On Sun, Jan 25, 2015 at 12:25 AM, Kay Diederichs <
kay.diederi...@uni-konstanz.de> wrote:
> Here, I subtracted the "Phenix and Refmac" entries from the total Phenix
> count, because it seems likely that Phenix was used for other purposes than
> refinement.
>
Actually, based on my skimming of meth
On Wed, Jan 21, 2015 at 12:24 PM, Keller, Jacob
wrote:
>I think this will probably never happen, but maybe there could be a
> confidence value associated with each atom in structures a posteriori,
> although it might be difficult to find the right automatable criteria for
> this value. The el
On Wed, Jan 21, 2015 at 10:17 AM, Keller, Jacob
wrote:
> I see your point about not knowing that it’s a chloride, but I think you
> would agree that it is certainly more likely a chloride than map-noise, and
> perhaps more likely than water as well. Would you agree that chloride is
> the best gu
On Wed, Jan 21, 2015 at 9:05 AM, Keller, Jacob
wrote:
> Not sure why there is this level of suspicion about the poor halide when
> waters generally get assigned so haphazardly. I would say that there are
> probably more “wrong” waters in the PDB than wrong chlorides, but there’s
> not much fuss
On Wed, Jan 21, 2015 at 12:16 AM, Engin Özkan wrote:
> Carbon in chloride's coordination sphere? To me, it looks like you have
> serious vdW violations, and neither water nor chloride could go there.
>
Halides can interact with carbon too - discussed in Dauter & Dauter (2001)
- although I think
On Wed, Dec 31, 2014 at 10:11 AM, Faisal Tarique
wrote:
> I request you to please tell me the three letter code for pyridoxine..
>
You can find the appropriate residue code for any molecule previously
deposited in the PDB - which includes pyridoxine - by simply searching for
the conventional nam
On Mon, Dec 8, 2014 at 7:24 PM, Keller, Jacob
wrote:
> FYI, sometimes native nucleotides can make it through protein
> purifications if binding is tight.
>
This is especially true for G-proteins, since tight binding to GDP is an
essential part of their function. I don't know what to expect fro
On Thu, Nov 6, 2014 at 5:20 PM, Oliver Clarke wrote:
> I wonder if a solution might be to create new residues containing alkyl
> chains of various lengths, named something like U01, U02, U(n), where N is
> the length of the alkyl chain that fits the density. Sort of similar to the
> way one might
On Wed, Oct 29, 2014 at 8:53 PM, luzuok wrote:
> I think it is better for COOT to solve this issue.
>
Coot already can be used to solve this issue - I think the automation is
somewhat lacking, but it's vastly preferable to anything involving a text
editor or shell commands.
1. Load molecule
On Fri, Sep 26, 2014 at 8:17 PM, Kimberly Stanek
wrote:
> Before refinement in phenix the R/Rfree gap is rather small, however even
> after one round of refinement I am finding that this gap increases to
> almost 0.06. I have a feeling that the high symmetry present has something
> to with this
The tests that output twinning fractions are *not* diagnostic for twinning;
they merely estimate what the twin fraction would be if the data were in
fact twinned, which can only be decided on the basis of abnormal intensity
statistics. (Any version of Xtriage since July should state this more
clea
In Python scripting (Calculate menu):
set_rotation_centre(x, y, z)
I assume there's a Scheme equivalent.
-Nat
On Tue, Sep 9, 2014 at 1:17 PM, Alejandro Virrueta <
alejandro.virru...@yale.edu> wrote:
> Does anyone knowhow to move the center pointer to a specific x,y,z
> coordinate? Or to place
On Thu, Sep 4, 2014 at 4:05 PM, CPMAS Chen wrote:
> Do you guys have some recommendation of the criteria? phenix reported
> anomalous measurability, CCP4/aimless has RCRanom. Sometimes, they are not
> consistent.
>
The "measurability" isn't always useful - it's definitely correlated with
how eas
On Tue, Aug 12, 2014 at 10:28 PM, Keller, Jacob
wrote:
> A somewhat similar question, with a quick answer I hope: when programs
> output CC's of 1/2 datasets, are several random halvings compared/averaged,
> and if not, does this make a difference, or are the scores so similar
> there's no point?
On Wed, Jul 23, 2014 at 3:25 AM, MARTYN SYMMONS <
martainn_oshioma...@btinternet.com> wrote:
> The practice at the PDB after deposition used to be to remove water
> alternate position indicators - although obviously to keep their partial
> occupancies.
