[ccp4bb] DIALS spot finding

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

Re: [ccp4bb] FFT map coefficients only for certain chains

:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UKCCP4BB@JISCMAIL.AC.UK] *On Behalf Of *zhang yu *Sent:* Sunday, February 19, 2012 11:47 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] FFT map coefficients only for certain chains Dear CCP4ers, Is that possible to generate map coefficients

[ccp4bb] FFT map coefficients only for certain chains

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

Re: [ccp4bb] 5-Bromo-2′-deoxyuridine monomer in coot and Jligand

/2011 21:03, zhang yu wrote: 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

[ccp4bb] 5-Bromo-2′-deoxyuridine monomer in coot and Jligand

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

Re: [ccp4bb] 5-Bromo-2′-deoxyuridine monomer in coot and Jligand

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 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

[ccp4bb] I/sigma for h+k=2n+1 and h+k=2n

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

Re: [ccp4bb] I/sigma for h+k=2n+1 and h+k=2n

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 (1/2, 1/2 ,0). Theoretically the dataset should show systematic weak spots of h+K

[ccp4bb] Non-crystallography symmetry operator

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

Re: [ccp4bb] Non-crystallography symmetry operator

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@JISCMAIL.AC.UK Copie à : Objet : [ccp4bb] Non-crystallography symmetry

[ccp4bb] coot torsion angle restraint

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

Re: [ccp4bb] Denzo/HKL2000 for Pilatus 6M detector

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 petr.lei...@epfl.ch Dear all, What is the status of Denzo/HKL2000 availability/support

Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'

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 nano...@gmail.com Dear Yu,

[ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'

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

Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'

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 ccp4f...@gmail.com wrote: Dear colleagues, Sorry to present the stereo issue to the board

Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'

don't wear prescription eye glasses, but I do have long modeling sessions without any discomfort wearing these. They come with several inter-changable nose-pieces so you can pick the one that fits you most comfortably. On Fri, May 6, 2011 at 11:27 AM, zhang yu ccp4f...@gmail.com wrote: Dear

Re: [ccp4bb] Copy NCS chain in coot

2011/3/31 Javier Garcia gar...@ysbl.york.ac.uk Dear Zhang yu, I also found that same problem recently. I think is a small bug from Coot. It will only copy NCS if the molecule's name you want to copy is molecule A. So maybe will work if you rename your built chain as A. Good luck! Javier

[ccp4bb] Copy NCS chain in coot

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'.

Re: [ccp4bb] Molecular replacement question

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 pholl...@umd.edu Hello fellow crystallographers, I am trying molecular replacement for a protein crystal dataset that has very high

Re: [ccp4bb] Fab:Peptide complex crystallization

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 christine.har...@fda.hhs.gov Hi all, I was