-- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Mon, 18 Jul 2011 12:21:16 -0700 From: Modeller Caretaker modeller-care@salilab.org Subject: Re: [modeller_usage] Help with modeller 9.9 in windows To: "Greene, Brandon Lee" blgree2@emory.edu Cc: "modeller_usage@salilab.org" modeller_usage@salilab.org Message-ID: 4E2487AC.1000003@salilab.org Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 7/18/11 7:22 AM, Greene, Brandon Lee wrote: > There are three inorganic residues in the first chain and one in the > second placed as "." in my ali file. Your alignment file does not match the PDB. Modeller reads the residues sequentially, so what it will see is - A chain amino acids - B chain amino acids - A chain ligands - B chain ligands So your sequence should also be in this order (XXXXXX/XXXXXX/.../.). Alternatively, you can edit the PDB file to place the A chain ligands immediately after the A chain amino acids and leave your alignment unchanged. > Using this structure and the template ali file to do the alignment (w/ > salign) I get poor alignment in the PAP file, but not in the PIR file??? > (P/---XXXX instead of P---/XXX in PAP). Those two alignments are identical. Since neither gaps nor chain breaks are "real" residues, their relative ordering is irrelevant - it only matters which "real" residues (amino acids or ligands) they come between. > "No aligned template residues for BLK residue; number of templates: 1 > Make sure that each BLK residue in your target sequence is aligned with > your templates..." Just like it says, a BLK (".") residue in the target sequence must be aligned with a residue in the template. Usually this means you need a "." residue in the template in the same place as the "." in the target. You can't align a "." with a chain break or gap, because "." means to copy the aligned residue directly from the template to the target, so it needs a "real" residue to copy from. Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 3 Date: Thu, 21 Jul 2011 00:16:06 -0700 (PDT) From: Daniel Li leeyuhang@yahoo.com Subject: [modeller_usage] Multiple Sequence Alignment vs Single Alignment To: modeller_usage@salilab.org Message-ID: 1311232566.71184.YahooMailClassic@web161902.mail.bf1.yahoo.com Content-Type: text/plain; charset="iso-8859-1" Hi, I have been reading about modeller usage for awhile and ran some tests with different models from the dual specificity phosphatase family. However, whenever I run the modelling with salign for multiple templates, my GA341 score is many folds lower (under 0.1) and the dope score/molpdf scores are lower as well compared to just a single template.?The templates that I use all give me a decent 50%+ identity based on output from build profile and I generally use 3 templates for my multiple template modeling.From reading it seems as if multiple templates should usually generate better scores but running 3 trials of 600 with different sets of templates for different proteins I still get better results from my single template models. So is there something I have to manipulate with the scripts and parameters?I'm sorry for the vague question because I'm not too sure what kind of additional information to provide but I hope someone can provide me with more insight into this. Thank you! Daniel