>
This has not been my experience - see for
On Wed, Jul 9, 2014 at 5:14 PM, Chris Fage wrote:
> Despite modelling completely into great electron density, Rwork/Rfree
> stalled at ~38%/44% during refinement of my 2.0-angstrom structure
> (P212121, 4 monomers per asymmetric unit). Xtriage suggested twinning,
> with <|L|> = 0.419, = 0.245, a
On Thu, Jul 3, 2014 at 7:50 AM, Nat Echols
wrote:
> On Thu, Jul 3, 2014 at 6:53 AM, Dirk Kostrewa
> wrote:
>
>> yes - unfortunately, in my hands, phenix.xtriage reads the XDS_ASCII.HKL
>> intensities as amplitudes, producing very different output statistics,
>&g
On Thu, Jul 3, 2014 at 6:53 AM, Dirk Kostrewa
wrote:
> yes - unfortunately, in my hands, phenix.xtriage reads the XDS_ASCII.HKL
> intensities as amplitudes, producing very different output statistics,
> compared both to the XDS statistics and to an mtz file with amplitudes
> created from that XDS
On Tue, Jul 1, 2014 at 3:10 PM, Katherine Sippel wrote:
> My google-fu has failed me once again so I am turning to the collective
> knowledge of the bb. I'm working on a blobology challenge at the moment and
> have hit a wall. Is anyone aware of an ion that coordinates to lysine and
> prefers oct
On Fri, May 16, 2014 at 7:12 AM, wrote:
> Short of storing images, which is the ultimate preservation of primary
> information, I have always been puzzled by the fact that the PDB only
> stores
> unique reflections i.e. no Friedel pairs even when provided. Is this
> outdated
> perhaps ? I remembe
regard this published structure as unreliable since a
> misconduct investigation by the University of Alabama at Birmingham has
> concluded that it
> was, "more likely than not", faked [1]
>
> [1] http://www.nature.com/news/2009/091222/full/462970a.html
>
>
>
>
&
On Thu, May 15, 2014 at 9:53 AM, Patrick Shaw Stewart wrote:
> It seems to me that the Wikipedia mechanism works wonderfully well. One
> rule is that you can't make assertions yourself, only report pre-existing
> material that is attributable to a "reliable published source".
>
This rule would
On Wed, May 14, 2014 at 10:53 AM, Mark Wilson wrote:
> As for the meaning of integrity, I'm using this word in place of others
> that
> might be considered more legally actionable. A franker conversation would
> likely more clearly draw the line that we're wrestling with here.
>
The reference t
On Wed, May 14, 2014 at 10:26 AM, Mark Wilson wrote:
> Getting to Eric's point about an impasse, if the PDB will not claim the
> authority to safeguard the integrity of their holdings (as per their
> quoted statement in Bernhard's message below), then who can?
I think this may in part boil down
On Tue, May 13, 2014 at 9:20 PM, Felix Frolow wrote:
> Phenix does even more, it adds TER after ions and ligands, so again manual
> messing is needed.
> However they may have a jiffy to fix it.
>
phenix.sort_hetatms will remove them for you, although why this "problem"
was apparently beyond the c
On Wed, Apr 23, 2014 at 6:15 AM, wrote:
> This discussion is very informative to fresher like me. Moreover, with
> most of the reading suggested in this discussion I read about the
> positively charged metal ions like Na, Ca, Mg and many more. I am curious
> about Cl in specific which could occu
On Wed, Apr 23, 2014 at 8:43 AM, Cygler, Miroslaw
wrote:
> I have inquired at Schrodinger about the licensing for PyMol. I was
> surprised by their answer. The access to PyMol is only through a yearly
> licence. They do not offer the option of purchasing the software and using
> the obtained versi
On Mon, Apr 21, 2014 at 3:36 PM, Faisal Tarique wrote:
> Just in the continuation of my previous mail i again want to ask few
> question on the metalloprotiens..Apart from factors like occupancy, B
> factor, coordination sphere and metal ion-ligand distances to distinguish
> Mg or calcium, can ano
On Fri, Apr 4, 2014 at 10:39 AM, Alastair Fyfe wrote:
> Reconstructing the refinement may be necessary in some cases but there
> are other applications (pdb-wide map statistics, development of map
> analysis tools, quick model vs map checks) where access to the depositor's
> final map would be s
On Fri, Apr 4, 2014 at 9:36 AM, Alastair Fyfe wrote:
> The topic brings up a question that I've been wondering about for some
> time, perhaps someone can enlighten me. Why is it not standard practice to
> deposit map coefficients along with structure factors ? Unlike image
> deposition there are
On Fri, Apr 4, 2014 at 1:57 AM, Tim Gruene wrote:
> A more up-to-date reason is that programs calculate R values very
> differently. If you take a PDB file refined with program X and put it
> into program Y you easily get discrepancies greater than 5%.
