Hi,
Which program outputs the symmetry operator (rotation and translation)? I
have a dimer in the asymmetric unit and need to know the symmetry operator
to get a tetramer, the active molecule.
James
Dear CCP4bbers,
I am facing CCP4-6.3.0 installation problem. Unable to run make.
Configuration is done. Getting error while running make (command not
found). Please help.
Thanks in advance, James
Dear Crystallographers,
Is there any rule of thumb for Protein concentration and molecular weight
for crystallization trials of a soluble protein? Looking for high molecular
wt. protein ~50kDa.
James.
Dear CCP4bbers,
Is there any tool to calculate the Matthews coefficient from a
crystallographic model of RNA-protein complex?
Thanking you.
James.
Dear ccp4bbers,
I wonder if someone can help me defining proper weight matrix term in
Refmac5 to lower the R-FreeR gap. The log file indicates weight matrix of
1.98 with a gap of 7. Thanks for suggestions in advance.
James
Dear CCP4BBers,
Refmac is giving the error No reflections in resolution bin??? It seems
there is no SigFP column. I wonder how to fix the problem.
Thanks in advance.
James
Dear All,
What would be the range of B-factor (Maximum temperature factor) for a
metal in a protein-metal complex?
Thanks in advance for the help.
James...
Dear All,
Sorry for the non-ccp4 query.
I am looking for an option to increase the atom radius in chimera. Can
anyone help me out?
Thanking you.
James
Dear all,
I just wonder, How to save the LSQ output in coot.
Thanks in advance.
J...
Dear All CCP4bbers,
Please help me in finding *R-sym I *(observed), *R-merge I*(obseved), *R-Free
Error i*n the data provided below. If I am not wrong, Can anyone suggest me
the difference between R-sym and R-merge?
Thanks in advance for the help.
James*
*
R-values of internal consistency :
Dear all,
What are the standard methods for the crystallographic model judgment? What
parameters should be included in the final refinement statistics in relation
to the model error? What is Cruinkshank DPI and how can it be calculated and
what information it gives about the quality of the model?
Dear ccp4bbers,
Can anyone suggests the acceptable range of DPI value as an coordinated
error and except sfcheck, what other programs calculate it?
Thanks in advance.
James...
Dear All,
I am using Refmac5 and have metal in the structure. The refmac program is
not reading this from the library file and hence not refining this metal
ion.
What is the way to solve this problem.
Thanks in advance.
J...
Dear All,
Wish you all a very Happy New Year, 2010.
Can anyone give me some information regarding the number of peaks in
molecular replacement.
What is the co-relation between no of peaks and the solution in molecular
replacement and where the no. of peaks are indicated in molrep or phaser
Dear All,
Sorry for the non-ccp4 query.
I have solved a crystal structure of an enzyme and woring on its biochemical
aspect. We have a mutant of this enzyme and we are comparing some
thermodynamic parameters of this enzyme with mutant( lke delH and delS,
delG). we have done the expt at different
Dear All,
I need help regarding installing Automar in ferora. After gunzip and untar
the file when I run automar/autiomar-install , it says commant not found.
Can anyone suggest why it is happening and its solution.
Thanks
james
Dear All,
Please suggest the Peak wavelength of SeMet and the corresponding f_prime
and f_doubleprime.
In one of the journal I got it is 0.97905 A and Phenix manual shows f_prime
and f_doubleprime to be -3 and 4 respectively.
How can one deduce f_prime and f_doubleprime for any HA at a
Dear All,
Please suggest the Peak wavelength of SeMet and the corresponding f_prime
and f_doubleprime.
In one of the journal I got it is 0.97905 A and Phenix manual shows f_prime
and f_doubleprime to be -3 and 4 respectively.
How can one deduce f_prime and f_doubleprime for any HA at a
Dear All,
I need some suggestions regarding the SAD phasing using home source. What
the the most commonly used HA for SAD phasing for Cu anode.
All suggestions are welcome.
Thanks.
James
Dear crystallographers,
Sorry for the non-ccp4 query. I am new to this field and need some
suggestions. My question is, why some protein takes longer time to
crystallize, say 6-8 months, and it is the only condition to get the
crystals.? What are the ways to get the crystals faster.
The crystal
Dear CCP4bbers,
Can anyone suggests how to make seed-stocks if one is not having
seed-beads... Is there any other methods to crush the crystals for the same
purpose. What if it is simple vortexed. Off-course there wold be all sorts
of sizes, the intact crystals as well.
Please suggest.
Thanks a
Dear CCP4bbers,
Please comment on the stabilizing solution for seed stocks. If the crystal
is in 30% MPD and coming after 2-3 days, what should be the stabilizing
solution for seeding.
Thanks.
James
Deal all,
Sorry for the non-ccp4 query once again.
I need suggestions regarding the improvement in crystal quality. I have
crystallized a protein in MPD. The crystals grow like a thin plates and the
plates are stacked together. So, the mosaicity is very high and also
indexing is difficult even at
Dear all,
Sorry for the non-ccp4 question. Recently I have got some long needle of on
35 kDa protein with 65% MPD at 4 degree C at pH 3.6 (50 mM NaOAc buffer).
The protein contains 50mM of salt. The florets are very thin. I need some
suggestions regarding the optimization of the crystallization
Deal all,
Sorry for the non-ccp4 query.
I am new to this field and need some suggestions regarding the improvement
in the crystallization qual
I have crystallized a protein with 65% MPD in 0.1M Acetate buffer pH 3.6 at
4 degree. The florets appear after 2 days and covers the whole drop. What
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