I didn’t see the following solution in any other responses. It’s probably the
most reasonable one given the constraints of collaboration and publishing.
In the absence of using the best software, I found it practical to write the
equations in MathType and save them as MathType PDF equations and
On May 12, 2015, at 3:08 PM, Douglas Theobald wrote:
> On May 12, 2015, at 4:50 PM, wrote:
>> I like the open source model, but there are problems with this model along
>> with the others. One major problem is that the authors are expected to
>> support their software after others have gone in
Making the software OSS solves many problems. For example, it solves the
problem of interdependency. Many tools these days aggregate the functions of
several different software packages into pipelines. If one step in that
pipeline is unavailable then the pipeline can be rendered unusable.
Most
of renewed funding and having to cut
> staff that had the knowledge?
> I'm pretty sure you only know part of the story.
>
>
> On Tue, May 12, 2015 at 11:48 AM, James Stroud wrote:
> I hereby call on the broadest community of academics and researchers,
> including scien
On May 12, 2015, at 12:29 PM, Roger Rowlett wrote:
> Was the research publicly funded? If you receive funds from NSF, for example,
> you are expected to share and "make widely available and usable" software and
> inventions created under a grant (section VI.D.4. of the Award and
> administrati
I hereby call on the broadest community of academics and researchers, including
scientists, historians, economists, sociologists, psychologists, and whoever
else has ever published a paper or read from the literature thereof, to reject
any and all papers that describe new software that itself is
You may want to drop the symmetry to see what is happening with the loop.
James
On Jun 10, 2014, at 11:48 AM, Nicholas Keep wrote:
> Am refining a structure in P3(1)21 with three copies in the ASU. It is pretty
> close to completion R/Rfree 18/21 with 2A data.
> However in one copy a section t
On Aug 7, 2013, at 2:35 PM, Ed Pozharski wrote:
> If I understand your proposal and reference to SQL correctly, you want some
> scripting language that sounds like simple English.
I didn't say anything about being English-like. English and other natural
languages are ill-adapted to describing th
On Aug 7, 2013, at 1:06 PM, Ed Pozharski wrote:
> On 08/07/2013 01:51 PM, James Stroud wrote:
>> In the long term, the MM structure community should perhaps get its
>> inspiration from SQL
> For this to work, a particular interface must monopolize access to structural
> d
On Aug 5, 2013, at 4:33 AM, Eugene Krissinel wrote:
> I just hope that one day we all will be discussing a sort of universal API to
> read/write structural information instead of referencing to raw formats, and
> routines to query MX data, which would be more appropriate than grep (would
> many
On Jun 5, 2013, at 10:41 PM, Nat Echols wrote:
> 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 i
I think there are some mitegen loops that are flat. They will probably be
useful for your crystals given what you say about the 2.2 Å anisotropic
diffraction, which is probably caused by deformation of your plates in
"conventional" loops.
Some others on the list may have a more specific recomme
On Apr 12, 2013, at 12:44 PM, eugene.krissi...@stfc.ac.uk wrote:
> What, I'm afraid, people rarely realise these days, is that their desktops
> are, essentially, GUIs to various OS features, so they obviously use GUI more
> frequently than they think :) After all, this is all matter of habits an
The concept of a "domain" in a DNA structure is a bit obscure. Could you be
more explicit about what you are trying to do? Do you mean protein domains in a
protein-DNA complex?
James
On Apr 12, 2013, at 12:18 AM, Veerendra Kumar (Dr) wrote:
> Dear CCP4 members,
> Is there any program to supe
On Apr 11, 2013, at 6:17 AM,
wrote:
> Sorry that this was unclear. We assume that updater is used primarily from
> ccp4i, where nothing changed (and why it should be used from command line at
> all ?:)).
Scriptability.
On Apr 11, 2013, at 10:34 AM, Jim Pflugrath wrote:
> I think James get
ns that I found (6.3.0-020). I only figured out what information was trying to be communicated because of your message (see attachment).JamesOn 11 Apr 2013, at 03:54, James Stroud wrote:Hello All,I downloaded a crispy new version of CCP4 and ran update until the update update script disappeared. Is th
Hello All,
I downloaded a crispy new version of CCP4 and ran update until the update
update script disappeared. Is the reason that CCP4 has reached its final update?
James
The underlying issue is that the implementation of OS X dynamic linking is
dependent system architecture. As I understand it, OS X 10.5.8 has a 32 bit
kernel, so its dynamic linking is not forward-compatible with 64 bit OS X
versions, for which SHELX-2013 seems to built.