>
This is actually pretty rare - usually it
On Tue, Mar 18, 2014 at 6:59 PM, Remie Fawaz-Touma wrote:
> how do you place the pointer if there is no bond there? (just density) I
> am trying to connect 2 sugars creating 2 bonds to one oxygen that I have to
> add (oxygen does not exist now).
>
On my Mac, I can change the pointer position by h
On Thu, Mar 6, 2014 at 11:45 AM, Keller, Jacob wrote:
> I was curious whether there has been a rigorous evaluation of ion binding
> sites in the structures in the pdb, by PDB-REDO or otherwise. I imagine
> that there is a considerably broad spectrum of habits and rigor in
> assigning solute blobs
On Tue, Feb 18, 2014 at 8:19 AM, Jan van Agthoven wrote:
> I'm filling out my table for NSMB, about a structure of protein ligand
> bound to a receptor. They ask for 3 different lines regarding number
> of atoms & bfactor. 1) Protein 2) Ligand/Ion 3) Water.
> Does my protein ligand belong to Prot
One comment (not a complaint) on all this: it seems like the same questions
get asked over and over again. If there is a good place for a general
crystallography FAQ list it is well past time for one to be put together -
or maybe it just needs to be better advertised? At a minimum, for instance:
On Mon, Dec 16, 2013 at 1:36 PM, Xiao, Junyu wrote:
> Dear all, sorry if this topic does not interest you. I wonder whether
> anyone has experience with freezing crystals grown in ~0.2 M Magnesium
> Formate. Garman and Mitchell suggested that "A major anomaly is solution
> 44, 0.2 M magnesium fo
On Wed, Nov 6, 2013 at 12:39 AM, Bernhard Rupp wrote:
> Hmmm….does that mean that the journals are now the ultimate authority of
> what stays in the PDB?
>
> I find this slightly irritating and worthy of change.
>
http://www.wwpdb.org/UAB.html
"It is the current wwPDB (Worldwide PDB) policy that
On Tue, Nov 5, 2013 at 12:22 AM, Bernhard Rupp wrote:
> Given their otherwise almost paranoid sensitivity to ultimate author
> authority
>
> (resulting in things like still having 2hr0 etc in the bank because
> certain authors go AWOL or ignore major issues)
>
In defense of the PDB, it's not just
On Wed, Oct 23, 2013 at 1:10 PM, Kristin Low wrote:
> I’m looking at upgrading my current laptop to a newer MacBook Pro. I’m
> torn as to whether I need integrated vs discrete graphics for structural
> biology, including molecular modelling, especially since the latest
> advances by Intel in term
On Thu, Oct 17, 2013 at 6:51 AM, Lucas wrote:
> I wonder if there's a list of problematic structures somewhere that I
> could use for that practice? Apart from a few ones I'm aware of because of
> (bad) publicity, what I usually do is an advanced search on PDB for entries
> with poor resolution a
On Wed, Oct 9, 2013 at 6:56 PM, Marco Lolicato wrote:
> Anyway, for those reasons and more, I was wondering if maybe is nowadays
> needed to revisit the peer-review process.
>
Apologies for the lengthy response, but I really do think the current
publication system is broken, just not for the sa
Levitt also contributed to DEN refinement (Schroder et al. 2007, 2010).
-Nat
On Wed, Oct 9, 2013 at 2:29 PM, Boaz Shaanan wrote:
> Good point. Now since you mentioned contributions of the recent Nobel
> laureates to crystallography Mike Levitt also had a significant
> contribution through the
On Wed, Aug 14, 2013 at 10:31 PM, Edward A. Berry wrote:
> If you refine once in phenix you can use phenix.cc_star to calculate cc*
> and compare with R and R-free; from the output mtz file and your unmerged
> .sca file.
