With regards to the image that Bohdan sent and Eleanor's statements, I'm
curious if the splitting of B-factors in Bohdan's image is due to the
increased amount of data (which may diminish the extent of uncertainty), due to
the diminished ensemble of structures within the crystal, or both. What
? Thanks.
Best wishes,
Reza
Reza Khayat, PhD
City College of New York
Associate Professor
Department of Chemistry and Biochemistry
Co-Director NIH G-RISE program
To unsubscribe from the CCP4BB list, click the following link
The clash score is also impressively high. Your map may have the incorrect
hand. Have you tried flipping it?
Best wishes
Reza
From: CCP4 bulletin board on behalf of Martyn Winn -
STFC UKRI <7c0f4d7fc2b7-dmarc-requ...@jiscmail.ac.uk>
Sent: 10 January 2024
structure. The structures were
predicted with the Robetta server and all have, as expected, geometry better
than most experimental structures.
Best wishes,
Reza
Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry and Biochemistry
New York
has written below. My question
was regarding the geometry of the structure. I also understand that outstanding
geometry does not indicate an accurately predicted structure -the helix example
indicated by Tristian. Nonetheless, the server links sent earlier are extremely
helpful.
Reza Khayat
that minimizes the geometry to
improve its statistics. Nonetheless, the journal has asked me for such a
report. Thanks.
Best wishes,
Reza
Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031
?Try using the psi-blast package and search against the PDB.
Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031
From: CCP4 bulletin board on behalf of Cryo EM
Sent: Sunday, September 5
Thank you Robbie.
Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031
From: CCP4 bulletin board on behalf of Robbie Joosten
Sent: Saturday, March 13, 2021 9:09 AM
To: CCP4BB
Hi,
For DNA/RNA models, is there an equivalent to a poly-Ala model? Something like
a poly-dN perhaps? This is in case you don't know the nucleic acid sequence.
Thanks.
Best wishes,
Reza
Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry and Biochemistry
?Does anyone know how AlphaFold performs on sequences with little conservation?
Virus and phage proteins are like this. Their structures are homologous, but
sequence identity can be less than 10%.
Reza
Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry
?Hi,
Has anyone been able to compile a windows version (non cygwin) of probe and
reduce? I'm asking for the windows version of coot. Thanks.
Best wishes,
Reza
Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031
been considered?
Reza
Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031
From: CCP4 bulletin board on behalf of Jon Cooper
<488a26d62010-dmarc-requ...@jiscmail.ac.uk>
Sent: Thursday
Hi,
Can folks suggest programs for objectively docking ATP/ADP molecules into
density? Our density is not so good, probably because of occupancy, and we'd
like a less subjecting approach for modeling. Thanks.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
City College of New York
?You can generate maps using UCSF Chimera then convert these to binary masks.
This means you can drag PDB around to generate a mask where ever you like.
Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031
Hi,
I've installed the entire CCP4 7.1 package (ShelX and arpWarp); however, I
can't find the arp/Warp binaries/scripts (e.g. auto_em.sh). Are these not
included with the CCP4 package? If not, why not? Thanks.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
City College of New York
?Hi Lei,
Rosetta uses something very similar to this for designing proteins that bind to
ligands/proteins. Perhaps look there.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
From
?Isn't the entire idea of using ITC that you are measuring an equilibrium
constant? Wouldn't this eliminate the nuances of what you're looking for (i.e.
kinetics)? Perhaps you should use SPR to tease out this model?
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
City College of New
?The interface doesn't appear to be extensive. What is the buried surface area?
Is the molecule a dimer in solution, or is the dimerization caused by crystal
packing?
Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
freezing conditions
become the bottle neck of cryo-EM.
?
Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
From: CCP4 bulletin board on behalf of Patrick Shaw
Stewart
Sent: Tuesday, July 23, 2019 1:35 PM
Hi,
Sorry for the non-crystallography question. We have a protein complex with
nucleic acid and would like to know if the nucleic acid is DNA or RNA. Is there
a sensitive method for doing this where we don't need buckets of the sample?
Thanks.
Best wishes,
Reza
?
Reza Khayat, PhD
Assistant
Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
From: Clarke, Oliver
Sent: Saturday, March 16, 2019 8:36 PM
To: Reza Khayat
Subject: [EXTERNAL] Re: CCP4BB Digest - 15 Mar 2019 to 16 Mar 2019 (#2019-81)
Hi Reza
?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
Reza Khayat, PhD
Assistant Professor
City College of New York
Department
Thanks everyone. I did two things:
1. Extract the MW from the cif file as suggested by David (see below)
2. I extracted the RNA sequence from the cif file and ran it through an
oligo calculator with ssRNA as the option
Both give similar results.
