[ccp4bb] superimposing Mtz maps

Hi, I have two maps from two different crystals with the same space group, both show an unknown density in the same place. I wanted to superimpose the maps to see if it is the same/similar density. Any ideas how to do this ? Thank you, Regards Rana

Re: [ccp4bb] superimposing Mtz maps

COOT can help you. If you have coordinates in both crystals COt can superpose the coordinates ( LSQ superpose) and carry the density with the coordinates. see under COOT extensions maps Transform maps by LSQ model fit Eleanor Rana Refaey wrote:

Re: [ccp4bb] superimposing Mtz maps

Hi Rana, You could use cphasematch to put the two maps on the same origin. To do this you will need to CAD the two data sets together then give cphasematch the phase columns to use. Typing cphasematch on the command-line should tell you how to do this. It's a tool from the clipper library, so

Re: [ccp4bb] superimposing Mtz maps

This sounds a little like multi-crystal averaging without the averaging. If you were using the Uppsala program suite, you could perhaps do the following: [define one xtal as reference, the other as target] 1. Make mask in map grid for reference xtal (program MAMA) 2. Establish operator for

[ccp4bb] more than one ligands for CNS generate.inp and refine.inp files

Dear colleagues, please help me with a CNS syntax. In the refine.inp, I could provide as many topology (or parameter) files as necessary: {refine.inp} {* topology files *} {===} topology_infile_1=CNS_TOPPAR:protein.top; {===} topology_infile_2=CNS_TOPPAR:dna-rna.top; {===}

[ccp4bb] Ligand PDB

Dear All, What is the best way to find the coordinates of a ligand. I do not find teh ligand in Pdb.org. I am trying to draw it in prodrug but the server is showing error. Also if I draw it how do I make sure that the geometry is correct. Thanks, Mariah -- Mariah Jones Department of

Re: [ccp4bb] Ligand PDB

Dear protein.chemist: Try elbow.builder or phenix.elbow or whatever it is currently called. It will optimize the geometry. Good.luck Bill.Scott On Tue, July 21, 2009 1:23 pm, protein.chemist protein.chemist wrote: Dear All, What is the best way to find the coordinates of a ligand. I

[ccp4bb] Self Rotation map in R32?

Hi all I'm trying to understand why there is a peak that is perpendicular to the c axis on my kappa = 180 and kappa = 90? The chapter entitled Characterizing a Crystal From an Initial Native Dataset from Sawaya says that R32 shouldn't have a central peak in kappa = 180 nor 90. Thanks

Re: [ccp4bb] superimposing Mtz maps

Rana Refaey wrote: Hi, I have two maps from two different crystals with the same space group, both show an unknown density in the same place. I wanted to superimpose the maps to see if it is the same/similar density. Any ideas how to do this ? Thank you, Regards Rana Hi, you might

[ccp4bb] Bioinformatics Technician Position - Center for the Study of Systems Biology, Georgia Tech

Bioinformatics Technician Position Available - Center for the Study of Systems Biology, Georgia Tech Job Summary Assists research staff in the integration, management and analysis of biological data, with a focus on the development, updating and maintenance of internal and public

Re: [ccp4bb] Self Rotation map in R32?

-Original Message- From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Francis E Reyes Sent: 21 July 2009 22:22 To: ccp4bb@jiscmail.ac.uk Subject: Self Rotation map in R32? Hi all I'm trying to understand why there is a peak that is perpendicular

Re: [ccp4bb] Self Rotation map in R32?

Ian Thanks for the quick reply. I enclose the missing kappa=90 slice. It is on the same scale as the kappa=180 slice. The log doesn't report any peaks for the kappa=90 slice (using a 10 sigma cutoff). The unit cell parameters are 104.63 104.63 109.80, 90 90 120 and based on the contents

Re: [ccp4bb] Self Rotation map in R32?

By 'on the same scale' do you mean it is 40% of the height of the K=120 peak? Could it be a 'tail' of the kappa=120 degree peak? If you look at 95, 100, 110 etc does the peak persist and get stronger? I'm not sure how meaningful this would be, but I just had a look at the polarrfn output of a

Re: [ccp4bb] Self Rotation map in R32?

On Jul 21, 2009, at 7:50 PM, Charlie Bond wrote: By 'on the same scale' do you mean it is 40% of the height of the K=120 peak? Could it be a 'tail' of the kappa=120 degree peak? If you look at 95, 100, 110 etc does the peak persist and get stronger? I'm not sure how meaningful this would

Re: [ccp4bb] Self Rotation map in R32?

This nicely illustrates the danger of using too low resolution data to compute the SRF (I'm referring to an earlier BB discussion on this subject, where it was suggested to cut out the high resolution data, against, it seems to me, all rationale). You should be using as high resolution valid data