Dear Herman,
If there are duplicate atoms in my PDB, Phenix refine GUI will post error
and crash (Sorry I haven't tried other refinement program). And there is no
.geo output file if program crash.
Phenix refine thought them as nonbonded atoms with distance equal to 0.
Because the
Postdoctoral Research Associate - Beamline I23
Beamline I23 at Diamond Light Source will be a unique facility for in-vacuum
long-wavelength macromolecular crystallography (MX). After more than five years
in design, construction and commissioning, we have recently collected first
diffraction dat
Dear Colleagues,
On behalf of the organizing committee, I call your attention to the upcoming
2015 West Coast Protein Crystallography Workshop (WCPCW), which is now open for
registration. Below you will find information reposted from the WCPCW listserve.
Nathan
Hi Luzuok,
Any validation program that detects clashes should hind these.
Cheers,
Robbie
Sent from my Windows Phone
Van: luzuok
Verzonden: 30-10-2014 10:58
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: Re: [ccp4bb] water at the same exactly position
Dear Nat,
But if t
Dear Lu,
I don’t see your problem. Why don’t you use the automatic water update option,
present in most modern refinement programs, as Pavel suggested? This should
take care of your problem.
Of course, having premium, 1st class hand-picked waters is still the gold
standard, but I don’t believe
Dear Lu Zuokun,
There are several methods you can use to locate these problem residues.
Here are 3:
a) manually step through your PDB file in coot (good practice anyway, this
is fundamentally what we as crystallographers should be doing when we are
model building)
b) identify waters with close co
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Dear Lu Zuokun,
it may appear tedious, but for a good quality model you should check
every position and decide yourself what to place there. Automation
will not replace your chemical understanding.
Regards,
Tim
On 10/30/2014 10:56 AM, luzuok wrote:
Dear Nat,
But if there are other solvent molecules, such as Mg2+, SO4-,, in the same
position.
How can this problem be solved?
Lu Zuokun
--
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南开大学新生物站A202
在 2014-10-30 12:57:31，"Nat Echols" 写道：
On Wed, Oct 29, 2014 at 8:53 PM, luzuok wrote:
I think it is better for COOT t
Hi,
I found that after upgrading to Yosemite and installing the latest version of
X11 (2.7.7), X11 was now in /opt/X11R6 rather than /usr/X11R6. In my case ccp4i
and coot both stopped working. I have no idea how the move happened, as no
options were presented during installation of X11 to put i
