Dear All,
We have obtained many tiny protein crystals in a condition
containing 0.1M citric acid pH 3.5, 2M ammonium sulfate. The crystals are too
small for mounting in loops.
We intend to vary the salt concentration pH to obtain larger
crystals.
Could
Dear All,
Thank you for your replies:
2 different methods were suggested for the citrate buffer preparation over a
small range of pH:
1. mixing citric acid with sodium citrate salts
2. mixing citric acid with NaOH
we found the latter method easier for our purpose.
Dear All,
Is there a way to superpose multiple, discontinuous stretches of
residues between two protein chains ?
Dali output shows that there are discontinuous stretches between the PDBs that
are being aligned. But I can not find any option to download the superposed
PDB. The
Dear All,
Whenever I open up imosflm GUI from the terminal, I get the
following error:
iMosflm version 7.1.1, 24th March 2014
ipmosflm is not compatible.
Please configure iMosflm with the correct executable.
clicking the Configure button at the bottom of the error message panel
plain from the message that
ipmosflm is not compatible'
that iMosflm is trying to run with an incompatible MOSFLM_EXEC (maybe from the
old ccp4 6.3 distribution, but there could be other reasons).
On 28 Apr 2014, at 13:05, sreetama das wrote:
Dear All,
Whenever I open up
Dear All,
Is there any protocol for preparing a sample from
(cleaning/dissolving) protein crystals for verifying their mass through mass
spectrometry or SDS-PAGE? How many protein crystals are required? Should they
all be from the same well, or can they be from different wells
Dear All,
What are reasonable values of Rmerge in the outermost resolution
shell?
Some of the recent discussions suggest going to those sheels where I/sig(I)
~2 and CC1/2 = 0.5. But I am getting Rmerge Rmeas 1 in the outermost shell
for those values of I/sig(I) and CC1/2, and
Dear All,
What are reasonable values of Rmerge in the outermost resolution
shell?
Some of the recent discussions suggest using data up to those shells where
I/sig(I) ~2 and CC1/2 = 0.5.
But I am getting Rmerge Rmeas 1 in the outermost shell for those values of
I/sig(I) and
hi,
I found the following reference in a paper-
Hubbard S. PhD thesis. University College of London, Department of Biochemistry
and Molecular
Biology; 1992. NACCESS: a Program for Calculating Accessibilities.
On Wednesday, 9 July 2014 8:20 PM, FOOS Nicolas
nicolas.f...@synchrotron-soleil.fr
Dear All,
I have a PDB file which does not have the REMARKS cards 465 (for
missing residues) and 470 (for missing atoms). This is not a deposited PDB
file. Is there any program to figure out the missing residues and atoms (some
programs complain about missing atoms) ? Or do I have
Dear all,
We are planning to buy electronic dispensing pipette (single
channel) and mechanical multi-channel pipette (8 channel) in the range 0.5 - 10
ul in our lab.
Currently, we are considering IKA PRECISION pipettes.
It will be helpful if we can get feedback on how these
Dear all,
Is there any CCP4 module/ other software/ web server which can
determine which particular residues form the surface of a pocket/ binding-site
in a protein?
Thanks in advance,
sreetama
: [ccp4bb] residues forming the surface of a cavity
On 10/04/2012 04:09 PM, sreetama das wrote:
Dear all,
Is there any CCP4 module/ other software/ web server
which can determine which particular residues form the surface of a
pocket/ binding-site in a protein?
Do you mean
check mail ...
Dear all,
I have a 20 KDa protein that has a single cysteine , about 42
residues from the C - terminal . The protein aggregates during crystallisation
setup (hanging drop, vapour diffusion ) . What ratio of protein and
mercapto-ethanol should be used during trials to prevent
Dear all,
I have a 20 KDa protein that has a single cys residue , about 42
residues from the C-terminal . The protein aggregates during crystallization
setup ( hanging drop vapour diffusion) . What ratio of protein and
mercaptoethanol is to be used to avoid aggregation and help in
Dear All,
Is there any module in CCP4/ other related software/servers which
can show a multiple alignment of homologous sequences from a protein family,
together with their secondary structures?
Thanks in advance,
regards,
sreetama
Dear All,
I am trying to superpose 2 chains from the same pdb file. I have
generated 2 separate pdb files, each with one chain, using PDBSET.
When I run LSQKAB with the 2 generated files (on UBUNTU 10.04, ccp4 6.2) it
fails to run. The 2 input files CONTAIN the columns for
Dear All,
I am trying to superpose 2 chains from the same pdb file. I have
generated 2 separate pdb files, each with one chain, using PDBSET.
When I run LSQKAB with the 2 generated files (on UBUNTU 10.04, ccp4 6.2) it
fails to run. The 2 input files CONTAIN the columns for
Dear All,
I am trying to superpose 2 chains from the same pdb file. I have
generated 2 separate pdb files, each with one chain, using PDBSET.
When I run LSQKAB with the 2 generated files (on UBUNTU 10.04, ccp4 6.2) it
fails to run. The 2 input files CONTAIN the columns for
Dear all,
I have a 17 KDa protein that gives crystals in a condition that has
0.1M bis-tris pH 6.5. The crystals are thin needle clusters and do not
diffract. I have tried additives, but they haven't improved the crystals. I
intend to vary the pH of the condition.
My
Dear all,
Is there any software which will print the RMSDs (residue wise, and
not chain wise) for more-than-2 chains (having similar/same sequences)
superposed together?
Thanks in advance,
sreetama
Dear all,
Is there any software or web server available to calculate the volume of a
ligand if the ligand coordinates are provided?
Google seems to come up only with options to calculate protein cavity volume.
Thanks in advance,
Sreetama Das,
phd student,
Physics, IISc
regions?
What is the best way to calculate the RMSD for superposition of the cores -
should I prepare a separate PDB file by removing the coordinates of the loop
residues and then superpose?
Thanks in advance,
Sreetama das,
PhD student,
Physics, IISc
Dear Users,
The option ValidateProbe clashes is disabled in coot (version 0.8/CCP4-6.5,
OS - ubuntu 12.04).How can this be enabled?Can I toggle between 'enable' and
'disable' according to need?
Thanks in advance.
SreetamaPhD student,IISc
Hi,Sorry for a slightly off-topic question.
I just noticed that for some pdb files, the value of R-factor shown on the PDB
web page is different from the value in the file obtained by clicking the link
display file. Why is this so?
examples where I noticed:4jzc , where the PDB page
Dear All,
I have a transferase, which is showing broad specificity for both the
substrates (nucleotides) in our organism of interest, but is highly specific in
other organisms.
Are there any references showing the applications of (bi-substrate) proteins
with such broad specificity towards
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