[ccp4bb] another quick question...
Good day all, In COOT, when I view my coordinate pdb file with my ccp4 map file (using Auto-open mtz), I have a couple residues for which only a part of the peptide chain is visible. E.g. for a Lys, only the terminal nitrogens at the end of the R-group chain are visible as bonds. The other parts of the residue (and even parts of adjacent residues) are visible only as stars/stellate points that may or may not be within my blue electron density. If I click on the stars, the atom names that appear are consistent with the missing peptide chain, and correspond to the missing amino acid that has the occassional visible R group. Just wondering what this means, that I am seeing stellate points that seem to be acting as place holders for my residues in a couple locations in my structure. The structure was obtained using molrep. Thank you, James Pauff Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos more. http://mobile.yahoo.com/go?refer=1GNXIC
Re: [ccp4bb] another quick question...
James, The stars are atoms in a residue that are no longer within recognizable bonding distances of other atoms. Somewhere along the way these residues were mangled to the point that some atoms are no longer within bonding distance of each other. (In Refmac, for example, this can happen if the X-ray weighting term is too high for the resolution of the data,and atoms start wandering off during refinement.) I'm not terribly familiar with Molrep, but most MR programs do rigid body searches, and do not normally alter the geometry of the search model. Is the original search model geometrically correct? Whatever the cause, you can at least snap residues back into line by doing a regularize zone in Coot. That should round up all the wayward atoms. Cheers, ___ 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: [EMAIL PROTECTED] -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of James Pauff Sent: Thursday, May 24, 2007 9:03 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] another quick question... Good day all, In COOT, when I view my coordinate pdb file with my ccp4 map file (using Auto-open mtz), I have a couple residues for which only a part of the peptide chain is visible. E.g. for a Lys, only the terminal nitrogens at the end of the R-group chain are visible as bonds. The other parts of the residue (and even parts of adjacent residues) are visible only as stars/stellate points that may or may not be within my blue electron density. If I click on the stars, the atom names that appear are consistent with the missing peptide chain, and correspond to the missing amino acid that has the occassional visible R group. Just wondering what this means, that I am seeing stellate points that seem to be acting as place holders for my residues in a couple locations in my structure. The structure was obtained using molrep. Thank you, James Pauff Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos more. http://mobile.yahoo.com/go?refer=1GNXIC
[ccp4bb] new version of MR pipeline BALBES
Dear all, A new version of an automatic molecular pipeline system - BALBES is now available. It can be downloaded from: www.ysbl.york.ac.uk/~fei/balbes The new options in this system are: 1) Use of user defined external PDB library 2) Use of a single PDB file as an input model for Molecular replacement 3) Use of assembles. You can give a multiple sequence and the program will assume that it is dealing with a complex of proteins 4) Search of domains from different molecules. For example if you molecule consists of two domains and one domain is in the molecule 1 and another is in a molecule 2 then the system will find both and try to assemble your molecule using molecular replacement Instructions how to use these options are in the README file. Of course difficult cases remain problematic. We are working on improvements of the BALBES to deal with these cases. Please send all your suggestions and/or comments to one of us. Fei [EMAIL PROTECTED] Alexei[EMAIL PROTECTED] Garib [EMAIL PROTECTED]
[ccp4bb] Maps look different from auto-mtz vs EDS vs FFT in Coot or CCP4MG.
I¹d like help in interpreting some mystery density in a structure. I¹m writing a paper about soaking the apo-estrogen receptor with different ligands. The apo structure is already released, as pdb code 2B23. The question is whether there is a mystery molecule in the pocket of the apo receptor. If you superimpose 3ERD, you can see where the ligand binds. The problem is that with some maps the pocket appears completely empty, and with others, there appears to be something there. Protein looks essentially identical with the different maps. We have used a few different approaches to identify the compound with LC-MS, and are pretty sure there is nothing there. For example, we can bind our protein to beads, soak it with estradiol, wash extensively, elute with organic solvent and find a great peak for estradiol, but nothing for the apo protein. We have also tried non-denaturing MS. If you look at the 2mFo-DFc map from EDS in Coot or CCP4mg, you see mystery density in the pocket. If I use the MTZ, you see density in Coot, but not CCP4MG. I then downloaded the structure factors from the PDB and made an MTZ. The map in CCP4MG shows some density, but much less that with the map from EDS. When I used FFT to make a 2mF1-1nF2 map, there is no mystery density in either CCP4MG or coot. I was ready to submit the manuscript with a picture of the mystery density, but now I¹m not sure if that is appropriate. Any suggestions, as far as how to interpret this mystery density would be greatly appreciated. Best Regards, Kendall -- Kendall W. Nettles, PhD Assistant Professor Department of Cancer Biology The Scripps Research Institute 5353 Parkside Dr. Jupiter Fl 33458 office 561-799-8851 fax 561-799-8805 cell 561-306-7566
Re: [ccp4bb] Maps look different from auto-mtz vs EDS vs FFT in Coot or CCP4MG.
Dear Kendall, I would suggest you to run a simulated annealing omit map around the region you are interested. The model bias will be reduced and you will get a more clear answer. Ciao, Joao Joao M. Dias Ollmann Saphire Lab The Scripps Research Institute 10550 North Torrey Pines Rd. IMM-2 La Jolla, CA 92037 USA tel (858)784-8925 On May 24, 2007, at 9:57 AM, Kendall Nettles wrote: I’d like help in interpreting some mystery density in a structure. I’m writing a paper about soaking the apo-estrogen receptor with different ligands. The apo structure is already released, as pdb code 2B23. The question is whether there is a mystery molecule in the pocket of the apo receptor. If you superimpose 3ERD, you can see where the ligand binds. The problem is that with some maps the pocket appears completely empty, and with others, there appears to be something there. Protein looks essentially identical with the different maps. We have used a few different approaches to identify the compound with LC-MS, and are pretty sure there is nothing there. For example, we can bind our protein to beads, soak it with estradiol, wash extensively, elute with organic solvent and find a great peak for estradiol, but nothing for the apo protein. We have also tried non-denaturing MS. If you look at the 2mFo-DFc map from EDS in Coot or CCP4mg, you see mystery density in the pocket. If I use the MTZ, you see density in Coot, but not CCP4MG. I then downloaded the structure factors from the PDB and made an MTZ. The map in CCP4MG shows some density, but much less that with the map from EDS. When I used FFT to make a 2mF1-1nF2 map, there is no mystery density in either CCP4MG or coot. I was ready to submit the manuscript with a picture of the mystery density, but now I’m not sure if that is appropriate. Any suggestions, as far as how to interpret this mystery density would be greatly appreciated. Best Regards, Kendall -- Kendall W. Nettles, PhD Assistant Professor Department of Cancer Biology The Scripps Research Institute 5353 Parkside Dr. Jupiter Fl 33458 office 561-799-8851 fax 561-799-8805 cell 561-306-7566
