Assuming that your homology model is that of a dimer, you could put it in a
large unit cell (just add CRYST1 record). The only interface you will get from
pisa will be your dimer interface.
If your homology model is a monomer, then pisa will not help, of course, and
you would need to
I suspect the question might be about converting intensities to anplitudes. If
so ctruncate is your friend.
Happy Connecting. Sent from my Sprint Samsung Galaxy S® 5
Original message
From: Eleanor Dodson eleanor.dod...@york.ac.uk
Date:01/03/2015 3:42 PM (GMT-05:00)
To:
Why? Merging waters like that in coot is a user error, and it does not happen
too often. I realize you are talking about changeable settings, but it would
be really annoying if a refinement program kept removing water molecules that
were placed manually because it does not fit some internal
Edit the ATOM records?
Sent on a Sprint Samsung Galaxy S® III
div Original message /divdivFrom: luzuok
luzuo...@126.com /divdivDate:10/23/2014 6:51 AM (GMT-05:00)
/divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: [ccp4bb] Merge PDB
chains /divdiv
/divDear all,
Sorry to
Yes, having different crystal forms in the same crystallization conditions is,
while clearly uncommon, not unheard of. I had a case once where at least four
different crystal forms were observed in crystals harvested from identically
prepared drops. It may be that there is some major set of
Try refining your model both ways (with and without covalent link) and see if
electron density maps give you an indication. At this resolution there will be
some model bias, so be critical.
Sent on a Sprint Samsung Galaxy S® III
div Original message /divdivFrom: rohit kumar
Probably the only way is to take unmerged scalepack output to aimless.
Sent on a Sprint Samsung Galaxy S® III
div Original message /divdivFrom: Faisal Tarique
faisaltari...@gmail.com /divdivDate:08/15/2014 9:40 AM (GMT-05:00)
/divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject:
Same here. Ultimately, the KD test must be used in the end to finalize the
resolution (keeping in mind recently discussed issues of effective resolution
given data completeness). I just want to add that at least some versions of
aimless report overestimated resolution based on CC1/2 cutoff
By all means, try it both ways and see whether the R-Rfree gap narrows with
random vs thin shell selection. Depending on resolution and data quality, you
may also consider imposing NCS restraints.
Sent on a Sprint Samsung Galaxy S® III
div Original message /divdivFrom: Xianchi
You may need to
1) modify _chem_comp.group to be DNA in the cif-file
2) import the resulting cif-file in coot
Cheers
Sent on a Sprint Samsung Galaxy S® III
div Original message /divdivFrom: Wang, Wei
wew...@ucsd.edu /divdivDate:07/15/2014 5:14 AM (GMT-05:00)
/divdivTo:
Try to put your crystal into oil drop?
Sent on a Sprint Samsung Galaxy S® III
div Original message /divdivFrom: Frank von Delft
frank.vonde...@sgc.ox.ac.uk /divdivDate:07/07/2014 12:32 PM (GMT-05:00)
/divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: [ccp4bb] emergency
There is no actual requirement to use Kabat numbering, you can avoid it
alrogether. Some argue that L27A is actually 28th amino acid in the protein
sequence, and labeling it as L27A is simply incorrect. I would suggest doing
refinement with plain numbering (no insertion codes) and changing it
Or, if for whatever reason sphere refine isn't an option, fix the metal and all
of its ligands
Sent on a Sprint Samsung Galaxy S® III
div Original message /divdivFrom: Paul Emsley
pems...@mrc-lmb.cam.ac.uk /divdivDate:06/05/2014 3:51 AM (GMT-05:00)
/divdivTo:
This may not work if a program implements its own algorithm for parsing command
line parameters
Sent on a Sprint Samsung Galaxy S® III
div Original message /divdivFrom: Tim Gruene
t...@shelx.uni-ac.gwdg.de /divdivDate:06/03/2014 8:27 AM (GMT-05:00)
/divdivTo:
Would a no-space symlink resolve this?
Sent on a Sprint Samsung Galaxy S® III
div Original message /divdivFrom: Mark J van Raaij
mjvanra...@cnb.csic.es /divdivDate:06/03/2014 8:03 AM (GMT-05:00)
/divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: Re: [ccp4bb] baverage:
no
Try refining without disulfide bond - from the way density looks it might work.
Whether this is what happens in vivo is a different question entirely.
