ossibility
these days.
best
jon
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]Im Auftrag von Careina
Edgooms
Gesendet: Dienstag, 14. August 2018 11:59
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] crystals that dont diffract :( :(
I got the most beautiful crystals I have
I got the most beautiful crystals I have ever seen and they don't diffract at
all. Not poor diffraction, NO diffraction. Anyone know why this could be and
how I can go about fixing it? I had three beautiful crystals and not one
diffracted. I did leave them in the drop for about 3 weeks before
Hello everyone
I am giving talk about refinement and model building. I wonder if anyone knows
of latest relevant papers on this topic that you could suggest for me?thank you
Careina
To unsubscribe from the CCP4BB list,
Dear all
What programs are best used for validate homology models? I know of molprobity
but if there are no coordinates I cannot use it. Is there a way to use such
programs with homology models?
Also I wish to use pdbepisa for to charaterise dimer interface but again for
homology model this
HelloI have two questions if anyone can help:1. Does anyone know how PDBe Pisa
calculate if the residues interact? I can't find an explanation for this.
2. Also, I want to do SAXS on a liquid sample using a rigaku smartlab x-ray
diffractometer. It is set up for powder and the software they use
Hi
I have not been in the game of solving structures for years. In the past I used
the program combat in ccp4 to convert my hkl output file from SAINT into mtz
file. Now I don't see combat anymore as an option in ccp4 programs and none of
the programs recognise my SAINT output file. Please
Dear CCP4 members
I do not have any good experience with chemical cross linking, it has not
worked for me and I am curious how others have got it to work. In my latest
attempt I wished to crosslink two monomers with DSS. The protein is exclusively
dimeric according to SEC. I incubated the
Dear all
I wish to do some docking work between a protein structure that I have and a
DNA model that I have created using the programme DelPhi. This can be done but
i would also like to create an electrostatic map of the interaction. Apparently
DNA and protein is to be protonated to generate
Sorry for off topic question, just wondering if anyone has come across a study
that shows the residue pka of certain amino acids is different in vitro
compared to in vivo?
Best
Careina
Briggs
about.me/david_briggs
On 13 August 2014 12:40, Careina Edgooms
02531c126adf-dmarc-requ...@jiscmail.ac.uk wrote:
Sorry for off topic question, just wondering if anyone has come across a study
that shows the residue pka of certain amino acids is different in vitro
compared to in vivo
Can anyone recommend a good docking program to look at protein-DNA interactions?
Dear CCP4 board
I have a protein that exists in equilibrium between monomer and dimer and I'm
trying to calculate KD using size exclusion. The problem is that the column
dilutes my sample so that if I put 20 uM on to the column, I only recover 0.5
uM in dimer fraction and 2 uM in monomer
Can anyone recommend a good modelling program to use to model protein-DNA
interactions. I have tried Haddock. Any suggestions?
Best Careina
Hi all
Any advice on how to get bigger crystals from conditions that give showers of
tiny crystals? I am getting small pretty looking individual crystals but they
are too small and they don't seem to grow. In fact, in some instances if left
for a couple of days they actually dissolve. I have
Dear ccp4 bulletin board
Sorry for off topic question. I'm working with a protein with pI 9.5 and yet it
will not bind to a cm sepharose column when equilibrated at pH 6.5. I have
removed all salt from the buffer but it still will not bind. I wonder if anyone
has suggestions as to why this
Just a quick question, does anybody know if ethidium bromide binds to
poly(dI-dC)?
Careina
Hi
Does anybody know how long one could store a crystal in liquid nitrogen for
before it will no longer diffract well? I'm talking in the order of weeks to
months...
careina
Dear ccp4
I have been performing trials on a protein DNA complex for a while now and have
not seen any crystals form. Today I checked an old plate (over a month old) and
I see 4 large crystals. *excitement* Three of them look tetragonal in shape
(like a pyramid) and one of them looks
Hi
Has anyone found the coomassie in a BN PAGE to be interfering with the
oligomeric structure of their protein? If so, how did you deal with this?
Thanks
Careina
by
varying the ratio.
Best,
Clemens
JPK
On Thu, Feb 28, 2013 at 2:06 AM, David Briggs
drdavidcbri...@gmail.comwrote:
You might want to try Disulfide by design
Cheers
Dave
On Feb 28, 2013 6:55 AM, Careina Edgooms careinaedgo...@yahoo.com
wrote
Dear CCP4 members
I wish to engineer a disulfide bond at the dimer interface of a protein I am
working with. Does anyone know of any available software to assist with this?