>
FYI, this should also work with structures refined in Refmac, assuming it
On Wed, Aug 7, 2013 at 2:36 PM, James Stroud wrote:
> Although it is likely the "best" library for working with structural data,
> CCTBX requires a loop just to change a specific chain ID (to the best of my
> knowledge):
>
> ...
>
> I don't intend to pick on CCTBX specifically (because the CCTBX
On Wed, Aug 7, 2013 at 12:54 PM, James Stroud wrote:
> All that needs to happen is that the community agree on
>
> 1. What is the finite set of essential/useful attributes of macromolecular
> structural data.
> 2. What is the syntax of (a) accessing and (b) modifying those attributes.
> 3. What i
On Mon, Aug 5, 2013 at 12:37 PM, Boaz Shaanan wrote:
> There seems to be some kind of a gap between users and developers as far
> the eagerness to abandon PDB in favour of mmCIF. I myself fully agree with
> Jeffrey about the ease of manipulating PDB's during work, particularly when
> encounterin
On Mon, Aug 5, 2013 at 11:11 AM, Phil Jeffrey wrote:
> While alternative programs exist to do almost everything I prefer
> something that works well, works quickly, and provides instant visual
> feedback. CCP4 and Phenix are stuck in a batch processing paradigm that I
> don't find useful for thes
On Mon, Jul 22, 2013 at 6:11 PM, Katherine Donovan <
katherine.dono...@pg.canterbury.ac.nz> wrote:
> *PHENIX – XTRIAGE*
> * *One possible pseudo merohedral twin operator
> 2-fold axis
> h, -k, -h-l
>
> /**2 = 2.032
> **2/ = 0.787
> <|E**2-1|> = 0.734
> <|L|>, = 0.490, 0.321
> Multivariate Z scor
On Mon, Jul 22, 2013 at 10:19 AM, Stefan Gajewski wrote:
> The maps shows signs of over fitting, the B-factors do not look correct in
> my opinion.
What do "correct" B-factors look like? What refinement strategy did you
use for them?
> Note that the R-free value in the 3.4A shell is lower tha
On Fri, Jul 12, 2013 at 1:08 AM, Stefan Krimmer <
krim...@staff.uni-marburg.de> wrote:
> in some of my macromolecular crystal structures with resolutions between
> 1.1 - 1.4 Å, several round positive Fo-Fc electron density blobs are
> detectable which show after assignment of a water molecule to t
On Sat, Jun 22, 2013 at 3:18 PM, Frank von Delft <
frank.vonde...@sgc.ox.ac.uk> wrote:
> In what scenarios would these improved estimates make a significant
> difference?
>
Perhaps datasets where a unusually large number of reflections are very
weak, for instance where TNCS is present, or where
On Thu, Jun 13, 2013 at 8:15 AM, Andrea Edwards wrote:
> I have some rather (embarrassingly) basic questions to ask. Mainly.. when
> deciding the resolution limit, which statistics are the most important? I
> have always been taught that the highest resolution bin should be chosen
> with I/sig no
On Fri, Jun 7, 2013 at 8:37 AM, Pete Meyer wrote:
> On the other hand, programming an implementation of something is a good
> way to make sure that you really understand it - even if you end up using
> another program.
I would argue that it's not really necessary to understand the column
format
On Thu, Jun 6, 2013 at 2:37 PM, GRANT MILLS wrote:
> My script seems to miscount the columns and read the two as one column,
> does anyone know how to avoid this? (PS, I've googled this like crazy but I
> either don't understand or the link is irrelevant)
>
You should resist the temptation to w
On Mon, Apr 15, 2013 at 11:47 AM, James Holton wrote:
> However, I'm sure the day is not far off when phenix.refine or the like
> will check if the starting R factor is too high and just "automatically"
> invoke a run of MR to see if something clicks.
>
I think the latest Phaser code actually do
On Fri, Apr 12, 2013 at 2:45 PM, Boaz Shaanan
wrote:
> Whichever way the input file for the run is prepared (via GUI or command
> line), anybody who doesn't inspect the log file at the end of the run is
> doomed and bound to commit senseless errors. I was taught a long time ago
> that computers a
On Fri, Apr 12, 2013 at 10:27 AM, James Holton wrote:
> But, when it comes to GUIs, I have always found them counterproductive.