Sent on a Sprint Samsung Galaxy S® III
div Original message /divdivFrom: Eze Chivi
ezech...@outlook.com.ar
My suggestion is to ignore Rmerge when making decisions about resolution
cutoff. While cc1/2 may still perhaps qualify for the recent discussion tag
(is two years recent?), deeply flawed nature of the Rmerge concept is over a
decade old.
Sent on a Sprint Samsung Galaxy S® III
div
there are other dedicated methods to do it that suffer less
from side effects. Including the docking approach.
Kind regards, Baerbel
Quoting Ed Pozharski epozh...@umaryland.edu:
If I understand the original post correctly, the binding sites in
question are not chemically identical
are solid methods to determine some sort of relative
affinities. I'd suggest to design mutants for either binding site and
ITC measurements with the mutant proteins. This might also tell you if
some sort of co-op exists between both sites.
Baerbel
Quoting Ed Pozharski epozh...@umaryland.edu
http://www.ccp4.ac.uk/html/watertidy.html
On 10/29/2013 04:43 PM, Elise B wrote:
Hello,
I am working on a project with several (separate) structures of the
same protein. I would like to be able to compare the solvent molecules
between the structures, and it would be best if the waters that
May I ask a question?
This is a catch-22 situation. If you ask permission to ask a question,
you are already asking a question. Answering this with no would
probably create a wormhole. I'd also like to see a bulletin board where
asking questions requires separate permission.
When we
On Thu, 2013-08-22 at 10:07 -0400, Bosch, Juergen wrote:
Yes, I'm also surprised why people run gradients for the capturing
step ?
Because we can. Joking aside, I've seen some examples where protein
eluted at relatively low imidazole and upon running the gradient there
remains some (minimal)
On Thu, 2013-08-22 at 13:58 -0400, Bosch, Juergen wrote:
well if we hit the timer after lysis, say via cell disruptor then I
have my eluted protein in less than 1 hour, including 40 minutes batch
binding.
then proceeds to wait six weeks for crystals to appear... :)
Cheers,
Ed.
PS. There
On Thu, 2013-08-22 at 14:22 -0400, Bosch, Juergen wrote:
But when it sits and crystallizes it is cleaner - unless some
opportunistic fungal contamination helps you trim off those nasty
loops that you would have omitted anyhow from your model.
Jurgen,
Good point and admittedly I never
According to Qiagen
Since imidazole absorbs UV radiation at 280 nm, an elution profile
measured at 280 nm while purifying a 6xHis tagged protein by FPLC will
show an increase in absorbance above the background signal allowing
quantitation of your protein. The absorbance of imidazole can vary
This question may be better suited for more small-angle-oriented forum,
e.g.
http://www.saxier.org/forum/
On 08/07/2013 11:22 AM, Remec, Mark wrote:
Dear CCP4bb,
I have a few questions concerning SANS data recently collected that
I'm having trouble analyzing. The data was collected at 2
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 data. Then maintainers of that victorious interface could
change the underlying
On 08/07/2013 03:54 PM, James Stroud wrote:
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
James,
On 08/07/2013 05:36 PM, James Stroud wrote:
Anyone can learn Python in an hour and a half.
Isn't this a bit of an exaggeration? Python is designed to be easy to
learn, but we probably talking about different definitions of learning
and anyone.
I.e. programs would look like this
On 08/07/2013 05:54 PM, Nat Echols wrote:
Personally, if I need to change a chain ID, I can use Coot or pdbset
or many other tools. Writing code for this should only be necessary
if you're processing large numbers of models, or have a spectacularly
misformatted PDB file. Again, I'll repeat
On 06/21/2013 10:19 AM, Ian Tickle wrote:
If you observe the symptoms of translational NCS in the diffraction
pattern (i.e. systematically weak zones of reflections) you must take
it into account when calculating the averages, i.e. if you do it
properly parity groups should be normalised
Dear Kay and Jeff,
frankly, I do not see much justification for any rejection based on
h-cutoff.
FrenchWilson only talk about I/sigI cutoff, which also warrants further
scrutiny. It probably could be argued that reflections with I/sigI-4
are still more likely to be weak than strong so F~0
The only thing that seems to make sense is bonds rmsd - but you should
ask the annotator for specifics directly. If it is bonds rmsd, this has
been discussed many times - just google rmsd bonds ccp4bb and look for
most recent entries.
On Mon, 2013-06-17 at 12:11 +0530, Faisal Tarique wrote:
I noticed something strange when processing a dataset with imosflm. The
final output ctruncate_etc.mtz, contains IMEAN and F columns, which
should be the conversion according to FrenchWilson. Problem is that
IMEAN has no missing values (100% complete) while F has about 1500
missing (~97%
in the morning when
I get into the lab and let you know.
