Good (?) afternoon,
I can't resist quoting the facetious answer, once given to me in a similar
situation by the dear departed Felix Frolow: '*proteins are bastards*'.
Well to be exact he used a much less socially acceptable term, and he said
it in Russian - but the point is that sometimes (most of
Hi,
I would like to input all 20 conformers of my ensemble into Molmol and chose
which of those 20 conformers is the best representation of all of the others. I
have been looking online for tutorials but I am coming up short. Does anyone
have any ideas?
Thanks.
Regards,
Robert Hammond
Thank you all for responses. I have added my reply below.
On 26 October 2016 at 17:02, Eleanor Dodson wrote:
> Are your 3 crystals isomorphous, and do they all refine well?
Yes, all C2221 crystal datasets refine to ~ 19/23 %
> I guess you struck lucky with DS3 - as suggested it could be a differ
Dear Kay,
Exactly. That is why we provided two Linux versions (called pdb2ins and
pdb2ins_oldlinux) on the SHELX server.
So far two versions seem to be enough and for Macs and Windows only one
version seems to be required. If
anyone finds this to be insufficient, please let Anna know giving
de
Hello Veronica,
There are 2 aspects to your enquiry:
1- The different number of ligands in your structure could be easily sorted
out by a longer soak. You don’t have to stick with 1 minute soak. A day or
longer (I’ve heard of a case in which the soak went on for 30 days), would fill
up as
In line with Kay's message this sounds like pdb2ins having being linked
statically with glibc.
AFAIK this can be problematic since glibc in reality can never be
completely statically linked. This may cause version conflicts if the
same version of glibc is not present on the users system. To avoi
Hi Liuqing,
As Eleanor suggested, if your structure is expected to contain alpha
helices, you might
want to give ARCIMBOLDO_LITE a try, as your resolution is still within the
scope of the method.
In case you have any suspicion of the fold that might be and it contains
beta sheets,
you can try ARCI
Hi Phil,
the error message occurs because your glibc is too old for this binary. The
glibc cannot easily be updated, it is tied to the distribution, in your case
RHEL6. A newer kernel does not change this, nor would an update to RHEL 6.8
This is why distributed Linux software should be built on
What is the height of non-origin Patterson function peak for your data sets?
C-centered cells:
216.5 345.8 145.290.090.090.0
and
147.0 354.3 217.490.090.090.0
are very different; however, they have common subgroup F222 with similar
unit cell parameters. In F
Are your 3 crystals isomorphous, and do they all refine well?
I guess you struck lucky with DS3 - as suggested it could be a different
soaking, different crystal size, etc, etc..
If isomorphous I would compare all 3 structures in COOT and look for subtle
differences..
Your C222 and C2221 cells a
Are these three crystals in order of harvesting (with different soaking times)?
How big is your ligand. How accessible is the binding pocket (and is there a
clear difference in accessibility between chains)?
T
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University
Hi Valentina,
> I just solved a NCS-tetrameric (biological assembly is just a dimer) crystal
> structures with ligand soak (same plate - same conditions). No density for
> ligand is observed in the first map. In the 2nd, I have 1 ligand bound. In
> the 3rd, I have 2 ligands bound. Is there any
Dear Veronica,
with 1st, 2nd, 3rd map you mean the density for the same dataset after
three consecutive cycles of building-refining or three different maps from
three different crystals?
If it's the first case, it could be fine, it may mean that at each cycle
you improve the map so you see signal
Hi,
it seems you haven't found a solution. If there is no model you might
want to try experimental phasing. With that resolution and the right sg
a S-SAD might be possible. So you might not even need a HA derivative.
Cheers
Christian
Am 26.10.2016 um 14:53 schrieb SUBSCRIBE CCP4BB Liuqing
Can you push the resolution higher?
Is there any anomalous signal?
Maybe you could try Archimoldo to look for helical fragments?
BUT these approaches work better the higher the resolution data...
Speaking as one who has failed many times with sort of problem!
Good luck Eleanor
On 26 October 2016
Hello!
I have a crystal diffracted to 2Å, and have no homology structure. As, i can't
repeat the crystallization, so i try using Balbe and MorDa program, the MorDa
give a partial model with Q socre 0.46, Rwork/Rfree 0.50/0.51. it's hard to
rebuilt using coot, and when i use Buccaner or Arp/w
Dear Phil,
as far as I understand, SL version 6 builds on kernel 2.6.32, which was
released nearly a decade ago. Maybe it's time to update?
Even the rather conservative Debian stable uses 3.16 ...
Best,
Tim
On Wednesday, October 26, 2016 12:11:25 PM Phil Evans wrote:
> Hi George
>
> I’m not s
Hello all,
I just solved a NCS-tetrameric (biological assembly is just a dimer)
crystal structures with ligand soak (same plate - same conditions). No
density for ligand is observed in the first map. In the 2nd, I have 1
ligand bound. In the 3rd, I have 2 ligands bound. Is there any reason for
this
Dear Phil,
Thank you for the information.
We made two versions for Linux available;
one packaged on an up-to-date Linux computer and one from an 'older'
system.
Should there be a library problem with the 'linux' version, the
'oldllinux' version could work.
best wishes,
Anna
On 10/26/2016 12
Mac version runs OK!
Martin
_
Dr. Martin Martinez-Ripoll
Research Professor
xmar...@iqfr.csic.es
Department of Crystallography & Structural Biology
www.xtal.iqfr.csic.es
www.xtal.iqfr.csic.es/Cristalografia/
Telf.: +34 917459550
Consejo Superior de Investig
Hi George
I’m not sure that anyone here is using shelxl but I’ve just updated our general
64-bit Linux versions anyway. shell starts OK, but with pdb2ins I get a
complaint. Do you understand this? (I should probably ask our local guys)
Our system is
Scientific Linux release 6.7 (Carbon)
./pdb
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