Also, to be fair, it's
It seems like the problem is that the Indigo has an IP address that is not part
of the subnet that it is on, so this makes network access impossible. Is this
correct?
If so, you can just spoof the proper subnet in isolation. You can run dd-wrt on
a compatible router and assign any subnet you wa
On Jan 22, 2013, at 11:20 PM, Nat Echols wrote:
> The real difficulty is integrating Macs into a
> Linux-centric environment, for example configuring NFS, NIS, etc.
That's because NFS and NIS are antiquities left over from the days of
mainframes. Distributed file systems and user information data
I meant c.2006 iMac, of course.
James
On Jan 22, 2013, at 11:05 PM, James Stroud wrote:
> Get a quad-core. If you have iTunes going, some website running javascript
> without your knowing it, and you have a computational job running, then
> you've used up your dual core
Get a quad-core. If you have iTunes going, some website running javascript
without your knowing it, and you have a computational job running, then you've
used up your dual core and things get sluggish. It happens to me all the time
on my c. 1996 iMac, which is still (barely) good enough for me.
he two monomers should be
adjacent.
If it is T4 ("tetrahedral") symmetry, then you need two generators, with one
generator made from a pair of monomers opposite and one generator made from a
pair adjacent.
James
On Jan 10, 2013, at 6:05 PM, James Stroud wrote:
> The transfor
The transformation matrix describing the symmetry is sensitive to the
coordinate system origin. You should center the entire tetramer on the origin
(0, 0, 0), where the origin coincides with the point symmetry element. If you
have a tetramer with true point symmetry, then the center of the tetr
In O, the command is called symm_sphere.
http://xray.bmc.uu.se/alwyn/A-Z_of_O/everything_s.html#anchor536668
James
On Nov 18, 2012, at 10:14 AM, Bosch, Juergen wrote:
> Hi Pavel,
>
> does this also work for symmetry related atoms ?
>
> Jürgen
>
> ..
> Jürgen Bosch
> Joh
On Nov 16, 2012, at 12:01 PM, Ed Pozharski wrote:
> On 11/16/2012 12:54 PM, Kendall Nettles wrote:
>
>> I wouldn't go into the lab and say "did you cryo-cool those crystals yet?"
>> or "check out this nice crystal. Its ready for vitrification".
>>
>
> If we speak the way scientific articles a
t of vitrification
> (anticrystallization) mixtures .."
>
> Perhaps we should call it anticrystallization?
>
> George
>
> On 11/15/2012 09:15 PM, James Stroud wrote:
>>
>> On Nov 15, 2012, at 10:59 AM, Tim Gruene wrote:
>>> I have heard this discussi
On Nov 15, 2012, at 10:59 AM, Tim Gruene wrote:
>
> My Pengiun English Dictionary states (amongst other explanations)
> freeze: "to make extremely cold",
I forgot to mention that if any dictionary is an authority on the very cold, it
would be the Penguin dictionary.
James
On Nov 15, 2012, at 10:59 AM, Tim Gruene wrote:
> I have heard this discussion before and reminds me of people claiming
> strawberries were nuts - which botanically may be correct, but would
> still not make me complain about strawberries in a fruit cake I
> ordered at a restaurant.
>
> My Pengiun
Isn't "cryo-cooled" redundant?
James
On Nov 15, 2012, at 11:34 AM, Phil Jeffrey wrote:
> Perhaps it's an artisan organic locavore fruit cake.
>
> Either way, your *crystal* is not vitrified. The solvent in your crystal
> might be glassy but your protein better still hold crystalline order (cf
I meant "where the drops have the concentration of ammonium acetate needed".
James
On Nov 9, 2012, at 10:06 AM, James Stroud wrote:
> This sounds like a job for ammonium acetate. Use it as your salt. Purify your
> complex in it and then set up drops where they wells ha
This sounds like a job for ammonium acetate. Use it as your salt. Purify your
complex in it and then set up drops where they wells have the amount of
ammonium acetate needed to keep your protein stable and the wells have none, or
a range of concentrations. The ammonium acetate will equilibrate b
The agism in the advertisement doesn't do the institute much credit. I'm
inclined to believe Sham, given the Institutes stated policies:
"Applicants, preferably below 35 years"
James
On Oct 29, 2012, at 11:28 AM, Narayana VL Sthanam wrote:
> Sham, who so ever you are, if you have such a long
Related to PDB embedded objects, I'm wondering if there would be much interest
in my releasing an implementation of a language designed to make fairly
elaborate illustrations in PyMOL. The reason I ask is because it would take
some time to document and distribute, but I would do it if the demand
This sounds like something that a PDB file is not intended to do. I think
everyone has universally agreed to the PDB specification at the RCSB, which
makes no provisions for arbitrary objects, as cool as they would be.