Jeff
On Mon, Jun 17, 2013 at 5:04 PM, Ed Pozharski epozh...@umaryland.edu
mailto:epozh...@umaryland.edu wrote:
I noticed something strange when processing a dataset with
imosflm. The
final output ctruncate_etc.mtz, contains
On 06/14/2013 07:00 AM, John R Helliwell wrote:
Alternatively, at poorer resolutions than that, you can monitor if the
Cruickshank-Blow Diffraction Precision Index (DPI) improves or not as
more data are steadily added to your model refinements.
Dear John,
unfortunately the behavior of DPIfree
On Thu, 2013-06-13 at 08:44 -0700, Andrea Edwards wrote:
In this case, the author should report a correlation coefficient along
with the other standard statistics (I/sigI, Rmerg, Completeness,
redundancy, ect.)?
Won't hurt.
What about Rpim instead of Rmerg? and if Rpim is reported, what
. This
is based predominantly on Scala/Aimless.
Cheers,
Ed.
On Thu, 2013-06-13 at 18:20 +0200, Tim Gruene wrote:
On 06/13/2013 06:16 PM, Ed Pozharski wrote:
[...] With that said, I am pretty sure that in vast majority of
cases structural conclusions derived with I/s=2 vs CC1/2=0.5 vs
DR
ATOM records have fixed format so you can (and should) use string
slicing instead, like so (one-liner)
serial, aname, altloc, resn, chid, resi, insCode, x, y, z, occ, b,
element, q = line[6:11], line[12:16], line[16], line[17:20], line[21],
line[22:26], line[26], line[30:38], line[38:46],
On Thu, 2013-06-06 at 14:41 +1000, Nat Echols wrote:
You should resist the temptation to write your own PDB parser; that
way lies pain and suffering. There are multiple free libraries for
Python that can be used for this task - I recommend either CCTBX or
BioPython (probably the latter if you
On Wed, 2013-05-29 at 12:30 -0400, Jeremy Stevenson wrote:
In this particular case you can see the website was registered in
September of 2012, which is a good indication that it was set up just
to scam people.
Just curious - why registration date indicates unsavory nature of
Jieke?
--
After
I am wondering whether there is a function I could use to build the
missing bases in one strand of the DNA to base pair with the other
strand of DNA which is complete...
Calculate-Other modeling tools- Base pair...
--
Coot verendus est
It is probably a wrong question to ask here. Pretty much everything is
tolerated by PDB during deposition, the report you get is an advice,
not instruction. I wonder whether anyone has an example of the
RCSB/PDBe/PDBj ever turning down submitted structure.
The right question is whether the
On 05/27/2013 11:27 AM, ka...@ssl.serc.iisc.in wrote:
Sir,
Ok. It is an acetate ion which interacts with its symmetry
equivalent ion only one of its oxygen atoms is closer to
its symmetry equivalent and not the entire ion. So do I
need to give lower occupancy for this ion?
Thank you
Regards
On 05/27/2013 12:14 PM, Kavyashree Manjunath wrote:
Later I tried with 0.8, 0.99 for which the map was normal
and also validation did not report it as short contact.
Is it ok if I give 0.99 occupancy?
Validation most likely will not report any short contacts if occupancy
is 1. If the distance
Matt,
with this technique, how do you prevent crystal from drying up (other
than doing it fast)? I know Thorne's group does this trick under oil.
If you take no extra precautions, do you have an estimate of how often
diffraction is destroyed by this?
On the other hand, it's quite possible
,
Tim
On 05/21/2013 10:40 PM, Ed Pozharski wrote:
On 05/21/2013 04:35 PM, Francis Reyes wrote:
Since you're using buster, have you tried global phasing's own
pdbvconv tool?
Naturally, but it leaves file unchanged.
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland
On Wed, 2013-05-22 at 18:09 +0200, Tim Gruene wrote:
the answers you received were correct with respect to the question you
asked. If they are not satisfactory, you have not given sufficient
information.
Tim,
Not sure when I expressed any dissatisfaction with replies I received.
I asked
and give a helpful answer.
Regards,
Tim
On 05/22/2013 07:55 PM, Ed Pozharski wrote:
On Wed, 2013-05-22 at 18:09 +0200, Tim Gruene wrote:
the answers you received were correct with respect to the
question you asked. If they are not satisfactory, you have not
given sufficient
Does anyone have a script to convert pdb file with DNA atom records from
v3 back to v2? I can certainly right my own and asking only if you
already have it written. Strictly speaking, this is not ccp4-related -
apparently, buster expects the old format.
