Dear all,
I am just switching from HKL3000 to DIALS for processing data collected at
EIGER detectors because it is too slow for the HKL300 to handle over 1000
images per dataset.
Our crystals are not perfect and you would expect split spots or spots of
multiple crystals in most cases. Sometimes w
all
> (MODE SFCALC MAPIN).
>
> Paul.
>
> [1] use mask inversion
> [2] don't use mask inversion
>
>
>
> --
> *From:* CCP4 bulletin board
> [mailto:CCP4BB@JISCMAIL.AC.UK]
> *On Behalf Of *zhang yu
> *Sent:* Sunday, February 19, 2012 11:47 PM
> *To:* CCP4BB@JISCMA
Dear CCP4ers,
Is that possible to generate map coefficients only for certain chains? For
example, I have two chains, A and B, and I would like to output a map file
only contains coefficients for chain A. The "isomesh" command in Pymol
could generate similar images. But my purpose is not for presen
;
> > Make sure the flanking nucleotides of DNA can already be
> > regularised/refined with coot (a version dependent issue i think)
> > otherwise it won't link the BRU properly.
> >
> > Alan
> >
> >
> >
> >
> > On 23/10/2011 21:03, zh
;OH
> with the standard dNTP in the PDB
> - is the 3BrdU defined as 'DNA' in the cif file? (under 'data_comp_list')
>
> Maybe that helps!
>
> Sabine
>
>
>
> On 10/23/2011 09:03 PM, zhang yu wrote:
> > Hi,
> >
> > My DNA chain has a
Hi,
My DNA chain has a internal modification of 5-Bromo-2′-deoxyuridine (5BrdU).
I had a problem when I tried to model 5BrdU into my DNA chain by coot. I
will appreciate it very much if someone can solve it for me.
What I did...
1. Generate the cif dictionary and export the pdb for 5BrdU in "Jlig
e even better if the scaling program would directly take
> into account the bimodal distribution...
>
> HTH,
> Esko
>
>
> On 26.7.2011, at 15.51, zhang yu wrote:
>
> Hi,
>>
>> I had a dataset which is P21 but with a pseudo-translational symmetry of
>> (
Hi,
I had a dataset which is P21 but with a pseudo-translational symmetry of
(1/2, 1/2 ,0). Theoretically the dataset should show systematic weak spots
of h+K= 2n+1 compared to h+k= 2n. Is that correct?
I would like to have a close look at the reflections. for example, the
average I/sigma for ref
ation vector. Row by row for
> the matrix. Some programs use a column by column approach, the transpose of
> the rotation
> matrix, or a set of 3 angles (with several conventions possible)
>
> > Message du 25/07/11 19:24
> > De : "zhang yu"
> > A : CCP4BB@JISC
Hi,
Does any one know which software could calculate and output
non-crystallography symmetry operator?
I am working on a structure with two molecules in one ASU, and two identical
subunits in each of one molecule. I would like to know the
non-crystallography operator of the two molecules, and al
Hi,
I am confused by the "torsion angle restraint" for real space refinement in
coot. Is the "Torsion angel restraint" for side chain or for main chain?
Yu
--
Yu Zhang
HHMI associate
Waksman Institute, Rutgers University
190 Frelinghuysen Rd.
Piscataway, NJ, 08904
We could use HKL2000 for Pilatus 6M detector a few months ago in our lab. We
upgraded our HKL2000 to Version 0.98.701 and asked a new license file to
include Pilatus 6M detector.
Yu
2011/7/20 Petr Leiman
> Dear all,
>
> What is the status of Denzo/HKL2000 availability/support for the Pilatus 6M
Dear Duangrudee
Thank you for your information. Is there any hardware requirement for the
stereo in coot and pymol with Zalman monitor? It seems that Hign-End Nvidia
graphic cards (Quadro FX 3800, FX 4800 ) are not necessary.
Yu
2011/5/8 Duangrudee Tanramluk
> Dear Yu,
>
> Pymol also has a Za
"3D Vision Pro" is more geared toward having large meeting
> rooms and presentation halls equipped so everyone in the room can view 3D on
> a large screen driven by a 120 Hz DLP projector.
>
> 3. I don't wear prescription eye glasses, but I do have long modeling
> sess
700ish for 24". Any video
> card, any software. Glasses are the same as movie glasses ($2 per pair), no
> batteries, no flicker. Very nice really.
>
> Dave
>
> Sent from my iPhone
>
> On May 6, 2011, at 11:27 AM, zhang yu wrote:
>
> > Dear colleagu
Dear colleagues,
Sorry to present the stereo issue to the board again.
Since my old SGI CRT monitor only has 75 HZ refresh rate, the flickering in
stereo mode bothered me a lot. Recently, I want to update my old CRT to 120
HZ LCD. I have a "Nvidia Quadro FX3800" in my workstation. I would like
the right
molecule and Fill 'M' and 'residue ranges'.
Coot will give a few positions to fit the chain, just choose the right one.
Yu
2011/3/31 Javier Garcia
> Dear Zhang yu,
>
> I also found that same problem recently. I think is a small bug from Coot.
> It
Dear all,
I have two fold NCS in ASU. I could find phase by molecular replacement,
but I have to build other chains by myself, since the model is not complete.
During model building in coot, I built one chain in one NCS, and I merged
this chain into the previous molecule. Now it is the "chain M'.
Dear all,
I have a question about twin refinement of Refmac in CPP4. I was told that
the refmac (Phenix also?) will generate the detwined map after the
refinement with twin. My question is that If my crystal is a perfect
hemihedral twin, how can the refmac make a detwined map after the
refinement?
Maybe there is a domain shift of your protein compared to the model. If this
is the case, try to do the MP with successive domains.
2010/9/13 Paul Holland
> Hello fellow crystallographers,
>
> I am trying molecular replacement for a protein crystal dataset that has
> very high sequence similarit
Hi Christine,
Just have a try. When people want to co-crystallize complexes of a protein
and small molecular compounds, DMSO is often introduced into the drop, since
pharmacologists like to dissolve compounds in DMSO.
2010/7/19 Harman, Christine
> Hi all,
> I was wondering if anyone has had an
Why the Rfree value is lower than Rwork?
在 2010年7月19日 上午3:41，孙庆祥 写道：
> Dear Collins and all,
>
> Thanks for the reply. Please find the following pdb header. For your
> information, this is after refmac5 with twin-refinement option selected.
> This is the best R values that I'm getting. Cutting re
22 matches
Mail list logo