> In my humble opinion, the purpose of computers and other machines is to DO
> work for me, not create work for me, and I already have enough buttons to
> push each day
On Thu, Mar 28, 2013 at 11:28 AM, wrote:
> Although it is hard to imagine, there could be a mechanism by
> which you make all your data public, immediately when you get it and this
> public record shows who "owns" it.
http://deposit.rcsb.org
(or international equivalent)
> The advantage (in my
On Fri, Mar 8, 2013 at 11:38 AM, Raji Edayathumangalam
wrote:
> I am looking for two specific test cases (below) and appreciate anyone
> pointing me to known structures/examples for the same.
>
> (1) For a successful case of molecular replacement in which the search model
> has an overall sequence
On Mon, Feb 25, 2013 at 8:02 AM, lei feng wrote:
> I need your suggestion for slowing down crystallization for my protein
> my protein got hit in PEG/ION #5 ( 0.2 M MgCl2, 20% PEG 3350, pH 5.9), but
> it crystallize too fast. In 1 hr I can see tons of tiny needles.
> Can anyone give me some sugges
On Wed, Feb 20, 2013 at 12:39 PM, Jacob Keller
wrote:
> it has been my experience that homology modelling programs get folds pretty
> well, but sometimes the details are pretty obviously bad, like too-close
> contacts. One might think that the modelling software would put in a sort of
> "polishing
If SPG buffer is what I think it is, that means you have a significant
concentration of inorganic phosphate, which forms salt crystals when
mixed with divalent metal ions.
-Nat
On Thu, Feb 7, 2013 at 2:24 PM, amro selem wrote:
>
>
>
>
> Hallo my colleagues.
> i hope every one doing ok . i did s
On Mon, Feb 4, 2013 at 12:24 PM, Roger Rowlett wrote:
> It's possibly a transition metal ion. Zinc is a common adventitious
> contaminant of solutions. Typical Zn-O distances (tetrahedral or
> pseudo-tetrahedral coordination) are 2.0 A. ICP-OES or ICP-MS of the protein
> solution might offer a clu
On Mon, Jan 28, 2013 at 8:39 AM, Robbie Joosten
wrote:
> DSSP recently went open source with a very liberal license. So you can
> consider using the real DSSP now. This may also be the moment to integrate
> DSSP in CCP4.
Based on the info here:
http://swift.cmbi.ru.nl/gv/dssp/
the license isn't
On Mon, Jan 28, 2013 at 8:04 AM, Antony Oliver
wrote:
> If you don't mind using the ksDSSP implementation, it is already installed
> with the phenix suite if you have it.
Correct, but although the method is supposed to be the same, the
output is not, and there are bugs in how it presents helix
a
On Fri, Jan 25, 2013 at 2:24 AM, Robbie Joosten
wrote:
> Phenix however needs to deal with the CCP4 type reflection binning. Now the
> size of the sets cannot be used which means that you have find a smarter
> solution. So I wonder how this is implemented. Does Phenix use the
> (reasonable) assump
On Thu, Jan 24, 2013 at 3:52 PM, Urmi Dhagat wrote:
> If Rfree reflections are refined my refmac upon switching from phenix to
> refmac then does this contaminate the Rfree set ? Should swiching between
> refinement programs Phenix and Refmac be avoided?
Repeating what was said earlier today: i
On Thu, Jan 24, 2013 at 10:34 AM, Leonid Sazanov
wrote:
> Most likely scenario is that Phenix by default assigns Rfree flag as 1, while
> ccp4/refmac - as 0.
> That would explain your Rfree going down - because your Rfree reflections
> were refined by refmac.
According to Garib, the current ver
On Tue, Jan 22, 2013 at 10:05 PM, James Stroud wrote:
> On Mac v. Linux where calculations come secondary to office-type
> calculations, you have to weigh your level of vendor lock-in. Do you run
> Libreoffice or Microsoft Office? Inkscape or Illustrator? Gimp or Photoshop?
> Etc. If you are lo
On Tue, Jan 22, 2013 at 9:59 AM, Cara Vaughan
wrote:
> I've seen from the archive that some people do use the Mac Mini for
> crystallography and I've got two questions:
> 1. Do I need the Quad core or is a Dual core processor enough?