Cheers,
Ed.
--
Oh, suddenly
On 05/21/2013 04:35 PM, Francis Reyes wrote:
Since you're using buster, have you tried global phasing's own pdbvconv tool?
Naturally, but it leaves file unchanged.
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian,
At this point you do have the scalepack2mtz output file (BTW,
imosflm/aimless is wholeheartedly recommended by this convert), and you
can easily extract all the info from there. There is mtzdmp, of course,
but it's easier to parse the actual mtz file (hey, the records are
actually text). Like
Don't believe such program/server does exist. Notice that you are asking for
something that *can* predict Kd. One can *try* making such predictions and
they may even be routinely in the ballpark, assuming that you are satisfied
with being routinely off by, say, an order of magnitude.
One
Protein-DNA complex crystal with channels too small for the dye is *extremely*
unlikely, imho.
Original message
From: Ulrike Demmer ulrike.dem...@biophys.mpg.de
Date: 04/15/2013 8:48 AM (GMT-05:00)
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] salt or not?
Dear
Doesn't lsqkab work? It just needs proper atom matching.
Coot definitely does superimpose DNA. One problem is that simple-lsq works on
a single chain, but you can trick it by changing chain id and renumbering the
other strand.
As for helix rotation, you can derive it from rotation reported
On 04/12/2013 06:03 PM, Nat Echols wrote:
On Fri, Apr 12, 2013 at 2:45 PM, Boaz Shaanan
bshaa...@exchange.bgu.ac.il mailto:bshaa...@exchange.bgu.ac.il 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
On 04/04/2013 04:51 PM, 李翔 wrote:
Hi everyone,
I met a problem when trying to build ideal DNA model in Coot. The
calculated DNA looks less than 10.5 bp/ turn, probably is about 10 bp/
turn. Is there a way for me to change the pitch to make it 10.5
bp/turn in Coot?
Thanks for your kind
On 04/04/2013 04:29 AM, Tim Gruene wrote:
Dear --,
Are we, the ccp4bb community, recently on the hunt to find new and
exciting ways to make sure people stop asking questions? Gentleman from
Moscow has clearly disclosed his full name and affiliation, but perhaps
I am wrong and subtle
As I recall, number of reflections set aside for cross-validation also affects
stability of sigmaA estimates. With 500 reflections and 20 resolution shells
you are down to 25 reflections per shell, which may be a bit too low.
Original message
From: Robbie Joosten
This might have changed, but in the past file formats were different.
Microcal files are text, while TA's are binary. I do have the actual
description of TA's format if anyone is interested, but it must be easier to
use native text export than write a converter.
Original message
On 03/23/2013 09:59 AM, Wei Feng wrote:
Can you help me to check out why these maps can not be converted by
sftools?
sftools is not for manipulating map files. Mapman from uppsala software
factory would be a good choice. xdlmapman, a gui frontend to it, used
to be part of ccp4.
--
Oh,
On 03/19/2013 02:41 PM, Jacob Keller wrote:
I don't understand this argument, as it would apply equally to all
features of the theoretical LUCA
No it won't. Different features would have different tolerance levels
to modifications.
Philosophically, one is wrong to expect that living
Jacob,
So you'd have to explain why the codon convention is so
intolerant/invariant relative to the other features--it seems to me
that either it is at an optimum or there is some big barrier holding
it in place.
Because altering codon convention will result in massive translation errors.
Check for translational NCS
And you are way too conservative with resolution. Even those holding
onto the Rmerge-dictated past would probably acquiesce to lower I/sig
cutoff. If you are using aimless, follow its recommendations based on
CC1/2, it's good for you.
Cheers,
Ed.
On Fri,
Pete,
Actually, I was trying to say the opposite - that the decision to
include something in the model (or not) could change the nature of the
error.
Duly noted
Pete
PS - IIUC := ?
IIUC - If I Understand Correctly
--
Bullseye! Excellent shot, Maurice.
Adam,
OK, seems like you are going with it's always statistical error we just
don't yet know what it is option.
Ed.
On Tue, 2013-03-12 at 16:15 +, Adam Ralph wrote:
Hi Ed,
You can have both types of error in a single experiment, however
you cannot determine
statistical
Kay,
the latter is _not_ a systematic error; rather, you are sampling (once!) a
statistical error component.
OK. Other words, what is potentially removable error is always
statistical error, whether it is sampled or not.
