Dear Kumar
you said 'shot from other conditions': we do not know then if you shot these
crystals or not.
Else:
- DNA should give you an X pattern, most of the time.
- protein should give you at least low resolution pattern, or faint rings if it
is powder pattern like
- salt should give you dif
Hi Joseph,
Are you having trouble getting bigger crystals. You said you shot them, and
they are not salt. Do they diffract at all? If they are diffracting to any
extent, you could optimize the crystallization condition to get better,
bigger crystals and shoot them. A simple way of growing fewer, b
Dear All
update 041 contains
* rdkit 2017_03_02
* acedrg
- update for new rdkit
* ccp4i2
- update for new rdkit and acedrg
* ccp4mg
- update for new rdkit
* coot
- update for new rdkit
Next up dials 1.6.1
All the best
CCP4 core team
Hi Joseph,
Could you post the UV fluorescence image? Oftentimes, UV absorbing
objects that do not fluoresce (such as nucleic acid crystals) show up
dark against a brighter background in UV fluorescence.
V. Nagarajan
JANSi
On 6/19/2017 7:20 AM, Joseph Ho wrote:
Dear all:
I would like to s
Dear Joseph,
I think, you already did the most classical test to determine what is in
your crystal.
Maybe you can try a destructive approach by washing the crystal prior to
put them in Agarose gel do a short run and color with ethydium bromide.
Simpler, you can also melt the crystal after wa
Dear all:
I would like to seek your opinion on our crystal hits. We are working
on protein/dsDNA complex. By changing different protein and DNA
(14-22bp) constructs, we recently got some hits from commercial
screens using sitting drop vapor diffusion (very small xtals). The
precipitant is PEG and
Just a reminder that there are still places available...
We are proud to announce a pair of workshops held at the University of
Leeds exploring the crossover between EM and MD.
http://www.ccpem.ac.uk/training/leeds_em_md_2017/leeds_em_md.php
(1) Computation for Biomolecular Cryo-Electron Microsc
Thank you Robbie.
I guess ligands do not (or should not) appear in SEQRES therefore should
not have a TER record.
Eleanor
On 19 June 2017 at 11:04, Robbie Joosten wrote:
> Hi Eleanor,
>
> From PDB format 3.3:
> * Every chain of ATOM/HETATM records presented on SEQRES records is
> terminated wit
On 19/06/17 09:54, Chris Ulens wrote:
I am looking to get feedback from others who have recently built and
refined bond lengths and angles of an N-linked glycosyl chain in Refmac.
I observed in Coot that the bond between O3 of BMA303 and C1 of MAN304
does show while the bond between O6 of BMA3
Hi Eleanor,
From PDB format 3.3:
* Every chain of ATOM/HETATM records presented on SEQRES records is terminated
with a TER record.
* The TER records occur in the coordinate section of the entry, and indicate
the last residue presented for each polypeptide and/or nucleic acid chain for
which the
Dear CCP4BB
On Tuesday 4th July 2017 at 3.30pm British Summer Time PDBe will be
presenting a webinar on using our REST API service.
In this webinar we will introduce the PDBe REST API service and show you
how to access macromolecular structural data programmatically.
This webinar is part o
Hi Jan,
I do the same thing, but it would be nice if there was a consistent target. I
noticed that the targets (and their sigmas) used by the PDB validation software
don't fully coincide with the 'ideal' values from their own Chemical Component
Dictionary. How are supposed to correct the restra
These do seem to multiply wonderfully in the PDB output files and
sometimees to have have strange effects/ affects in COOT?
As I understand there should be a TER record after a protein chain? but not
after a ligand.
Dont know about carbohydrate chains.
Eleanor
The correspondence about N linked
Hi Chris,
Not a direct answer to your question, but I notice that there are two TER
records for the same residue. We've been noticing a lot of problems with
leftover TER records. Any idea where they came from? It probably won't help,
but try deleting those.
Cheers,
Robbie
> -Original Mess
Dear Nick,
I would contact some MassSpec people and ask if they could find out the mass of
your mystery ligand. I would also carefully look at the neighboring protein. It
might be an alternate conformation of a partially disordered loop. Finally, I
would check literature to see if a natural lig
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