You can survive with the dual, but I would definitely spring fo
On Wed, Jan 16, 2013 at 2:53 PM, Roger Rowlett wrote:
> When you are a building a metalloenzyme model you should really have some
> solid evidence that a metal ion is present by (1) inclusion in the
> crystallization medium, (2) direct determination by an analytical technique,
> (3) UV-visible spe
On Mon, Jan 14, 2013 at 11:18 AM, Tim Gruene wrote:
> I admit not having read all contributions to this thread. I understand
> the "John Henry Challenge" as whether there is an 'automated way of
> producing a model from impossible.mtz'. From looking at it and without
> having gone all the way to a
artfast:~/uni/datasets/nk/xds_run3$ adxv -sa
>> DX-CORRECTIONS.cbf DX-CORRECTIONS.tiff
>> Adxv Version 1.9.8
>> Copyright (C) 1994-2011 by Andrew Arvai, Area Detector Systems Corporation
>> Recognized CBF format data.
>> Warning: Could not find diffrn_frame_data or diffrn
On Mon, Jan 7, 2013 at 1:28 AM, Xiaopeng Hu wrote:
> We recently resolved an enzyme/inhibitor complex structure. The enzyme
> contains two NCS related active site and we did find extra density in both of
> them.However we observed that the two inhbitor moleculors are not NCS
> related, but part
On Thu, Nov 8, 2012 at 12:20 AM, Mark J van Raaij
wrote:
> Depends on what you call a "solved structure".
> For deposition to the pdb ideally there should be very little clashes like
> Nat writes.
> But perhaps you are referring to the clash score just after molecular
> replacement, like that ou
On Wed, Nov 7, 2012 at 4:02 PM, Meisam Nosrati wrote:
> I want to know what is considered an acceptable Clash Score for a solved
> structure.
The recommendation from MolProbity is less than 10. If you have
low-resolution data and don't have a high-resolution starting model,
it could be a little
On Tue, Nov 6, 2012 at 12:06 PM, saleem raza wrote:
> I have to put water molecules in my model but It's difficult to judge that
> electron density is for water of something else. How to differentiate
>
> How the electron density look like for metal ions like Ca and Na???
Sodium can't be dist
On Tue, Oct 30, 2012 at 12:12 PM, Jim Pflugrath
wrote:
> How would you distinguish between a mixture of Ca and Zn in the same
> locations?
How often would they be likely to bind in the same place? Some of the
other transition metals are difficult to tell apart, but Ca and Zn
have very different
On Tue, Oct 30, 2012 at 7:44 AM, Jacob Wong wrote:
> Dear all, I have this (3.0 A) structure that has 8 molecules per ASU -
> Phaser was able to find 7 molecules correctly, but not the last one, as
> indicated by the .sol file (TFZ=5.1) below and the resultant density map. I
> tried to delete the
On Tue, Oct 23, 2012 at 9:55 AM, Meindert Lamers
wrote:
> Is there any convention on the numbering of residues in a fusion protein?
>
> I have a structure of two domains fused together but would like to keep the
> biological numbering intact.
> 1st domain: residue 200-300 (protein A).
> 2nd domain
On Tue, Sep 25, 2012 at 6:51 AM, Tim Gruene wrote:
> I would assume that someone who publishes crystallisation conditions has
> given up solving the structure or some other reason to encourage others
> to pick up the project, i.e., no, I don't see much point NOT
> publishing your data.
I always a
On Wed, Sep 12, 2012 at 12:49 PM, James Stroud wrote:
> Also, python (aka python 2) and python 3000 (aka python 3) are considered
> two different languages. It's not reasonable to consider them one language
> and then complain that they are incompatible. Python 3 was created as a new
> language (a
On Wed, Sep 12, 2012 at 7:32 AM, Jacob Keller
wrote:
> since this probably comes up a lot in manipulation of pdb/reflection files
> and so on, I was curious what people thought would be the best language for
> the following: I have some huge (100s MB) tables of tab-delimited data on
> which I woul
On Thu, Aug 23, 2012 at 10:44 AM, Jim Pflugrath
wrote:
> Singly-measured reflections should have a sigma from Poisson counting
> statistics, so that should not be a problem. A problem might occur if the
> X-ray background is exactly zero and the observed (sic) intensity is exactly
> zero.
Or the
On Thu, Aug 9, 2012 at 12:52 PM, Lee, Ting Wai wrote:
> May I ask a very general question? I am going to buy a laptop. I am going to
> do a lot of structural biology work on it using programs such as CCP4,
> Phenix, Coot and Pymol. Mac or PC, which is better?
See this morning's thread. Short ans
On Thu, Aug 9, 2012 at 8:14 AM, Quentin Delettre wrote:
> I have seen that in the last Mac Os, X11 have been removed... But can still
> be used with some package installation.
