[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 fold proteins are trimer protein. can i run MR in this case . how i should proceed. i m trying for MIR also . regards vandana
[ccp4bb]
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 assymetric unit. the homologous fold proteins are trimer protein. can i run MR in this case . how i should proceed. i m trying for MIR also . regards vandana I suggest that you ccp4i, then phaser within ccp4i (or Alexeai Vaguin's program, Molrep i think it's called). The easiest and perhaps most clever approach would be to give as a search model the trimer, and look for 2 copies in the asymmetric unit. Otherwise (if your protein does not assemble as trimers, for example as a dimer of trimers) then you give as a search model a single monomer, and look for 6 copies. But this can be tricky. You may have to edit your search model before. In any case, you should always remove the waters present in the pdb of your search model. HTH, Fred. PS how do you know you have 6 molecules in the asymmetric unit?
[ccp4bb]
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 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 fold proteins are trimer protein. can i run MR in this case . how i should proceed. i m trying for MIR also . regards vandana
[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
[ccp4bb] Graduate Teaching assistant/Phd Student Birkbeck University of London
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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 to handle that. Alternatively, you could try to place 6 monomers, but this number of protein assemblies is usually extremely challenging for either program. You will have to search all alternative space groups of P622 [e.g., P6(1)22, etc.] and see which one generates appropriate packing and sensible electron density maps. Both Phaser and OpenEPMR will search all alternative space groups in one go if you set the option. We just solved an MR structure recently where three dimers gave the perfect Matthews number, but alas, there was no way to fit three dimers in the ASU with the proper symmetry. Two or four dimers were way out on the fringe of the Matthews probability, but it turns out that the ASU actually has only two dimers (a biological unit tetramer), and the solvent content of the crystal is a whopping 67%. So you might have to consider alternative packings. Phaser will usually complain about clashes or lack of unit cell volume if you try to stuff too much into the ASU. Do be pretty liberal with allowed clashes in Phaser or you won't get any solutions. We usually allow 30 or more clashes for initial searches, as required, to allow for solutions to be revealed. This is especially important if your search models are significantly different from your protein. In worst cases, you might want to trim your search model back from the N- or C-terminus to a more compact domain to avoid clashes that are present in the search model but not your target protein. Cheers, Roger Rowlett 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 assymetric unit. the homologous fold proteins are trimer protein. can i run MR in this case . how i should proceed. i m trying for MIR also . regards vandana -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu
[ccp4bb] Postdoc positions, Florida, USA
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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 alignment .pir file to include the alignments for both chains? thanks for in advance for your help! Ronnie
[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 of fold prediction actually homology modeling on a protein with similar fold? Feeling skeptical today, Ed 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 assymetric unit. the homologous fold proteins are trimer protein. can i run MR in this case . how i should proceed. i m trying for MIR also . regards vandana
[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 pdb file, which can then be used as input for another EMBL-Hamburg program, crysol. This approach does what I want. Nice. Em2dam hasn't been released yet, but is available for testing upon request (ashku...@embl-hamburg.de). http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html HYDRO can also calculate scattering form factors from dummy-bead models, but I didn't try that out. From the group that wrote HYDRO comes hydromic, a program that calculates, from an EM map, a distance distribution and a P vs. h list whose usefulness didn't immediately reveal itself to me. Those more familiar with SAXS might find that this program is just what they want. http://leonardo.fcu.um.es/macromol/programs/programs.htm The program vol2pdb, which is part of the situs package, converts spider format em maps to dummy-bead models. I couldn't suppress the feeling that the pdbs obtained with em2dam were closer to the truth. Situs also has a SAXS tutorial that might be useful. http://situs.biomachina.org/tutorial_saxs.html The EMAN program proc3d with the calcsf option can calculate scattering curves. The output file contains the F**2/s distribution for the map with max=0.0. Some scaling might be required. I didn't try this. http://blake.bcm.tmc.edu/eman/ Chimera might have a SAXS function. I didn't check. http://www.cgl.ucsf.edu/chimera/ Thanks to all who contributed ideas and suggested approaches, and special thanks to Alex for sharing em2dam. Andreas On 23/07/2010 11:54, Andreas Förster wrote: Dear all, the other day I obtained SAXS data from which a low-resolution structural model was calculated. The model is simpler/less complex than one of the same protein that we obtained with cryo-EM. Is there a way to estimate theoretical SAXS data from a cryo-EM reconstruction to compare with the obtained raw data? Is there a program that does for a reconstruction what CRYSOL does for pdbs? I understand that there would be a huge amount of handwaving involved, but it might help us reconcile our models. Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
[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
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 ccp4bb.l...@gmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, July 28, 2010 1:31 PM Subject: [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 *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu ***
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 dimer interfaces (a "dimerization" and a "tetramerization" interface) giving a biological unit with multiple 2-fold axes. So far, it will crystallize in unit cells C2, a "double-size" C2 on c, C222(1), P4(1)2(1)2, P6(5), P3(2), and I2(1)2(1)2(1) depending on the variant and ligands bound. My students seem extra-talented in generating new unit cells and space groups of the same protein for us to puzzle out via MR. Cheers. On 7/28/2010 2:31 PM, Fred wrote: 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 -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu
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 tetramers? If I have a tetramer composed by 4 identical subunits, it'll always have a P4 point group symmetry? Thank in advance, Tomb -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
[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 be responsible. Redimension and recompile. 264 seems rather small. Has anyone had any program issues after recompiling with a larger string size? Thanks! -Ian
