Hi,
i am trying to crystallize a protein. i got phase separation in many
conditions. can anybody tell me about phase separation? Is this good or not?
My protein concentration is 17mg/ml. shall i increase it?
Thanks in advance.
parveen
Good morning ccp4bb-ers!
I have two protein-protein complex structures, and the orientation of one of
the components shifts slightly with respect to the other component between
the two structures.
If I run superimpose on the shifting component I get this:
CROWTHER ALPHA BETA GAMMA 12.41607
Hi all,
I'm starting using pymol to generate movies to show my structure.
While its seems fairly easy to generate simple movies with rocking or
rotating molecules, I have been finding some difficulties
understanding how to generate more complex movies.
For instance, I'd love to generate a
Dear All,
I am trying to build a molecular replacement model in arp/warp in space group
P22121.
Refmac alone seems to be fine with refining the model in P22121; but arp/warp
fails, as far
as I can see at the first Refmac refinement stage. In the log-file it says
this space group is
not
Hi -
ARP/wARP only likes standard space groups, like P21212,
P22121 is not-standard ... oh well ...
(Eleanor is complaining about it for about 13 years ... but never
mind that she is right)
Just re-index your sg to be P21212 (refl. utilities, reindex, in ccp4i).
Choose 'Entering reflection
Dear Florian,
ARP/wARP supports 65 space groups where proteins crystallise and it
indeed uses the Hermann-Mauguin convention as given in the International
Tables. The space group P22121 (number 3018 in the CCP4 symop.lib) is
not supported by ARP/wARP. The standard for it would be number 18,
Go to the Pymol community wiki (www.pymolwiki.org) and install SLERPY, a
python plugin that allows you to create multiple scenes and transitions
in Pymol. It is possible to create some pretty sophisticated animations
using slerpy, including fading transitions of surfaces. If you ray-trace
the
Hi all
i am having Ca2+ and Cl- as hetroatoms in my protein structure. while doing
refinement with REFMAC i m getting following warnings:
I am reading library. Please wait.
mon_lib.cif
WARNING : residue: CA994 chain:XX
different element name: file:C
POSTDOCTORAL POSITION IN PROTEIN CRYSTALLOGRAPHY
An NIH-funded POSTDOCTORAL position is available immediately to study the
structure and function of (1) ATP-dependent molecular machines [e.g. Cell
(2003) 115:229; Mol. Cell (2007) 25:261] and (2) multi-component protein
assemblies [e.g. EMBO J.
the phaser docs/tutorial indicate that phaser calculates what could be
called (ensemble) / (sequence) to get a percent composition, however i
cannot seem to find the direct result from this in any output (.sol, .sum,
.pdb, .log... other?)
any tips appreciated as to if this can be found /
i wrote
(ensemble) / (sequence) to get a percent composition
i forgot to emphasize that i do not mean the Vm or the Z composition,
but the composition as one would enter e.g.
COMPosition ENSEmble mol1 FRACtional 0.22
or
COMPosition SCAttering SCATTERING
-bryan
Dear Vineet,
It seems, in your input PDB file the atom level for CA and CL in the last
column is C. It should be CA CL respectively. The atom name in the
input file and Dictionary doesn't match.
all the best
Manish
Vineet Gaur [EMAIL PROTECTED] wrote: Hi all
i am having Ca2+ and Cl-
I used to do that in POVray.
you can use any program that writes POV output and can generate all the
objects you want. I used to write each object I want to manipulate to a
separate file and #declare ed it as a POVray object. Then I wrote a
'master' povray file, that #include d the aforementioned
Hi, All,
After lunching pymol, if I drag the Xterm window produced by PYMOL using
mouse, my computer will suddenly freeze, the keyboard seems no longer
functioning. The only thing I can do is to re-boot my Linux system.
This problem makes it almost impossible for me to use PYMOL on my LINUX
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