But you could put your information into REMARK records, which are free-form.
The design of python was influenced by the ABC language which itself was meant
to be a replacement for BASIC. So the similarities you observe are not by
chance.
If you are looking for a free online experience that will stretch your computer
literacy, try this:
http://mitpress.mit.edu/sicp/full
The fit seems to be driven by the high number of points in the area of the
graph where many points overlap. The points that catch your eye and establish
the visible balance probably do not contribute much.
Maybe this one should have been plotted as log in the abscissa for appearances.
James
You might get better help if you post links (not attachments) to diffraction
images from several angles and an image of the crystal that gave the image, and
maybe several images of typical crystals.
Also, you could post dimensions of the crystal, and if your lab is set up for
it, a picture of t
You could do homology modeling of several homologs using
http://protein.cribi.unipd.it/Homer/ . Then calculate the electrostatics of the
homologs.
Better though would be actual structures. How much identity do the homologues
have? If they are so close that homology modeling works, then you may
On Sep 13, 2012, at 10:30 PM, Eric Bennett wrote:
> [woz:~] bennette%
> /Library/Frameworks/Python.framework/Versions/2.6/bin/python pytest.py
> Traceback (most recent call last):
> File "pytest.py", line 2, in
>number = int(example_string)
> ValueError: invalid literal for int() with base
On Sep 13, 2012, at 11:02 AM, Patrick Shaw Stewart wrote:
> Like most computer users and many scientists I don't write scripts to
> organize or analyse my data unless I get desperate. I've used both Python
> and Perl a few years ago, but it would take quite a lot of time and effort
> and starin
rogrammers put no more effort than any other programmer. It's
just that python has more advocates (for good reason) so the apparent effort is
amplified.
Don't hate us because our preferred programming language is beautiful.
James
--
James Stroud
http://www.jamesstroud.com
On Sep 12, 2012, at 1:00 PM, George Sheldrick wrote:
> It is the lack of compatibility between different versions mentioned by Ethan
> that really put me off learning PYTHON.
Python is backwards compatible. I have reams of code I wrote in python 2.3 that
still works in 2.7 without modificatio
Python sorting 1 records of 1 floats for each record, finding the max,
min, and mean of entire 100,000,000 32 bit float array (400 MB) on a 6 year old
white imac.
*11.6 seconds.
*This doesn't include the time to generate the 400 MB of random (normal) data.
Try it on your own comp
On Sep 12, 2012, at 9:11 AM, Pete Meyer wrote:
> That said, I'd take a look at python, octave or R. Python's relatively easy
> to learn, and more flexible than octave/R; but it doesn't have the built-in
> statistic functions that octave and R do.
import scipy
Now it does!
You should choose an OS that interfaces well with your phone.
James
On Aug 9, 2012, at 7:55 AM, Jacob Keller wrote:
> Dear List,
>
> I guess this is somewhat of a perennial issue, but I am faced with choosing
> an OS for a new computer, and am curious about benefits and drawbacks with
> rega
The hydroxyls were on the wrong carbons in the previous picture I sent. These are correct.JamesOn Jul 11, 2012, at 1:37 PM, Lukacs, Christine wrote:Hi all- I have a protein that crystallizes in I422, and diffracts well, between 1.3-1.7A. Beautiful density, slightly higher final R-factors than you
It looks like dityrosine, usually caused by radiation damage (I think UV is the usual culprit).http://www.nugowiki.org/images/thumb/c/ca/HMDB06045.png/220px-HMDB06045.pngJamesOn Jul 11, 2012, at 1:37 PM, Lukacs, Christine wrote:Hi all- I have a protein that crystallizes in I422, and diffracts well,
I think delphi doesn't need to know about connectivity, only the atom
identities. So the distinction between DNA and protein should be irrelevant and
thus the input files would be the same.
If you just want to visualize the delphi EP, try this page:
http://structure.usc.edu/howto/delphi-surfa
On Jul 9, 2012, at 11:02 AM, Tim Gruene wrote:
> Dear Fulvio,
>
> http://lmgtfy.com/?q=somore+molecular+replacement
>
> should help you out, especially the but last paragraph of the first
> link provided.
Not Found
The requested URL /~djamrog/somore.html was not found on this server.
