There are CCD modules (often come with lenses, which can be taken off) sold on
Amazon, eBay or aliexpress (or even better, Taobao) costing USD 20-40. These
modules should be capable of taking full HD movies (MPEG or YUV2 compressed) at
30fps these days. Some may allow 120fps@640x480 or promise h
Hi Orly,
REMARK 290 should be the easiest way for generating symmetry mates. Other
routes are just going to give you the same results. As Jonathan already pointed
out, the symm ops do not garantee that the symm copies are close to each other.
The most simple-minded solution to this problem wou
Hi all,
If anybody is interested in non-viral stable expression, we have a
piggybac-based, doxycycline-inducible system. It is the reference 40 in the
lentiviral paper that Tomas directed to. We’d be happy to distribute the
plasmids.
Zhijie
> On Jan 25, 2020, at 3:26 AM, Tomas Malinauskas
Hi all,
I was confused when I saw mysterious new glycan chains emerging during PDB
deposition and spent quite some time trying to find out what was wrong with my
coordinates. Then it occurred to me that a lot of recent structures also had
tens of N-glycan chains. Finally I realized that this
gt;>> In generally I like the treatment of carbohydrates now as branched
>>> polymers. I didn't realise there was an exception. It makes sense for
>>> unlinked carbohydrate ligands, but not for N- or O-glycosylation sites as
>>> these might change during
If the data files generated from trusted computers carry digital signatures
it would be more trustworthy. Otherwise, a person with proper knowledge can
still manipulate the data files, even if it is in binary. If the image
processing software routinely incorporate encrypted key information of th
Hi,
Why not give macroseeding a try?
On the other hand, did your try additive screens? You might find something that
modifies the growth behavior of your crystals. In some cases simple
manipulation of ionic strength could have great effects. I had a crystal that
had a long axis, but the crysta
Hi Lu,
Cadmium(II) seems to be in the standard monomer library in both Coot and CCP4.
Thus you do not need to make it by yourself. I guess your problem was due to
that you have put a "Cd" instead of "CD" when adding it in Coot. Refmac is case
sensitive when identifying the compounds or atoms. A
Corrections of my previous email:
According to wikipedia:
"Although cadmium usually has an oxidation state of +2, it also exists in the
+1 state."
So there is probably no Cd(III) for us to worry about.
From: Lu Yu
Sent: Monday, November 28, 2011 3:16 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [cc
Hi,
There is a interesting paper/tool that might shed a little light on the
debate here:
The paper: http://www.ncbi.nlm.nih.gov/pubmed/19956261
The tool:
http://ucxray.berkeley.edu/ringer/Documentation/ringerManual.htm#Utility
As I remember, this tool claimed to be able to extract information
Hampton sells an adjustable mounted loop for this purpose.
http://hamptonresearch.com/product_detail.aspx?cid=24&sid=136&pid=385
From: Frank von Delft
Sent: Wednesday, March 07, 2012 1:26 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] How to reduce no. of overlaps
You probably have to t
Hi,
Besides aligning the long axis with the rotation axis, which is the most
important, there are a few more things that may help:
1) Try optimizing the freezing to reduce the mosaicity (if not ideal), or shoot
at RT if possible. With higher mosaicity, the shape of the reflections are
elongate
Was this crystal shot frozen? With new crystals it is always a good idea to
take some room temperature shots first to get an idea of how good the
diffraction could possibly be. If you shoot the crystals at room temperature
and the spots look fine, then the obvious answer is to optimize the freez
Hi,
If those are spams, then Kevin must be the most successful spammer I have
ever encountered, as I have actually read all his posts and linked web
pages.
About the twitter idea, I am not sure if I would ever become a twitter user
in the near future. Compared to following tens of authors, I
Hi,
If it is under a UNIX-like system, I would probably make a new user for myself,
say, projects_2012, etc.. It is not perfect, but it is a simple solution.