Best wishes,
Reza
Reza Khayat
Hi,
I'm not an RNA person. Can anyone suggest a method to calculate the mass of a
RNA PDB? I'd like the protons to also be considered in the calculation. Thanks.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
Department of Chemistry
City College of New York
85 Saint Nicholas Terrace
wishes,
Reza
Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
wishes,
Reza
Reza Khayat, PhD
Assistant Professor
Department of Chemistry
City College of New York
85 Saint Nicholas Terrace, CDI 2.318
New York, NY 10031
http://www.khayatlab.org/
212-650-6070
?Hi,
Has anyone established a robust method to calibrate the pixel/voxel size of a
cryo-EM image reconstructions using a known PDB? Thanks.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
I think this is an excellent opportunity to combine MD calculations with your
structures to see what role(s) this flexible region may play in your structure.
Reza
Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
detecting and
calculating RMSD, but I'd like to have the spread for each atom in the final
graph that Coot generates. Thank you.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
eza
Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
Hi,
Is there a server/program that can generate a chemical picture/PDB from the
sequence of a polysaccharide and the type of connections? I'm not so interested
in the minimized structure at this point. Thanks.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
Department of Chemistry
City
Hi,
Is it possible to run Coot without the use of GUI? We have some Coot scripts
for a pipeline and we'd like to do without the GUI. Thanks.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
Department of Chemistry
City College of New York
85 Saint Nicholas Terrace, CDI 2.318
New York
Dear Chen,
Is this an icosahedral virus crystal structure, or a highly symmetric structure
where the RNA may have different binding modes to each subunit and thus
averaged out in the crystal?
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
City College of New York
Department
wishes,
Reza
Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
such criterion is by
no means trivial. Thanks again for the help.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
From: Reza Khayat
Sent: Sunday, April 9, 2017 6:07 PM
To: CCP4
one another to
warrant a closer look? I think the most important aspect of the analysis would
be defining a threshold (possibly based on resolution and structure statistics)
that would identify sufficient difference between structures. Thanks.
Best wishes,
Reza
Reza Khayat, PhD
Assistant
Hi,
Sorry for another non crystallography question. Can someone suggest a fraction
collector to collect fractions from a CsCl/glycerol/sucrose/... gradient from
an ultracentrifugation run? Thanks.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
City College of New York
Department
I don't think this is taught in Biochem101. You didn't miss it. The cytoplasm
is quite viscous, like jello.
Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
From: CCP4 bulletin board [CCP4BB
elute later because it may
interact with the matrix. Thanks.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
Hi,
With the hopes of not reigniting the heated "Chloride or water" CCP4 discussion
in Jan. 2015, what experimental method is suggested for identifying chlorides
in a x-tal?
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
Ne
I would have to agree with Tim. I'm a little surprised that your R/Rf is 27/32.
Are the images representative of the entire model/map fits, or a small section
of it?
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
Department of Chemistry
City College of New York
85 Saint Nicholas
I Agree with Edward. No discussion of politics, religion, or sex at work.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on
I've done this sort of analysis in the past and it can be very useful depending
on your story is. I'm not sure if any software offers this. My solution was to
write a script to do the comparison after the superposition was done.
Unfortunately I can't find the script.
Best wishes,
Reza
Reza
Hi,
Sorry for the non-crystallography question, does anyone know how to produce
milligram quantities of single stranded DNA? Thanks.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
Department of Chemistry
City College of New York
85 Saint Nicholas Terrace, CDI 12318
New York, NY 10031
That's interesting. Enantiomer differences can be detected at worse than
20Angstrom resolution in EM reconstructions. What do you think is the reason
for this?
Reza Khayat, PhD
Assistant Professor
Department of Chemistry
City College of New York
85 Saint Nicholas Terrace, CDI 12318
New York
Hi,
Follow up question on SAXS. Does SAXS have an enantiomer problem like electron
microscopy? In other words, does the calculated model possess the correct
handedness or can both handedness of a model fit the scattering profile just as
well?
Best wishes,
Reza
Reza Khayat, PhD
Assistant
Hi,
Try using 100mM Ammonium Citrate pH 8.5 as the buffer for your lysis -add salts
as well. The Citrate will inhibit metalloproteases and is Ni-NTA friendly. It
solved our proteolysis problems and may help with yours.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
City College of New
,
Reza
Reza Khayat, PhD
Assistant Professor
Department of Chemistry
City College of New York
New York, NY 10031
http://www.khayatlab.org/
212-650-6070
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Radisky,
Evette S., Ph.D.