Best
Careina
Dear ccp4
I apologise for the straightforward question. I'm just a bit confused about the
observed reflections quoted in tables. What exactly is this and should it
include outer shell separately?
Best
Careina
Dear ccp4
Apologies for the off topic question. I was wondering whether anyone could
suggest a good tool or methodology to use to predict protein solubility and
ability to fold from the sequence? I am working with a large protein of
multiple domains. I would like to work with as close to the
Dear CCP4
I wish to crystalise a transcription factor in complex with DNA. Are there any
good papers you can recommend on protein-DNA crystallisation?
Also any helpful tips on protein:DNA ratios, protein concentrations or buffer
conditions that have worked for any of you would be most helpful
Dear CCP4
I have data that is twinned with an L statistic of 0.43. It seems all the
crystals that I produced were twinned sadly. Is there anything I can do to
twinned data to make it easier to analyse?
I have tried to use the detwin software but it won't let me input a
twinning operator for a
Anyone have any advice on how to detect whether my protein is forming
oligomers? It is monomeric in the native state but I have reason to believe
that it may be oligomerising in mild concentrations of urea (intermediate
state).
I have tried cross linking and BN PAGE and they are inconclusive.
Anybody know of any software out there that can predict potential interaction
sites between two proteins? They have been shown to interact via y2h screens
but I have no idea if they would interact on their own in vitro. Before I clone
them into a vector and purify them I would like some sort of
Dear ccp4ers
I just wonder whether anybody knows if the PISA software could be used/modified
to detect potential interfaces of interaction of different proteins? This would
be very useful as a tool to validate protein-protein interactions detected by
in vivo methods such as yeast 2 hybrid
Dear ccp4
I ask a very fundamental question because I have not had formal training in
this and I would like to understand.
How can I obtain the multiplicity (z) from the space group? So for example if
the space group is P222 how do I know that there are 4 monomers in the unit
cell? Or if it
Dear ccp4 bulletin board
I apologise for off topic question. I wonder if anybody knows of a good method
to detect oligomerisation?
I suspect an equilibrium intermediate is forming oligomers based on tryptophan
fluorescence showing an exposed tryptophan becoming buried in a hydrophobic
region.
Good morning CCP4 members
I have a question about a 2F0-Fc difference map that I calculated with Refmac.
In some instances it gives me negative (red) density around part of a side
chain and no positive density in sight. Furthermore the entire residue fits
well into the blue density of the
Dear all
Simple question, is there a way I can upload my own data into the EDS server? I
see only place for it to take from data already published in the PDB.
Apologies for non ccp4 based question
Careina
/
//
//
/
/
*From:*CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK]
mailto:CCP4BB@JISCMAIL.AC.UK] on behalf of Careina Edgooms
[careinaedgo...@yahoo.com] mailto:careinaedgo...@yahoo.com]
*Sent:* Friday, September 02, 2011 11:41 AM
Dear ccp4 bulletin board
I just have a slight concern regarding my Rwork Rfree difference. I have a
structure that I have solved. I am reasonably content that it is complete
because it has refined well, it no longer has bad geometries and contacts and
all the rotamers, ramachandra, bond
Dear ccp4 members
I have something that surprises me with molecular replacement. I have obtained
a
solution for a single point mutation using Phaser, the solution seems ok. I do
one round of refinement with refmac and I check the structure using molprobity
before I even start really to refine
Dear ccp4 members
I have question about how to interpret polarrfn log. I wish to know if my
crystal display NCS. I am not sure how to interpret the file. I see it have two
peak, one is origin and the other is not that high to me. I have attach copy of
the file. If someone could assist me to
Dear ccp4 users
I would like to know, is there a way to check that heavy metal has bound to
crystals before I take it to synchrotron which is far away?
thanks
Careina
Dear CCP4 members
I have a confusion with molecular replacement. I wish to solve a monomeric
protein in P21 where there are 2 monomers in asymmetric unit. I have a search
model that also has 2 monomers in asymmetric unit.
First I try using Phaser. I use only one chain of the monomer model
Dear CCP4 mailing list
I have a relatively simple question. How do I get sequence file in .pir format
which is required for many programs? I normally use fasta format but some
programs eg arpwarp do not allow me to use that
Thanks for your help
Careina
Dear CCP4 bulletin board
I am trying to solve structure with molecular-replacement. I have got good
solution using Phaser. The refined structure fits well to electron density and
appears reasonable in terms of geometry, ramachandran, rotamers etc. The
problem I experience is that there are
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