Re: [ccp4bb] convert map coefficients to phases and FOM

Hi Matt, If you use the ccp4i-GUI, choose "Map&Mask Utilities" and open the "Clipper Map Utilities" Section, there is an entry called "Map to structure factors" which might do what you want - except for the FOM part which I consider impossible in that direction. Cheers, Tim On Wed, Nov 10, 2010

[ccp4bb] convert map coefficients to phases and FOM

Hi, I am trying to calculate phases and FOM from a model map. However, CNS 1.2 model_map.inp does not output map phases and FOM. Instead, it only gives map coefficients. My question is how to convert these map coefficients to phases and FOM. Does anyone have a script to do that? Thanks so muc

[ccp4bb] sunrider

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[ccp4bb] Crystal structures of phosphorylated proteins

Hi Sally, Crystallization of proteins with multiple phosphorylation sites is often a difficult problem. Like you said it is often an issue of inhomogeneity. Several suggestions that may be helpful: First, I would use a bit of your protein sample for Mass Spec analysis. It is possible (though m

Re: [ccp4bb] Crystal structures of phosphorylated proteins

To make it clearer, I'm looking for successful examples of crystallization of phosphorylated proteins, especially ones containing multiple phosphorylation sites, and would like to access crystallizability of these protein types. I want to produce and crystallize protein at its phosphorylation state

Re: [ccp4bb] Bruker Smart and Mosflm

Dear George, You said: > By far the easiest way would be to use the programs (SAINT and SADABS) > provided by Bruker. We get excellent data, e.g. for in-house S-SAD > phasing, using these programs (either offline or as part of the Bruker > GUI) for data collected on our SMART6000. For a detail

Re: [ccp4bb] Pymol import error

You need to define the environmental variable PYMOL_PATH first, which for example in Ubuntu with pymol installed from repositories should point at /usr/lib/pymodules/python2.6/pymol. Try this from python prompt to verify from imp import find_module print find_module('pymol')[1] You may also need

Re: [ccp4bb] COOT water retention problem...

Thanks for all the helpful suggestions. An upgrade of COOT to 6.1 actually enabled the delete item option which did nothing when I click it before. Myron -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Folmer Fredslund Sent: 10 November 2010

[ccp4bb] too much of questions (P21-C221 pseudo-translation/PHASER/SHELX/autoSHARP)

Dear all, I have less experience in this field. My Protein (200 aminoacid residues) is stable in high salt buffer(1M KCl); however after extensive optimization by salting-in (in 4-5 weeks time), am getting very thin and improved plate-like single crystals with a size of 50 X 50 X (don't ask me

[ccp4bb] too much of questions (P21-C221 pseudo-translation/PHASER/SHELX/autoSHARP)

Dear all, I have less experience in this field. My Protein (200 aminoacid residues) is stable in high salt buffer(1M KCl); however after extensive optimization by salting-in (in 4-5 weeks time), am getting very thin and improved plate-like single crystals with a size of 50 X 50 X (don't ask me

Re: [ccp4bb] COOT water retention problem...

Dear Myron, What is wrong with using the "Delete Item" option from the menu? It's gives you a couple of choices, one of which is waters. Means that you will only delete waters when selecting in the main window. That is the way I do it anyway. Best regards, Folmer Fredslund 2010/11/10 Smith, My

Re: [ccp4bb] Crystal structures of phosphorylated proteins

Perhaps you might pose a more directed question... Do you want to produce phosphorylated protein? Are you having trouble crystallising a protein that is phosphorylated? Atlanta On 10 Nov 2010, at 11:09, Sally Pham Thanh Van wrote: Dear all, Could you please tell me any information reg

[ccp4bb] COOT water retention problem...

Has anyone ever accidentally placed a water molecule onto the exact position of selected atom and tried to delete it? How was that achieved? I actually saved the pdb file and deleted the text line of the coordinates for the offending water, then reloaded the file. Is there any other procedure that

[ccp4bb] Pymol import error

Hello: I am trying to use Pymol in the python script but I am facing very simple error: "No module named pymol". I guess this is very simple error. I have installed binary file of Pymol. When I tried to import the pymol, the error message was displayed. >From where I could get Pymo

[ccp4bb] Crystal structures of phosphorylated proteins

Dear all, Could you please tell me any information regarding to crystal structures of phosphorylated proteins? Your input would be appreciated. Best regards, Sally.