declining to comment based on lack of data. I think it is exactly the
> same as omitting residues one cannot see in the density.
No
On Thu, Mar 31, 2011 at 7:42 AM, Jacob Keller <
j-kell...@fsm.northwestern.edu> wrote:
> Why not have the "b-factors take care of it" until some magic cutoff
> number? When they reach the cutoff, two things happen:
>
> 1. Occupancies are set to zero for those side chains, to represent our
> lack o
On Tue, Mar 15, 2011 at 4:20 AM, John Chipperfield <
john.chipperfi...@postgrad.manchester.ac.uk> wrote:
> Therefore does anybody know of a quick way to build the remainder of a
> residue around its alpha carbon, short of manually building in COOT etc. I
> need to carry out this task on many pdb
On Mon, Mar 7, 2011 at 1:21 PM, wrote:
> We have found videomach, which costs a very small amount of money to
> obtain. Similarly, Adobe Premiere is affordable for an educational
> institution. We don't mind paying, but before we go there, does anyone have
> experience with making MPEG movies fro
On Fri, Feb 25, 2011 at 2:10 PM, Sean Seaver wrote:
> I've been curious if there has been discussion about moving data processing
> and refinement to a software as a service (SaaS) deployment. If programs
> were web accessible then it may save researchers time and trouble
> (maintaining and inst
On Fri, Jan 7, 2011 at 2:34 PM, Matthew Franklin wrote:
> However, I'm not sure if you're doing the right thing by leaving SIGF
> unassigned. I believe this should be assigned to the experimental error,
> which is usually called 'SIGF' in your mtz file. I don't know if FFT
> actually uses this
On Fri, Jan 7, 2011 at 10:49 AM, James Holton wrote:
> But what about MolProbity? and all those neat inter-digitating hydrogens?
> Should it not be possible for the refinement program to be "smarter" about
> where it puts riding hydrogens? Well, that is always possible, but I don't
> think MolP
On Mon, Dec 20, 2010 at 7:34 AM, Zhibing Lu wrote:
> Recently I solved a structure in which some water molecules have Bfactors
> at 0 and overall wilson Bfactor is 0.654 based on PHENIX refinement. Is it
> possible?
>
Very unlikely - it might be worth trying the latest nightly build and seeing
On Mon, Nov 29, 2010 at 6:50 AM, Tim Gruene wrote:
> But you have to make sure that refmac5 uses the same integer for flagged
> reflections as refmac does. If I remember correctly, the default in the
> ccp4i
> gui for refmac is 0 or 1 (out of usually 0-19 for 5% of flagged
> relfections),
> but I
On Fri, Nov 19, 2010 at 11:33 AM, Jacob Keller <
j-kell...@fsm.northwestern.edu> wrote:
> I took a look at his slides--looks pretty interesting, and I would
> have liked to have heard the talk! I am not sure I would be ready to
> advocate having no more journals, but I am interested in thinking
>
On Fri, Oct 29, 2010 at 5:46 PM, Tom Huxford wrote:
> I'm working with good quality relatively complete x-ray diffraction data
> collected to a resolution limit 2.6 Å from a crystal of a protein with a
> small molecule ligand bound. I ran MR from 10-4 Å and then did maximum
> likelihood rigid bod
On Wed, Oct 27, 2010 at 2:20 PM, Ed Pozharski wrote:
> One can also release structure in the PDB prior to submission - I
> believe the HPUB option is rarely (if ever) justified.
>
What's to prevent your closest competitor from downloading the structure and
using it to solve and refine his or her
On Tue, Sep 21, 2010 at 7:10 PM, William G. Scott <
wgsc...@chemistry.ucsc.edu> wrote:
> In fact, the only source-code I can find for pymol is on the fink mirror,
> for the OS X fink package I have been maintaining, i.e.,
>
> http://distfiles.master.finkmirrors.net/pymol-1.3-src.tar.bz2
How abou
On Sun, Sep 19, 2010 at 8:45 AM, wrote:
> I wanted to know which type of graphics card is more suitable for a
> notebook which is going to be used for structural biology. Integrated or
> dedicated? ATI or NVIDIA? At the moment I have to choose between an
> integrated Intel HD Graphics or a dedic
On Fri, Sep 3, 2010 at 4:53 PM, Jin H. Park wrote:
> I have solved the structure. But, there seems oddly strong density above
> histidine residue.
> What could this density be?
> The protein was in Tris buffer, with NaCl and DTT, and crystallized in
> NaSCN with PEG.