Zhijie
From: wtempel
Sent: Tuesday, April 03, 2012 9:52 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] ccp4i project display
Dear co
Hi,
Regarding the online image file storage issue, I just googled "cloud storage"
and had a look at the current pricing of such services. To my surprise, some
companies are offering unlimited storage for as low as $5 a month. So that's
$600 for 10 years. I am afraid that these companies will fe
Hi Intekhab,
With 6 copies of the complex in ASU, NCS averaging might give you a better map.
Uppsala software factory has everything you need to do that:
http://xray.bmc.uu.se/usf/. Check the RAVE package. Particularly, have a look
at the average.csh script listed in the RAVE package page in th
-loss
-Eric
On Apr 3, 2012, at 9:22 PM, Zhijie Li wrote:
Hi,
Regarding the online image file storage issue, I just googled "cloud storage"
and had a look at the current pricing of such services. To my surprise, some
companies are offering unlimited storage for as low as $5
Hi
This is what I do:
Validate>Highly coordinated waters
From: Andre Godoy
Sent: Friday, April 13, 2012 3:57 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Good way to check ion sites on Coot
Dear all.
can someone tell me what is the best way to check for ion binding sites on my
structu
Hi,
At such concentrations, it might be necessary to concentrate the medium.
Otherwise you are likely to be working well below the KD of the affinity beads.
At 0.5mg/L, 50KDalton gives you 10nM. The KD of Ni-NTA should be around 1uM,
according to published SPR data
http://www.sciencedirect.co
Hi,
My first thought was same with David: the truncation won't change the
crystal's space group. The symmetry of the crystal is reflected by the
symmetry of the amplitudes of many many reflections across all resolutions.
Ellipsoidal truncation itself only removes some very weak reflections fro
--
From: "chen c"
Sent: Sunday, April 29, 2012 6:09 PM
To: "Zhijie Li"
Subject: Re: [ccp4bb] Anisotropic diffraction
I accept your advice. In fact, this is the first time I am involved in
anisotropic issue. And I learned a lot from all the above discussion.
Any thoughts on determining flexible regions, trying mutations, truncations,
different sequences from difference species?
It is essentially the protein that crystallizes, so I tend to think of making
changes to the protein itself.
From: ruby singh
Sent: Friday, May 04, 2012 3:09 AM
To: CCP4
Hi Pradeep,
On the stability issue:
Roche sells an EDTA-free protease inhibitor cocktail (other companies probably
also do). It is very effective. You can figure out the lowest needed
concentration and add it to your protein stock solution.
On the other hand, if you can accelerate the nuclea
Hi Xinghua,
The total intensity of each reflection needs to be accurately quantitated in
order to calculate the structure factors. Not only the dots need to be well
separated in the 3D reciprocal space, but also a small area around the dots are
often needed to calculate the background for subtr
Hi Faisal,
Please read this thread:
http://www.mail-archive.com/coot@jiscmail.ac.uk/msg00645.html
BTW, I had a look at my CCP4(6.2.0) and COOT lib files, it seems the CYS-BME
link is not in the mon_lib_list.cif file yet. Instead, I have two MPR-CYS links:
MPR-CYS MPR ..CYS
Hi Gloria,
I asked for a little baker's yeast from a lab in our department and PCRed
both the SMT3 domain and the SUMOase gene from its genomic DNA, then cloned
them to E coli vectors. The good thing about yeast is that most of its genes
are single exon so one do not really need to find cDNA f
Hi,
If you feel the refinement to be too slow, you may turn off the smooth
centering (in preferences) or change the centering steps to a smaller number
to save unnecessary graphical calculations. To go extreme, you may even
remove the real time display commands in the scripts - also a way to te
nt model's "backup state":
backup_state(imol)
Zhijie
--
From: "Xiaopeng Hu"
Sent: Tuesday, March 29, 2011 9:02 AM
To: "Zhijie Li"
Subject: Re: [ccp4bb] step refine speed of wincoot
Dear Zhijie,
Thanks f
Totally agree with Chun.