The star is usually for sugar atoms, not for the bases. I don't remember what
curves wants.
Does your PDB have apostrophes instead of stars? If so you should just do a
global search and replace.
If you still have a problem, you should copy-paste the error message.
James
On Jul 2, 2012, at 12
't be recognized.
Thank you for any input,
James
--
James Stroud
http://www.jamesstroud.com
Hello All,
I would like to discuss symmetry axes, but I'm not sure what the notation
convention is. For example, I'd like to say something about a 2(1) along the
x-axis, but the phrase "the 2(1) symmetry axis along x" is a bit cumbersome to
repeat many times or to put in a table. So I'd like a
If you want to use se-Met, you might want to start by labeling only one protein
at a time. For example, if you have A,B,C,D, grow crystals like this:
se-A, B, C, D
A, se-B, C, D,
etc.
Then try combinations of 2, then 3, then if you haven't got the phases you
need, try all 4.
And remember, if
On Apr 13, 2012, at 1:24 PM, James Holton wrote:
> I tried downgrading the operating system to 32-bit, but that reduced the
> number of "CPUs" available in the system from 24 to 8. Still don't know why
> that is
I'm probably wrong, but I'll guess that a 32 bit operating system can only
spar
Yes.
File -> Save Molecule...
James
On Apr 11, 2012, at 1:17 PM, Harman, Christine wrote:
> Hi All,
> Sorry for the dumb question, but if there was a way to export coordinates
> from PyMol. Is yes, then how?
>
> Thanks
>
> Christine
>
On Apr 3, 2012, at 7:19 PM, Katherine Sippel wrote:
> I would also consider looking into adding an RSS feed to your site so that
> those people interested in your articles can be informed without spamming the
> boards.
Why continue to punish him? Adding an RSS feed means installing and configu
I read the first part of the page you linked to. I'm not sure what the decent
into troll etymology says about the CCP4BB community--especially in response to
your seemingly innocent post.
My understanding is that the goal of the CCP4BB is to educate and not belittle
the naivety of other members
On Mar 30, 2012, at 1:04 PM, Bryan Lepore wrote:
> On Fri, Mar 30, 2012 at 4:02 AM, Kevin Jin wrote:
>> Here is way I have used for [...]
>
> I hate to be a curmudgeon, but can a list member please explain why
> this is not specifically blogspam or spam - or whatever it is exactly?
It's not rea
I feel compelled to throw a few references into the ring.
NFAT is a protein where you get a good sampling of snapshots:
1. Folded up as a monomer when interacting with partner proteins:
http://www.ncbi.nlm.nih.gov/pubmed/9510247
http://www.ncbi.nlm.nih.gov/pubmed/16873067
2. Extended as a
Use 5' overhangs of two and make the DNA 10, 11, 15, 20, 21 25, 26, 30, or 31
bases in length. Count the overhangs in the length.
If you don't know where to start, try 15, 25, and 26 first because they will
make 2(1) screws, which are good for crystals.
James
On Feb 15, 2012, at 1:06 AM, LISA
.
James
On Feb 10, 2012, at 1:51 PM, Jacob Keller wrote:
> Interesting to juxtapose these two responses:
>
> James Stroud:
>> How could they not be snapshots of conformations adopted in solution?
>
> David Schuller:
>> How could that possibly be the case when any structur
conformations
that are accessible in solution.
On the point of physiological relevance, it wasn't mentioned in the original
question.
James
On Feb 10, 2012, at 1:34 PM, Nat Echols wrote:
> On Fri, Feb 10, 2012 at 12:29 PM, James Stroud wrote:
>> How could they not be snapshots of conform
How could they not be snapshots of conformations adopted in solution?
James
On Feb 10, 2012, at 1:25 PM, Jacob Keller wrote:
> Dear Crystallographers,
>
> I am looking for references which discuss the validity of the
> assertion that multiple crystal structures of the same or similar
> protein
Hello All,
Two people named Rob told me that the the 3 letter code is "N".
http://ligand-expo.rcsb.org/reports/N/N/index.html
Coincidentally, the old 3 letter name is "ROB".
Thank you for your help!