> (electron density in the pic
On Thu, Sep 2, 2010 at 5:31 AM, wrote:
> The other question is: why does phaser write 'R 3 :H' in the mtz? When
> the problem with the P21221 space group first popped up last year, Randy
> told me that space group numbers like 2018 are non-standard, and that
> space group 18 with the name P21221
On Wed, Aug 25, 2010 at 2:11 PM, George M. Sheldrick <
gshe...@shelx.uni-ac.gwdg.de> wrote:
> I would like to propose that we rename this list to the "Phenix (and
> CCP4) Bulletin Board". What have people got against sending purely
> Phenix questions to the Phenix list?
>
Actually, people who don
On Fri, Jul 2, 2010 at 11:29 AM, Tim Gruene wrote:
> I agree to this.
> What are the actual reasons against attachments?
> If one really has a slow network connection and cannot use IMAP instead of
> POP3
> (if I understand correctly, with IMAP one does not need to download the
> emails
> until o
On Wed, Jun 30, 2010 at 10:59 AM, Pavel Afonine wrote:
> I am refining a structure at 2.25 A using Phenix.refine. I am using TLS
> parameters for refinement but as i use TLS, phenix does individual
> anisotropic refinemnt also.
>
> No, it doesn't: it does not do "individual anisotropic refinement
On Fri, Jun 25, 2010 at 12:41 AM, Francois Berenger wrote:
> When you say "After molecular replacement you should check the result
> with the model building program of your choice and correct as many
> errors as possible before running a refinement program."
>
> Can this step be automated in some
On Wed, Jun 23, 2010 at 8:21 AM, Graeme Winter wrote:
> There will be a cctbx.python dispatcher now which should set
> everything up - however if you source setpaths_debug I think this
> should make for a happy python as it includes everything from the
> dispatcher.
>
Don't use setpaths_debug -
>
> atul kumar wrote:
>
>> dear all
>> I am trying to solve structure of data set at 1.9 A,r merge 9.3,it belongs
>> to space group P3221 unit cell 160.78 157.32 135.62 90.0 90.0 90.0,i has no
>> NCS ,i did tls as well but after water addition the r factor and r free is
>> stuck at 22 and 25 respec
On Mon, Jun 14, 2010 at 1:57 PM, Zhou, Tongqing (NIH/VRC) [E] <
tz...@mail.nih.gov> wrote:
> I have some problem in refining a structure. The data goes to 2.4A (with
> some 30% completeness at 2.15A), the structure was solved by MR with Phaser,
> refinement was done with Phenix, but the r and r-f
Most of what Kevin says applies equally well to Phenix - refinement is a
relatively complex series of calculations, much less inherently parallel
than what VMD is using GPUs for. There are many other things we could do to
speed up calculations that would probably be more useful and more effective.
On Thu, Jun 3, 2010 at 10:01 AM, Hailiang Zhang wrote:
> Not sure why, but sometime when I run it, it says
> "Max nr of points in map :4194304",
>
> some other times, it says
> "Max nr of points in map : 5000".
>
> All the runs are on the same machine, and I hope the latter ca
On Wed, Jun 2, 2010 at 3:06 PM, Eric Larson wrote:
> The authors need to take the initiative and let the PDB know when their
> structures have been published. The correspondence from the PDB people when
> they are curating the structure deposition says something along these lines:
>
Yes, and I'v
On Wed, Jun 2, 2010 at 12:07 PM, Andre Ambrosio <
andre.ambro...@cebime.org.br> wrote:
> We have recently obtained crystals from a small protein, and
> interestingly, at least for me, they are hollow trigonal rods (please see
> pictures attached).
>
> Just out of curiosity, has anybody ever seen
I thought that some of you might be interested that the journal Nature
has clarified the publication requirements regarding source code
accessibility. It is likely that some of you deserve congrats
for this. Cheers!
http://www.nature.com/nmeth/journal/v4/n3/full/nmeth0307-189.html
Although the
I'm not sure what "in desperation" means. You're trying to solve a
structure, so all options are open, right? They don't have to be elegant,
it just has to work. :)
Yes, but it's not worth wasting time and resources on something that is
guaranteed to fail. In this case, it's a 50kD protein tha
I had a debate with a coworker about using MR in desperation and I'm
curious what the most extreme case is where a very different model was
used to solve a structure. This could be highest RMSD, lowest % identity,
or most incomplete model. I'm also curious whether homology modelling has
ever
for ground state ATP analogues use AMP-PNP (or AMP-PCP) or ADP in complex
with beryllium fluoride.
In some circumstances ATP-gamma-S will work too. It's less resistant to
hydrolysis, so it's a bad idea for many enzymes, but the resulting active
site geometry can be different depending on whic
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