We are using a His tagged S219V construct that's very similary to the one
described in the Waugh paper. To my experience, agitation, 37C incubation, low
salt buffer, (etc.?), should all be avoided when using TEV. When using
relatively large amount of enzyme(0.1~0.2mg/m
ated with the pdb file being fitted.
Do not forget to turn it back on after the fitting:
turn_on_backup(imol)
To check the current model's "backup state":
backup_state(imol)
Zhijie
--
From: "Xiaopeng Hu"
Sent: Tu
Hi Heping,
Thanks for the list. It is very helpful and interesting. Out of curiosity:
how did you generate this list? Is there a way to search none-linear motifs
in PDB? Or did you write a script for searching database?
BTW, the ALA in 1xm7 looks unreal. A three-way tri-sulfide? The electron
Hi Anita,
Admittedly, there are proteins that naturally bind to Ni-NTA so tightly that
they co-elute with our His6-tagged proteins even on an imidazole gradient.
However, we do need some luck to come across a protein with such property. For
most proteins, they would just flow through the Ni-NT
Hi Bei,
First of all, I think you meant N-linked glycans, and the following discussion
are based on this assumption. I am not aware of any direct glycosylation on
lysines except for the O-glycosylation of hydroxylysines, which is really rare.
1. If you have enough protein, you should screen b
You may also want to have a look at this summary of a 2006 discussion:
http://www.mail-archive.com/ccp4bb@dl.ac.uk/msg01697.html
From: joybeiyang
Sent: Friday, April 08, 2011 2:06 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] off topic: Is deglycosylation necessary for crystallization?
D
Hi,
I have never done this myself, but as far as I know, DNA can be directly
conjugated through their primary amino groups to CNBr-activated beads or
NHS-activated agarose beads. These beads are supplied by many companies:
pierce, sigma, biorad, GE healthcare, etc.. - the same thing used for m
From: Engin Özkan
Sent: Saturday, April 09, 2011 10:44 PM
To: Zhijie Li
Subject: Re: [ccp4bb] off topic: Is deglycosylation necessary for
crystallization?
On 4/8/11 1:43 PM, Zhijie Li wrote:
5. Finally, to my knowledge, proteins produced from insect cells are mainly
high-mannose type (I
Hi,
Some anecdotes here for your reference:
One paper I read says that the authors were having trouble reproducing a
crystal from an initial screen. After some debugging, they realized that it
was because that they used a same pipette tip when making screens. Adding a
little solution from the
PS, it might be a good time to start an additive screen.
--
From: "Jun Yong Ha"
Sent: Tuesday, April 12, 2011 7:56 AM
To:
Subject: [ccp4bb] Reproducing crystals.
Hi all,
Recently, I produced crystals with MBClass1-64 which contains PEG4000,
HE
Hi Jobi,
I also had some crystals that were highly sensitive to glycerol. In one case, I
found that DMSO at 10-15% can cryo protect it, also the crystal could grow in
the presence of 10% DMSO which essentially eliminated a soaking step. In
another case, I grew the crystals in the presence of 5%
Hi,
This article says it is the Human Rhinovirus HRV3C Protease:
https://wasatch.biochem.utah.edu/chris/links/PrescissionProteaseProtocol.doc
The genome of this virus is here:
http://www.ncbi.nlm.nih.gov/nuccore/156254956
The gene record for the polyprotein is here:
http://www.ncbi.nlm.nih.gov/
Hello,
I just noticed that Hampton Research carries this adjustable mounted cryoloop
(HR5-900):
http://hamptonresearch.com/product_detail.aspx?cid=24&sid=136&pid=385
This looks quite interesting to me, as it seems that not every synchrotron
station's configuration can allow the use of an extend
Hi Tatyana,
It is funny that I just had that same problem a few days ago.
Here is the solution:
First of all, install Ghostgum and Ghostscript to your computer- which you have
done. I installed them to my C:\Program Files\ directory.