James
> On Fri, Jan 27, 2012 at 2:38 PM, James Stroud wrote:
Hello All,
Do any of you RNA structural biologists know what is the 3 letter code for
1'-deoxyribofurnaose-5'-phosphate (abasic site in RNA)? I found that the
1'2'-dideoxy is 3DR, but could not find a lead on the 1'-deoxy. I scoured
HIC-UP to no avail, which I think is the most comprehensive he
This reminds me of stride2pdb in case you want to use more than pymol with your
secondary structure assignments:
http://structure.usc.edu/stride2pdb/
James
On Jan 24, 2012, at 2:20 PM, Martin Hällberg wrote:
> You can try STRIDE2PyMOL:
>
> http://pldserver1.biochem.queensu.ca/~rlc/work/pymol
Try DSSP2PDB.
http://structure.usc.edu/dssp2pdb/
It's a perl script.
Crossover flame note: I spent a lot of time learning perl and I still don't
recommend the language ;-)
James
On Jan 24, 2012, at 1:57 PM, Ed Pozharski wrote:
> I am looking for a program/server that would determine second
On Jan 24, 2012, at 11:24 AM, Ian Tickle wrote:
> 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 working, such as on Windows
> working
I should know better than to touch a flame post, but, but here goes:
don't use anything but python. They are nightmare languages, sloppy, and force
you to format the code by inserting semantically redundant brackets and
semicolons in a specific way rather than dispensing these redundancies
alt
On Jan 23, 2012, at 9:46 PM, Yuri Pompeu wrote:
> Hello Everyone,
> I want to play around with some coding/programming. Just simple calculations
> from an input PDB file, B factors averages, occupancies, molecular weight, so
> forth...
> What should I use python,C++, visual basic?
> thanks
Pyt
On Jan 18, 2012, at 6:17 AM, Anastassis Perrakis wrote:
> Here at the NKI, we had formed a committee to look at ELN solution two years
> ago.
> We had interviewed three vendors, and run two tests with twenty users.
>
> A brief description of the outcome:
>
> 1. None of the twenty test-users was
use.
> Regards,
> Fred
>
>
>
> Em 12-12-2011 19:18, James Stroud escreveu:
>> This is not trivial. Assuming an arbitrary origin, the simplest 4-fold
>> symmetry operation (4-fold rotation) has 5 free parameters (translation
>> along the symmetry axis i
This is not trivial. Assuming an arbitrary origin, the simplest 4-fold symmetry
operation (4-fold rotation) has 5 free parameters (translation along the
symmetry axis is irrelevant). The biggest problem is determining the values for
these parameters. For example, once you apply the symmetry, you
Hello all,
Since no one offered a good utility for Ed Pozharski's idea to easily cut a
region of a density map, I made a permanent web location for my utility called
mapreg:
http://mapreg.bravais.net/
Enjoy.
James
On Dec 8, 2011, at 8:39 AM, Ed Pozharski wrote:However, I'd see no harm in posting just a small cutout of the map in the region ofinterest. It's not a difficult task (fft/mapmask or perhaps some usfmagic), but is there some user-friendly approach to cutting out a smallmap volume? There's probably
Usually you put a statistic like this in the tempFactor field (B) and then
color by "B-factor" in pymol or similar.
I'm certain there is a facility for filling this entry somewhere. If not, then
a fairly trivial server is waiting for someone to create it and claim the glory.
Google something li
With such a nice parting letter, we find it disheartening to let you go.
James
On Nov 29, 2011, at 7:44 PM, debanjan choudhuri wrote:
> To whom it may concern,
> I am writing this in request to the cancellation of my subscription to CCP4BB
> mail.
> It was indeed a very rewarding and a knowledg
On Nov 21, 2011, at 6:34 PM, Jacob Keller wrote:
> I am curious how all of this can be more than splitting hairs, i.e.,
> under what conditions can this 1Ang domain motion mean something
> biologically significant?
To engage in the discussion, I think we had to accept this:
On Nov 21, 2011, at 3
On Nov 21, 2011, at 5:23 PM, James Stroud wrote:
> except that you use Euclid's formula to calculate the distances in higher
> dimensions
I meant to say "Euclidian distance". "Euclid's formula" has a specific meaning
that is different.
On Nov 21, 2011, at 3:52 PM, Filip Van Petegem wrote:
> As mentioned for X-ray structures, a Luzzati analysis may give information
> about the positional errors, but there should be an increased resolution when
> comparing domain movements, because it's unlikely for all atoms to have an
> erro
On Nov 21, 2011, at 3:04 PM, Filip Van Petegem wrote:
> So the question is: how you can state that a particular movement was
> 'significantly large' compared to the resolution limit?
I can think of a different but related question. How significant is a
particular movement compared to a measure
On Nov 4, 2011, at 2:09 AM, Chris Morris wrote:
> One argument for archiving images has been that reprocessing could
> demonstrate deliberately deceptive structures.
