Re: [ccp4bb] Truncated protein structure

The convention for "P22121"s is P21212, which is used by both CNS and CCP4 and many else, if not all. The unit cell needs to be reindexed (a-b-c --> b-c-a in your case). Then please try again. Lijun > Thank you for your suggestions. > 1. The unit cell of my crystal is 47.41 99.67 114.97 90 90

Re: [ccp4bb] Truncated protein structure

Thank you for your suggestions. 1. The unit cell of my crystal is 47.41 99.67 114.97 90 90 90 space group P22121, different from PDB structure 64 64 113 90 90 90 P43212, which has the same growth condition. 2. Mathhews_coef indicate my crystal should be dimer if ~30kD. I used all monomer, dimer and

Re: [ccp4bb] Truncated protein structure

Hi Haitao, I need to ask you a few questions first: 1. Did you mean you could not solve your structure by molecular replacement? Did you compare your crystal's unit cell with the PDB file? Are they significantly different? If the assymetric unit has more than one monomer, have you tried doing

[ccp4bb] Truncated protein structure

Dear all, I repeated a protein crystallization which is reported in PDB with the almost same condition, and got a 2.6A data. But the problem is that I can not determine the right phases with neither CCP4 nor CNS. Then I found the protein in my crystal had been degraded from ~30kD to ~20kD by SDS-

Re: [ccp4bb] Definition of Fourier coefficients

Not sure for other software, but in phenix.refine you can request to output I*mFo-J*DFc map, where I and J are any user specified values. Pavel. On 7/7/2008 6:00 PM, Meyer, Peter wrote: It is redundant, but it adds an additional step if someone wanted to calculate something like a 3mFO-2DFc

Re: [ccp4bb] Definition of Fourier coefficients

It is redundant, but it adds an additional step if someone wanted to calculate something like a 3mFO-2DFc map. Thanks, Pete -Original Message- From: Kevin Cowtan [mailto:[EMAIL PROTECTED] Sent: Mon 7/7/2008 10:18 AM To: Meyer, Peter Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] Defini

[ccp4bb] coot 0.4.1 on ubuntu 8.04

Dear colleagues, I was able to install and finally run coot under ubuntu. However I cannot open mtz files and get the following error: ... >> CCP4 library signal ccp4_parser:Failed to interpret symop string (Success) raised in symop_to_mat4 << Spacegroup_registry: ASU warning, LGha

Re: [ccp4bb] Definition of Fourier coefficients

Probably because in the classic implementation it is redundant, D being derived directly from sigmaa. Some programs refine D and sigmaa (or equivalent terms, such as Lunin's alpha and beta) separately. This is conceptually equivalent to deriving D from sigmaa and refining the scale between Fo

[ccp4bb] dna-rna restraints in CNS

Dear colleagues does anyone know how to change the weighting of the Watson-Crick base pair restraints using the dna-rna_restraints.def restraints definition file in CNS? We are working with rather low resolution structures and I would like the restraints to be a bit tighter than they are by de

Re: [ccp4bb] Definition of Fourier coefficients

Hi Pete, phenix.refine outputs it all the time. Pavel. On 7/7/2008 7:59 AM, Meyer, Peter wrote: Slightly off-topic from the original question, but is there a reason that most programs don't output D for sigma_a coefficients? Pete -Original Message- From: CCP4 bulletin board on beh

Re: [ccp4bb] average B and TLS

Ariel Talavera wrote: Hi all, I am working with a 2.5 Šresolution structure with Wilson B factor 37,5 Ų. It is already 100 % built but after the TLS refinement the average B factor was quiet low (4.6 Ų) and of course also the B factors for each atom were also very low. For that reason I ra

Re: [ccp4bb] Definition of Fourier coefficients

Slightly off-topic from the original question, but is there a reason that most programs don't output D for sigma_a coefficients? Pete -Original Message- From: CCP4 bulletin board on behalf of Mayer, Mark (NIH/NICHD) [E] Sent: Sat 7/5/2008 2:39 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4

[ccp4bb] average B and TLS

Hi all, I am working with a 2.5 Šresolution structure with Wilson B factor 37,5 Ų. It is already 100 % built but after the TLS refinement the average B factor was quiet low (4.6 Ų) and of course also the B factors for each atom were also very low. For that reason I ran TLSANL program to res

[ccp4bb] Structural Biologist - permanent position in Central London

Structural Biologist - permanent position Central London (Reference XR0708) Cancer Research Technology (CRT) is a specialist technology transfer company which develops discoveries arising from Cancer Research UK and worldwide prestigious oncology organisations into potential therapies and d

[ccp4bb] Weakest protein-protein complex crystallised: summary

Hi, Many thanks to all who replied to my enquiry about the weakest protein- protein complex crystallised. The idea that crystals themselves are weak complexes had already crossed my mind and I was glad to hear it confirmed by others. My impression is that there are no hard and fast rules,

Re: [ccp4bb] Parameter MAXSAVE exceeded

You almost certainly have a wrong format statement - it is tricky getting them correct for more complex cns inputs. Eleanor Miller, Mitchell D. wrote: You could also try cns2mtz? http://www.ysbl.york.ac.uk/~cowtan/cns2mtz/cns2mtz.html Regards, Mitch -Original Message- From: CCP4 bul

[ccp4bb] baculovirus GFP vectors

Hi, bit off topic, but would anyone have baculovirus vectors that co-express GFP for checking infection (i dont want a fusion protenin) ??? such as the pUltraBac-1 by Philipps B, Rotmann D, Wicki M, Mayr LM, Forstner M. Time reduction and process optimization of the baculovirus expression system