Then in CCP4i->system configuration->Config CCP4interface->
Forgot to mention: the trick is, CCP4i uses the Linux/UNIX '/' to specify the
subdirectories, not the Windows '\'. That is why if you copy the path from
windows explorer and paste it it won't work.
From: Tatyana Sysoeva
Sent: Friday, June 17, 2011 12:53 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject
Hi,
I think inside a protein crystal, it is a macromolecular crowding
environment. According to what I read, it seems that in a crowding
environment, the KD of proteins to ligands may change - often gets tighter.
As we know, 20-80% of the total volume in a protein crystal is occupied by
the
coverDate=12%2F31%2F2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C50024&_version=1&_urlVersion=0&_userid=994540&md5=678db69356318fcf86da3f9a4d6f2164
Zhijie Li
Fab:Peptide complex crystallizationHi Christine,
I never worked with Fab, but I do have a little experience with DMSO.
I had a case in which I could grow my crystal in 10-15% DMSO - to use it as
cryoprotectant. But in another case, 5% DMSO inhibited my crystal's growth.
When I had DMSO as cryo
Hi Ivan,
Did you try using a buffer other than phosphate? Also maybe a different pH can
help keeping the IgG in solution. Although papain prefers pH 6-7, it is a
fairly robust enzyme and will cleave with >20% efficiency in the range of pH4-9
(Hoover S & Kokes E ,1946, http://www.jbc.org/content
...
Thanks in advance,
Zhijie Li
Biochemistry, U of Toronto
ut to optimize your molecular replacement
parameters.
Zhijie Li
Graduate student, Univeristy of Toronto
- Original Message -
From: Haitao ZHANG
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, July 07, 2008 10:27 PM
Subject: [ccp4bb] Truncated protein structure
Dear all,
I repeat
HI Vijay,
One thing I would like to mention first is that often when a DNA fragment is
smaller than or close to 1Kb, it could enter the low EtBr region on an agarose
gel if allowed to run to long. Its bound EtBr could be stripped off so
significantly that the corresponding band become very f
Hello Jacob,
The problem for native gel is that it is much more sensitive to a
single charge difference than size differences. Also, the gel pattern
may change greatly if you use a different buffer system. I had a case
2 years ago that my protein ran at 5 positions on a Laemmli(pH 8.8)
na
Hi Jiabao,
(1) The concepts of primary and logical partitions are due to the limited
number of partitions that one MBR on a physical harddisk can handle. The MBR
can only accomodate information for 4 partions. These 4 partitions that are
recorded in MBR are primary partitions and if any, one ex
I remember that the Geforce series are capable of doing stereo only under
the fullscreen OpenGL mode - which is only used in 3D games. This capability
is provided by the Nvidia video driver. Under this mode, the card takes the
3D model that the game software sends to it, and generates a stereo v
Hi Terje,
I think the circular polarizers are really linear polarizers with a 1/4-wave
retarder (which make the polarized light circular again) sticked to the back.
The reason for them selling the CPs these days is because that digital cameras
will have problem metering with LPs. But for human
Hi Matt,
Why not check the NEB pMal system manual
(http://www.neb.com/nebecomm/ManualFiles/manualE8000.pdf). It has a good
cold osmotic shock protocol that I've been using for my periplasmic MBP
fusions.
Zhijie
- Original Message -
From: "Matt Colins"
To:
Sent: Monday, February
Hi Jothi,
You can make the blue native gel by yourself. It is quite cheap and easy to
make. Other than the standard native PAGE supplies and some buffering
reagents (if you want pH~7, imidazole will do), what you need in addition is
commassie G-250. Please note, that commassie R-250, which you ma
Hello Jacob,
If no extra residue other than G or S is desired, I think the answer is LIC.
Or you may have to put the whole TEV site plus the restriction site on the
5' primer.