I guess it isn't distributed with the OS any more - but it is still available:
http://xquartz.macosforge.org/landing/
-
On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller
wrote:
> one. Are there any really reasonable arguments for preferring Mac over
> windows (or linux) with regard to crystallography? What can Mac/Linux do
> that windows cannot (especially considering that there is Cygwin)? What
> wonderful features am
On Wed, Aug 1, 2012 at 11:27 AM, Uma Ratu wrote:
> The protein is in tetramer form. I define this by using the residue number
> (1332) which is 4 x monomer.
>
> After run, Phaser only gave 9 partial solutions, and no solution with all
> components. The resulted PDB contains only dimer form of the
On Tue, Jul 24, 2012 at 10:33 AM, Ethan Merritt
wrote:
> As to the home source - no.
> Neither Cu nor Zn has appreciable anomalous signal when excited with a
> Cu K-alpha home source.
> http://www.bmsc.washington.edu/scatter
>
> An element's emission edge (Cu K-alpha in this case) is about 1 keV
On Tue, Jul 24, 2012 at 10:14 AM, Haytham Wahba wrote:
> 1- if i have anomalous peak of unknown heavy atom, How can i identify this
> heavy atom in general. (different methods)
>
> 2- in my case, i see anomalous peak in heavy atom binding site (without any
> soaking). preliminary i did mass spec.
On Mon, Jul 23, 2012 at 9:50 AM, Scott Foy wrote:
> We are computationally averaging several homologous protein structures into a
> single structure. This of course will lead to a single protein structure that
> possesses poor biophysical characteristics of bond lengths, bond angles,
> steric h
On Fri, Jul 13, 2012 at 2:19 PM, Radisky, Evette S., Ph.D.
wrote:
> Several have mentioned harvesting in the cold room to reduce evaporation. I
> used to do this also as a postdoc, but I worried whether I risked nitrogen
> gas poisoning from liquid N2 boil-off, since the cold room did not seem ve
On Sun, Jul 8, 2012 at 2:11 PM, James Garnett wrote:
> I have found a molecular replacement solution in I212121 using an NMR
> structure of the same protein and MR-ROSETTA/PHENIX (PHASER LLG=128
> TFZ=12.3), although I can not refine this below R ~45% and Rfree ~50%. The
> maps look OK in parts
On Wed, Jun 20, 2012 at 11:13 AM, sonali dhindwal <
sonali11dhind...@yahoo.co.in> wrote:
>
> I am working on a protein for last so many years and for which i have got
> crystal now in a tray which i kept 1 years ago. It diffracts well and
> resolution is 2.2A, which is good.
>
> I indexed in HKL20
On Tue, Jun 19, 2012 at 8:35 AM, RHYS GRINTER
wrote:
> There's no significant difference between the high res and low res proteins
> in the shared region (amino acid 38+) (r.m.s.d 0.46 A), and the while there
> is broken density for the first 38aa from the full length data it's too poor
> to mo
On Tue, Jun 12, 2012 at 8:53 PM, Frank von Delft
wrote:
> Finding 111 sites should be feasible without other tricks than very careful
> data collection (see below); if you have two or more copies in the ASU, you
> may find you need to do what the ribosome guys did, namely use other
> derivatives
On Sat, May 5, 2012 at 2:23 PM, Pavel Afonine wrote:
> may be I'm missing something but I think all you need to do is to place (add
> to PDB file) a Zn2+ into a blob of density that you believe that Zn belongs
> to, and then most of refinement tools will take care of it automatically. So
> I'm not
On Sat, Apr 7, 2012 at 9:50 AM, Roger Rowlett wrote:
> I don't know the state of current software, because I haven't tried
> recently, but when I set up my student crystallography workstations a few
> years back I noticed many packages (e.g. EPMR, Phaser) that had potentially
> long run times (whe
On Mon, Apr 2, 2012 at 11:00 AM, Maria Sola i Vilarrubias
wrote:
> About a wrongly fit compound, the reviewer can ask images about the model in
> a map calculated at a specific sigma and in different orientations.
This will often be insufficient, I'm afraid. We generally assume good
faith on the
On Thu, Feb 16, 2012 at 7:17 AM, Francis E Reyes
wrote:
> The problem is not developers ensuring their identities by signing their
> apps. It's that there's now a (small) barrier for the end user in installing
> unsigned apps.
>
> The implementation has yet to be seen, but will getting around t
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