[ccp4bb] CNS 1.3 error

While trying to add harmonic restraints to a 603 aa structure, I was unable to input all the necessary restraints because of a limit on the string length. A previous post suggested recompiling "PARAMETER (STRING_SIZE=264) in the file "cns.inc" would appear to

Re: [ccp4bb] non-symmetric tetramer ?

Dear Tomb, if your tetramer (oligomer in general) is part of the asymmetric unit the crystal's space group can be independent from the tetramer. Tim On Wed, Jul 28, 2010 at 03:31:45PM -0300, Fred wrote: > Dear CCP4bb, > Could someone please, point me to some references about non-symmetric > te

Re: [ccp4bb] non-symmetric tetramer ?

The symmetry of a homotetramer will depend (in part) on how many types of interfaces it has. Some sort of 2-fold symmetry is probably more likely. Crystallization unit cell is another matter, and depends on contact interfaces. We study a protein that is a homotetramer that has two different dim

Re: [ccp4bb] non-symmetric tetramer ?

I had a tetramer with 222 symmetry--1f38 and related entries. Is that what you mean? Jacob - Original Message - From: "Fred" To: Sent: Wednesday, July 28, 2010 1:31 PM Subject: [ccp4bb] non-symmetric tetramer ? Dear CCP4bb, Could someone please, point me to some references about

[ccp4bb] non-symmetric tetramer ?

Dear CCP4bb, Could someone please, point me to some references about non-symmetric tetramers? If I have a tetramer composed by 4 identical subunits, it'll always have a P4 point group symmetry? Thank in advance, Tomb

[ccp4bb] summary - SAXS EM comparison

Here's a preliminary summary of the suggestions I got from the ccp4 community regarding the problem stated below (calculate theoretical SAXS data from EM reconstruction): The program em2dam, currently developed at EMBL-Hamburg (where the magicians of SAXS live), converts a Spider map into a pd

[ccp4bb]

Dear Vandana, What kind of fold prediction? I have the impression that fold prediction will not give a sufficiently real model to use in MR What means "100 % identical fold" ? Do you have root-mean-square deviation of CA atoms between your predicted fold and the model? Or maybe was the last step

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Vandana, Roger gives some good advice and I agree with Fred about not knowing the number of mols in the AU. I routinely see solvent content in the 75% range for many different crystals, although they tend to diffract rather poorly. In addition, you may have to convert your search model to

Re: [ccp4bb] chainsaw with multiple chains

Sorry - i dont know the answer but why dont you divide the pdb into two parts, ditto the pir alignment and run two chainsaw jobs? Clumsy but it should work.. Eleanor Ronnie wrote: If i want to use chainsaw to prep a pdb file that contains two chains of different sequences, how do I format the a

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[ccp4bb]

For finding multiple copies of protein assemblies in the ASU, Phaser or OpenEPMR are the best choices based on our experience. If your Matthews probability prediction is correct (it definitely not foolproof) then I would try searching for two trimers per ASU. Phaser or OpenEPMR should be able t

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[ccp4bb] chainsaw with multiple chains

If i want to use chainsaw to prep a pdb file that contains two chains of different sequences, how do I format the alignment .pir file to include the alignments for both chains? thanks for in advance for your help! Ronnie

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MR may work - it is worth a trial. Are you sure the SG is P622 or could it be P6i 22? You can check al these with MR and hope to get a much better result in the correct SG Eleanor Vandana Kukshal wrote: hello sir , recently i have collected one data of 3.0 A of a protein having no sequence

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Vandana Kukshal wrote: hello sir , recently i have collected one data of 3.0 A of a protein having no sequence homology with any known PDB . but while fold prediction i got 100 % identical fold with some of the protein . space group of my protein is P622 and showing 6 molecule in a assymetr

[ccp4bb]

hello sir , recently i have collected one data of 3.0 A of a protein having no sequence homology with any known PDB . but while fold prediction i got 100 %  identical fold with some of the protein . space group of my protein is P622 and showing 6 molecule in a assymetric unit. the homologous