Here is the TEV site that I designed for our vector (The left half is
probably the only possible LIC sequence for EN
Hello Paula,
As I remember HKL2000 requires 900 pixels in its running window's vertical
resolution - otherwise it won't run. Although you can set the virtual
desktop
resolution greater than your screen's physical pixel number to make HKL2000
running on a smaller screen, it would a be more comfo
Hi Ed,
I guess by "24mL SD200" Peter meant the Superdex 200 10/300 column, which
most of us should be quite familiar with. According to GE healthcare, a new
Superdex 200 10/300 GL column should have TP >25000/m. For comparison, a new
Superdex200 16/600 PG, which uses bigger beads, has TP >1300
Hi Tom,
Yes, SC can be used for calculating protein-small molecule ligand SC. Simply
put the ligand and protein on two separate chains. You probably need to edit
the $CLIBD/sc_radii.lib file to add some atom radii for your ligand. For
example:
ABC N* 1.65
ABC C* 1.90
Zhijie
--
Izit is an aqueous solution of methylene blue, which you can prepare simply and
cheaply. Look here:
http://www.ysbl.york.ac.uk/ccp4bb/2000/msg00387.html
One word of warning: not every crystal stains. I found poking crystal with hair
or glass fibre to see if it cracks or breaks is more reliable
Hi Danilo and all,
A little trick for the glutaraldehyde "staining": you can hang a 1-2uL drop
of 25% glutaraldehyde (or the most concentrated stock solution you can find)
besides your crystal drop in the vapour diffusion chamber. The
glutaraldehyde will get into the crystal drop via vapour di
Hi Dmitry,
I think the best way is not to make a new monomer. MAN-SER and MAN-THR
linkages do exist in the ccp4 monomer lib. If you simply build a mannose
with its O1 removed and put the C1 ~1.4 Angstrom to the OG of the serine I
think refmac should be able to detect the linkage. When this hap
Hi Engin,
Thanks for the information! I didn't realize that O-glycans can also be
specified as specific linkages like N-glycans. Those two extra angle
restraints should be helpful.
Zhijie
-Original Message-
From: Engin Özkan
Sent: Thursday, November 21, 2013 1:00 PM
To: Zhij
Hi Dmitry,
COOT does have the MAN-SER linkage record in its monomer lib, but it won't
detect the bond for you. It also haven't provided an interface for the user
to specify the bond type yet.
The COOT procedure you described is perfectly fine for generating a generic
covalent bond record for a
It seem the LINK line I provided eariler was chopped by the email system.
Here it is again:
LINKRC1**MAN*C***1*OG**SER*B*912MAN-SER
Simply replace each * with a space and change the residue IDs.
Also to clarify the procedure of using refmac to generate the
Hi Dimetry,
The difference between LINK and LINKR can't be explained better:
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg11865.html
Older versions of COOT used to not display the LINKR record, but now the
newer versions display both LINK and LINKR records as dotted bonds. I assume
that
Hi Zhongzhou,
For laptops, the passive stereo (Zalman mode) would be the easiest way to go.
All you need to do is to plug that monitor to the VGA port of you laptop. The
halving of the vertical resolution under stereo mode only affects reading the
characters, which can be solved by setting the
Hi Richard,
I am not sure if this is what you are looking for: second order nonlinear
optical imaging of chiral crystals (SONICC). It is not based on a
computational algorithm but the nonlinear optical property of chiral
crystals to double the wavelength when illuminated by intense light.
S
note: the same applies to UCSF Chimera, where the volume data
(maps) control also requires you to specify the cut off or gradient in real map
values instead of RMSD.