Sent: Wednesday, April 22, 2015 3:40 PM
To: CCP4BB
Reza Khayat, PhD
Assistant Professor
Department of Chemistry
City College of New York
New York, NY 10031
http://www.khayatlab.org/
212-650-6070
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Victor
Lamzin
Sent: Tuesday, April 21, 2015 9:07 AM
To: CCP4BB@JISCMAIL.AC.UK
can define the regions
where NCS is applied and thus avoid loops/regions where the NCS is violated.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
City College of New York
160 Convent Ave, MR-1135
New York, NY 10031
(212) 650-6070
rkha...@ccny.cuny.edumailto:rkha...@ccny.cuny.edu
On Apr
lysed with the micro-tip. Same results were observed.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
City College of New York
160 Convent Ave, MR-1135
New York, NY 10031
(212) 650-6070
rkha...@ccny.cuny.edumailto:rkha...@ccny.cuny.edu
On Mar 19, 2015, at 11:15 PM, John Fisher
Hi,
Cultures are being properly cooled prior to induction (water bath supplemented
with ice).
Reza
Reza Khayat, PhD
Assistant Professor
Department of Chemistry
City College of New York
New York, NY 10031
http://www.khayatlab.org/
212-650-6070
From: lieh low [mailto:liehy...@gmail.com]
Sent
Hi Todd,
A concern of mine is that you may be looking at an artifact
of the domain. Whatever assays you decide to do, make sure
that they are also performed for the full sized protein.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry
Hi,
Has anyone used citrate as the sole cryoprotectant? If so,
what concentration was needed?
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
160 Convent Avenue
New York, NY 10031
Tel. (212) 650-6070
www.khayatlab.org
have reasonable phases to build a reasonable model.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
160 Convent Avenue
New York, NY 10031
Tel. (212) 650-6070
www.khayatlab.org
Original message
Date: Thu, 27 Nov 2014
Hi,
This is way off topic but relevant. Does anyone routinely
use the Rainin Classic Pipet series? If so, what are your
thoughts and how often do they need to be calibrated?
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
Hi,
Can people direct me to programs capable of detecting non-
contiguous protein domains from a PDB file? I realize that
some structures may be problematic.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
160 Convent Avenue
Hi,
The research group of Dr. Reza Khayat at the City College of New York
(www.khayatlab.org) is seeking candidate postdoctoral fellows to study host
pathogen interaction using a combination of cryo-electron microscopy (cryo-
EM), X-ray crystallography, biophysics and biochemistry. The research
on walls next to the FPLC
:)
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3055910/
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304934/
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
160 Convent Avenue
New York, NY 10031
Tel
Hi,
Does anyone have a protocol for getting rid of PEG3350 from a protein sample?
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
160 Convent Avenue
New York, NY 10031
Tel. (212) 650-6070
www.khayatlab.org
Hi,
I guessed glycerol by looking at the figs and not reading your text. Having
read your text afterwards, you do have glycerol in the solution. My guess is
glycerol.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
160
Hi,
A crazy solution may be to make a cuvette with a 3D printer. I'm not sure if
the available resins are transparent to DLS.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
160 Convent Avenue
New York, NY 10031
Tel. (212
observe. Are
there any chemicals that would disrupt short beta-sheet formation? Thanks.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
160 Convent Avenue
New York, NY 10031
Tel. (212) 650-6070
www.khayatlab.org
binding site.
Thanks.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
160 Convent Avenue
New York, NY 10031
Tel. (212) 650-6070
www.khayatlab.org
What does an omit map look like, if you omit both cysteines?
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
160 Convent Avenue
New York, NY 10031
Tel. (212) 650-6070
www.khayatlab.org
Original message
Date: Mon, 2
=1Posti
ngSeq=1
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
160 Convent Avenue
New York, NY 10031
Tel. (212) 650-6070
www.khayatlab.org
is not willing to disclose the contents for the media.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
160 Convent Avenue
New York, NY 10031
Tel. (212) 650-6070
www.khayatlab.org
Original message
Date: Mon, 19 May
Hi,
The research group of Dr. Reza Khayat at the City College of
New York (www.khayatlab.org) is seeking candidate postdoctoral
fellows to study host pathogen interaction using a combination
of cryo-electron microscopy (cryo-EM), X-ray crystallography,
biophysics and biochemistry
I think fungus dependent crystallization has occurred for some
labs. A paper that pops into mind is from my graduate
laboratory (not my work though):
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2225192/
Reza
Reza Khayat, PhD
Assistant Professor
The City College of New York
Department
Hi,
I think the experiment is doable, but how would you decouple
protein-protein interaction from folding of the unfolded
protein due to protein interaction?
Reza
Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
160 Convent Avenue
New York, NY
USCF Chimera can save maps as a VRML and other formats. You
can use 3D animation software to change formats from VRML to
anything else.
Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
160 Convent Avenue
New York, NY 10031
Tel. (212) 650-6070
? Here's
hoping that the solution is not dumping a bunch of Se-Met into
all the purification buffers...
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
160 Convent Avenue
New York, NY 10031
Tel. (212) 650-6070
Original
deposits on it with
every use.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
160 Convent Avenue
New York, NY 10031
Tel. (212) 650-6070
Original message
Date: Tue, 4 Feb 2014 12:40:51 -0500
From: CCP4 bulletin
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