>
> In fact, what is needed for this is not necessarily the image. It is the last
> data file that was produced by a trusted com
On Oct 27, 2011, at 5:22 PM, Francis E Reyes wrote:
> So I ask again, are there literature examples where reevaluation of the
> crystallographic data has directly resulted in new biological insights into
> the system being modeled?
This is a poor criterion on which to base any conclusions or dec
On Oct 26, 2011, at 9:59 AM, Patrick Shaw Stewart wrote:
> The principle is that the movie is written to the same area of memory,
> jumping back to the beginning when it is full (this part is not essential,
> but it makes the principle clear). Then, when the photographer takes his
> finger of
On Oct 24, 2011, at 3:56 PM, James Holton wrote:
> The PDB only gets about 8000 depositions per year
Just to put this into dollars. If each dataset is about 17 GB in size, then
that's about 14 TB of storage that needs to come online every year to store the
raw data for every structure. A two s
Since a crystallographic 3-fold generates the trimer (of dimers) then A1-B2 can be the ASU in this case.Just generate the symmetry mates with the A1-B1 dimer and then make a new PDB of A1-B2 then generate the symmetry mates of A1-B2 to see that the lattice is complete.I compulsively made and attach
On Oct 19, 2011, at 4:36 AM, Kayashree M wrote:
> We have a structure which is a homodimer in the asymmetric unit.
> PISA predicts most probable assembly as a dimer but this
> dimeric assembly is different from what is solved (offcourse
> we can generate the symmetry equivalent molecule and get tha
I should have said "not compelling".
James
On Oct 17, 2011, at 12:40 PM, James Stroud wrote:
>> The programs give me solutions with "reasonable" maps, but it is never
>> possible to refine to achieve Rvalues below 0.40.
>
> This strongly suggests a spa
> The programs give me solutions with "reasonable" maps, but it is never
> possible to refine to achieve Rvalues below 0.40.
This strongly suggests a space group issue.
If the systematic absences are compelling, you should try to drop it down to P2
first. Look at your packing in the C222(1). If
Each R-free flag corresponds a particular HKL index. Redundancy refers to the
number of times a reflection corresponding to a given HKL index is observed.
The final structure factor of a given HKL can be thought of as an average of
these redundant observations.
Related to your question, someone
First of all, are you sure those are ice rings? They do not look typical. I
think you might have salt crystals from dehydration *before* freezing.
Otherwise, I think your freezing went well. Maybe try a humidity controlled
environment when you freeze.
Second, I'm not so sure the bad stats come
I've used a technique called "annealing", which amounts to holding an index
card between the cryo stream and the crystal for a few seconds then removing
the card quickly.
In my experience, about 70% of the time the diffraction is worse and about 30%
of the time the ice rings will be gone with s
If you can reproduce the crystals and have the material
1. Harvest several large crystals.
2. Make several transfers to fresh mother liquor to wash.
3. Dissolve in DNA loading dye without SDS
4. Run on a native gel (e.g. 6% polyacrylamide, 0.5XTBE, etc.).
5. Include positive control lanes for prot
I think something in your workflow is inserting dos line feeds (\n\r or \r\n, I
can't remember which).
If I have guessed correctly, you want to remove those "\r"s before proceeding
(or never let them get in there in the first place).
You claim to open it with MS something, which would insert do
Hello All,
Is Table 6 of http://cci.lbl.gov/sginfo/hall_symbols.html the authoritative
mapping of space group numbers to Hermann-Mauguin symbols (i.e., can we count
on major software packages to honor this mapping if present in a PDB file)? I
notice that this web page was authored by a couple o
Check out Theseus: http://www.theseus3d.org/
You will need a sequence based alignment. This alignment can be provided
automatically by muscle if you have it installed
(http://www.drive5.com/muscle/)--this is different from pymol. Pymol seems to
do an SVD to obtain the alignment. I'm not up to d
One holistic way to view a reciprocal lattice (or subset thereof) without the
requirement for 3-d or moving frames is with a pole figure.
http://en.wikipedia.org/wiki/Pole_figure
See Palmer & Ladd for a better discussion.
I don't know what software can make a pole figure, though.
James
On
ld be intercepted, corrupted, amended, lost, destroyed, arrive
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I've found that predator is one of the best services of this sort:
Ref: PROTEINS: Structure, Function, and Genetics 27:329–335 (1997)
Server: http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::predator
The server is slow but the service is good.
James
On Jul 18, 2011, at 10:47 PM, Franco
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