Zhijie
From: hongshi WANG
Sent: Wednesday, February 19, 2014 3:47 PM
To: Zhijie Li
Subject: Re: [ccp4bb] Can not see density
Hi Debasish,
I would first use some of those crystals to make seeds and grow some new
crystals so that I would not lose the crystal. Dehydration, even done
systematically (eg,
http://www.mitegen.com/mic_catalog.php?c=jenCrystaloptdehydrate), may or may
not improve the diffraction. Like most ot
Hi,
Two things i would like to add:
1) Due to the dependence of A280 on amino acid composition, a simple
two-wavelength 280 and 340 or 320 comparison is not very ideal for
determining the scatter component of the UV absorption of protein/protein
aggregate particles (the usefulness of this sim
I beg to differ on this:
"Also, passive screens have a pol-filter in place, the fine lines of which you
will observe on a white background, the more disturbing the closer the viewing
distance to the screen is. So, for general office applications (writing text),
the screens are less useful. "
Our
Hi Bernhard,
I too suspect that it is some kind of metal chelating reagent causing the
problem (possibly used in medium for carrying Fe2+, as the free Fe2+ is toxic
to cells). One simple test would be to load a liter of the unused medium to the
Ni2+ column and see what happens. Do you concentra
Hi Kevin,
a)
If your goal is merely to display EM maps, then UCSF Chimera, COOT,
pymol, etc. should all do. The EM maps are saved in the MRC format (.mrc
or .mrcs). Despite a different extension and some minor differences in
the headers, the MRC format is essentially the same format as our
e
Hi,
At high concentration (1-2%) the published saturating SDS:protein binding ratio
is about 1.4:1 by weight, that is roughly one SDS molecule per two aa on
average. It is dense but not that dense to prevent any further interaction.
More importantly, as a quite hydrophilic small molecule SDS
Hi all,
On linux there are a few good GUI HEX editors. Here I’d like to recommend
BLESS, which conveniently displays all possible numerical interpretations of
the four bytes under cursor. It also allows the user to switch between big
endian or little endian through a checkbox. Unfortunately all
with Convex, Cray, Fujitsu, or VAX reals/strings?
> I’d be interested to see what those files actually look(ed) like.
>
> // Best wishes; Johan
>
>> On Nov 9, 2018, at 18:38, Zhijie Li wrote:
>>
>> Hi all,
>>
>> On linux there are a few good GUI HE
Hi Ethan,
Thanks for the information. My guess is that in MTZ only F-float is expected,
because it is the only 32bit form?
Zhijie
> On Nov 13, 2018, at 3:44 PM, Ethan A Merritt wrote:
>
>> On Tuesday, November 13, 2018 11:51:55 AM PST Zhijie Li wrote:
>> If somebody is g
4:54 PM
To: Zhijie Li
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] VERY old mtz file..
Hi Zhijie
It's definitely a factor 4. The code is in subroutine QTIEEE in the Fortran
source I mentioned previously at this line:
See line:
A(I)=((A(I)+SIGN(2,A(I)))/4.AND..NOT.MNAN).OR.MDN2
If you
It's also said here, at the end of file :
https://www.cs.auckland.ac.nz/~patrice/210LN/DR4.pdf
"add 1 to the left, with the binary point"
0.1.
From: CCP4 bulletin board on behalf of Zhijie Li
Sent: Tuesday, November 13, 2018 7:4
Hi Nick,
Our LE outputs are exactly the same. Rmerge=100.0%!
Zhijie
From: CCP4 bulletin board on behalf of Nicholas
Devenish
Sent: Wednesday, November 14, 2018 7:15 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] VERY old mtz file..
Hi Eleano
rpret it as half bytes!
Zhijie
From: Nicholas Devenish
Sent: Wednesday, November 14, 2018 8:54 AM
To: Zhijie Li
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] VERY old mtz file..
Hi Zhijie,
Looks like we both had the same thoughts!
On Wed, Nov 14, 2018 at 1:
are quite feasible for MTZ files (not maps because we can
put anything into MRC/ccp4 map). Yes, the idea is to try all possibilities
until we can recover miller indices that look normal.
Zhijie
From: Nicholas Devenish
Sent: Wednesday, November 14, 2018
Hi Tomas,
Some thoughts:
a) I guess the thermodynamic drive for all part of this small ectodomain to
fold into a single lowest energy conformation is not very strong. The cells
can’t know that the little artificial domain is supposed to be a monomer when
the oligomers are also sufficiently hydro
Yes, we have also seen some indication that overdriving the expression can
cause problems. In our cases this may range from bad aggregations or loss of
expression. Since we use induced stable cells we simply reduced the doxycyline
levels.