So is it fair to say that if there are some factors that I either do
the other
uncontrollable errors.
Cheers
-- Ian
On 11 March 2013 19:04, Ed Pozharski epozh...@umaryland.edu wrote:
Ian,
thanks for the quick suggestion.
On Mon, 2013-03-11 at 18:34 +, Ian Tickle wrote:
Personally I tend to avoid
OK. Other words, what is potentially removable error is always
statistical error, whether it is sampled or not.
Clarification - what I meant is potentially removable by proper sampling
and reducing standard error to zero with infinite number of
measurements. Not removable by better
Ian,
On Wed, 2013-03-13 at 19:46 +, Ian Tickle wrote:
So I don't see there's a question of wilfully choosing to ignore. or
not sampling certain factors: if the experiment is properly calibrated
to get the SD estimate you can't ignore it.
So perhaps I can explain better by using the same
Is there some way of opening a log file (specifically, the
pointandscale.log that imosflm bridge to scala generates) with qtrview
from command line?
I tried, of course, this
qtrview pointandscale.log
but it opens empty, no log-file. I tried qtrview -h and qtrview --help
and man qtrview but
Salve,
I would like to solicit opinions on a certain question about the
relationship between statistical and systematic error. Please read and
consider the following in its entirety before commenting.
Statistical error (experiment precision) is determined by the degree to
which experimental
Tim,
On Mon, 2013-03-11 at 18:51 +0100, Tim Gruene wrote:
I don't share your opinion about a single measurement translating into
a systematic error. I would call it a poorly designed experiment in
case you were actually iterested in how accurately you determined the
protein concentration.
Ian,
thanks for the quick suggestion.
On Mon, 2013-03-11 at 18:34 +, Ian Tickle wrote:
Personally I tend to avoid the systematic vs random error distinction
and think instead in terms of controllable and uncontrollable errors:
systematic errors are potentially under your control (given a
Pete,
On Mon, 2013-03-11 at 13:42 -0500, Pete Meyer wrote:
My take on it is slightly different - the difference seems to be more
on
how the source of error is modeled (although that may dictate changes
to
the experiment) rather than essentially depending on how the
experiment
was
By the way, am I the only one who gets this thing with every post? If
anyone can ask Jin Kwang (liebe...@korea.ac.kr) to either clean up his
mailbox or unsubscribe, that would be truly appreciated. Delete button
is easy and fun to use, but this has been going on for quite some time.
On Tue,
On 03/04/2013 10:02 AM, Marcin Wojdyr wrote:
It also puzzled me, but I haven't done more careful benchmarking yet.
What did you get after compiling refmac?
My numbers are not as impressive, but I also get quite detectable
improvement, from 35s to 27s (ccp4-6.3.0 vs compiled from source). This
checking by running the tests provided
with the suite. Aggressive optimization can be a source of bugs.
Best regards
Thierry
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ed
Pozharski
Sent: Monday, March 04, 2013 8:55 AM
To: CCP4BB@JISCMAIL.AC.UK
Adam,
On Mon, 2013-03-04 at 09:56 +, Adam Ralph wrote:
One of the first routines called by CCP4
progs is ccp4fyp. This initialises the CCP4 environment.
I think you might have missed in my original post that I get an error
when I *do* source ccp4 environment.
Does the error occur with
Indeed, the problem goes away when -static flag is omitted.
Interestingly, the resulting binary dependencies do not include any
ccp4-related libraries. For those interested, I was able to track the
segfault down to the close() operator - so basically it fails when
closing a file opened with
On Mon, 2013-03-04 at 11:37 +, Marcin Wojdyr wrote:
Running times were, correspondingly, 32.2s, 35.1s and 18.7s.
Numbers are almost too impressive to believe :)
How does it compare with ifort (which I thought should be the fastest
option on intel processors and thus unavailable (not free)
Adam,
I am not compiling CCP4, just refmac. IIUC, all that sourcing
ccp4.setup does is it sets $CLIB for refmac makefile to find libccp4c
and libccp4f. And presumably lapack and libblas, but that's a separate
issue.
On Thu, 2013-02-28 at 10:28 +, Adam Ralph wrote:
Hi Ed,
It looks
I am trying to compile refmac from source on a machine running Ubuntu
12.04. In a nutshell, after some troubleshooting I end up with
executable that generates a segmentation fault. Log-file states that
CCP4 library signal ccp4_parser:Failed to open external command
file (Success)
We might have just found a new recurring discussion - what to do with insertion
codes! I am sure the opinion split is close to 50/50.