Zhijie
> On Dec 14, 2018, at 1:13 PM, "r...@mrc-lmb.cam.
PCA?
On Jan 3, 2019, at 3:41 PM, Reza Khayat
mailto:rkha...@ccny.cuny.edu>> wrote:
Hi,
Happy new year to all! A bit of an off topic question. Does anyone know of a
method/program to extract the most distinct "n" (n>2) sequences from a sequence
alignment? Thanks.
Best wishes,
Reza
Re
Hi,
I believe that one can put a 50-100uL drop of fresh SigmaCote (in a tube cap)
with the glass pieces (surface well exposed), sealed in a dedicated (because
the container will be coated too) container (air-tight lunch boxes). After a
while the SigmaCote vapor should react with the glass and
Hi Nicola,
0.1-1mM Cysteine, GSH or BME will work fine. You can also try using very fresh
TEV without reducing reagent (or store it with BME and remove the reducing
reagent by some column just before use). Depending on how concentrated the
stock is, diluting it 3-5x could also sufficiently red
Hi Jan,
I guess you might be seeing a flat cut surface on the maps? It might be that
the map’s extent is not covering the protein molecule, which is usually the
case. When you rotate crystallographic maps it is usually no longer possible to
take adjacent unit cells to continue the density on the
Hi Jan,
Sorry I didn't read your script earlier. If you change your mapmask command to
output a map instead of a mask it may work for you:
mapmask \
mapin 2mol_2mFo-DFc.map \
xyzin 2mol_B.pdb \
MAPOUT B.map \
<< eof
border 2
eof
then you should get a map that covers the whole molecule
Hi Jan,
As Paul pointed out, you can use COOT to accomplish what you want. Particularly
you can take a look at the following functions in section 6 of the COOT manual
(these are in scheme):
(set-map-mask-atom-radius radius)
(mask-map-by-molecule imol-map imol-model invert-mask?)
(transfo
Sometime ago when I was watching a Youtube video on magnetron I learnt that at
least at at certain point of time the antenna port of the magnetron was sealed
using beryllium oxide ceramic(probably for its high thermal conductivity). The
video maker warned that this ceramic was extremely dangerou
Hi Jonathan,
We discussed about VAX floats last November:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1811&L=CCP4BB&O=D&P=63307
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1811&L=CCP4BB&O=D&P=65015
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In short
Hi Mintu,
I suggest using purified whole protein for ESI-MS. You will get a series of
protein peaks (if the substitution is not 100%, which is often the case), each
differ for 47 Dalton. You can determine how many Se each peak corresponds to if
you know the molecular weight of your protein. The
Hi Rob,
The BLAST nr database (fasta format) can be downloaded from the NCBI ftp:
ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/
As I remember it is the nr.gz file. When unzipped the file is called "nr".
According to BLAST the nr database does contain PDB entries.
http://blast.ncbi.nlm.nih.gov/Blast
Hello,
My apologies for sending the previous post to the wrong BB.
Zhijie
-Original Message-
From: Zhijie Li
Sent: Friday, August 08, 2014 11:10 AM
To: R.D. Oeffner ; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [phenixbb] local BLAST server
Hi Rob,
The BLAST nr database (fasta format) can
Hi Xiao,
I would poke the crystal with a piece of glass fiber or an oocyte needle to
make sure it is not salt. Some protein crystals can be a little tough
(rubber-like), but they react to poking very differently from rocks (salts) and
will eventually shatter. So far I have found this test to be
Have you done it?
1) Click “add residue...”
2) Click that “real space refine zone” button.
You will see what will happen.
From: Dialing Pretty
Sent: Wednesday, January 14, 2015 9:24 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Coot: How to connect N-terminal to neighbouring C-terminal
Dear
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