Personally, I don't think insertion codes make sense in the first place. Are
catalytic triad residues always the same distance from the N-terminus? No. The
There should be many ways to do this. You can split the file, renumber with
pdbset, and then reassemble it. This may be useful
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Useful_scripts_(aka_smart_piece_of_code)
Cheers,
Ed
Original message
From: Amar Joshi
Maybe you can try different energies hoping that damage is wavelength
dependent. It must be dose dependent though, so you may consider merging short
sweeps from multiple crystals.
Original message
From: Uma Ratu rosiso2...@gmail.com
Date:
To: CCP4BB@JISCMAIL.AC.UK
On Mon, 2013-02-11 at 09:56 +0100, Robbie Joosten wrote:
This is a 'compatability' option in Refmac that internally renames
atoms. If you comment out 'MMA .C7 CM' in your
mon_lib_list.cif file, the problem will disappear.
Robbie,
thanks a lot - this fixes it.
Is this
I see a strange issue with a model that includes O1-methyl-mannose
(three letter code MMA). Basically, refmac fails and says that C7 is
missing in the model while CM is absent from the library. The problem
is that there is no CM atom in the pdb file, while C7 is right there.
This happens
Patrick,
Something related:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Conditions_prone_to_salt_crystallization
Truth be told, we recently had a major breakthrough with the peg/fluoride
condition I came to consider a useless salt crystal generator. So tables like
these are
On Fri, 2013-02-08 at 09:13 -0500, Edward A. Berry wrote:
I like to take a 5-sec 180* oscillation which gives plenty of
spots in a nice pattern for a salt crystal
Second that
It also confuses bystanders really well - what a strange diffraction
pattern - half salt (small unit cell) / half
On Fri, 2013-02-08 at 14:53 +0400, Evgeny Osipov wrote:
Protein crystals behave rather as gelatine and not as solid
I'd have to disagree on that. Protein crystals are fragile but not
soft. If your crystals are like gelatine it's unusual. It has been
demonstrated that elastic properties of
On Fri, 2013-02-08 at 09:57 -0500, Jacob Keller wrote:
do you have a reference quickly on hand
http://www.ncbi.nlm.nih.gov/pubmed/8129868
and references therein
http://www.sciencedirect.com/science/article/pii/S0022024801010922
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1300955/
The last
On Feb 8, 2013, at 9:23 AM, Ed Pozharski wrote:
On Fri, 2013-02-08 at 14:53 +0400, Evgeny Osipov wrote:
Protein crystals behave rather as gelatine and not as solid
I'd have to disagree on that. Protein crystals are fragile
Try this
http://www.mac-forums.com/forums/os-x-apps-games/239657-gedit-command-not-found-terminal.html
Original message
From: LISA science...@gmail.com
Date:
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] gedit on mac terminal
Hi all,
I installed gedit on my mac
To what extent modern geometric restraints have been upgraded over
original EnghHuber? And where I can find a consensus set of values
(with variances)?
For example, Fisher et al., Acta D68:800 discusses how histidine angles
change with protonation, and refers to EnghHuber when it says that
Article in the Tables is the answer to my question about the latest
EnghHuber parameters. These still don't match Fig.6 from Fisher, but I
am OK with using Tables for my internal purposes.
Thanks to Mitchell and Dale for prompt response.
Cheers,
Ed.
--
After much deep and profound brain
On 12/10/2012 08:45 PM, Yuri Pompeu wrote:
hello everyone,
I have collected data on a problematic crystal. (first mistake...)
Images spanning phi angles 45-80 look ok and usable, also images 229-279 are
usable (index well and merge well too).
How can I combine the 2 separate .mtz files from
Francois,
I did not realize Phil Evans is god (perhaps a minor one as he did not
yet earn a capital G).
I do concur that insertion code is evil. I had to re-refine an old
antibody structure recently and it messes up coot sequence window and
breaks refmac bond restraints. Evil, evil,.evil.
On Wed, 2012-12-05 at 17:02 +0100, Robbie Joosten wrote:
Does 128A come before or after 128?
Robbie,
shouldn't it simply depend on which residue record comes first in the
pdb file?
Ed.
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
On Tue, 2012-11-27 at 21:46 -0800, William G. Scott wrote:
Are Mg++ ions ever observed to chelate primary amines?
MESPEUS reports, for example, 13 structure where magnesium is
coordinated by a lysine. 7 with arginines and a bunch of asn/gln side
chains as well. It does not prove, of course,
1 - 100 of 497 matches
Mail list logo
