Re: [ccp4bb] predicted secondary structure based alignment

Hi, check out http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Servers_and_programs_for_sequence_analysis HTH, Kay smime.p7s Description: S/MIME Cryptographic Signature

[ccp4bb] predicted secondary structure based alignment

hello everyone, Is there a good program to align two sequences based on their predicted secondary structure...something that could be useful to align low homology sequences ? Thanks

Re: [ccp4bb] good phasing, bad R-factors

Hi, Thanks to all of those who responded so far. Here's some more info: >The space group is consistent in the all mtz files. >I have run phenix.xtriage. No twinning was suspected. I have one molecule in the ASU. >According to the systematic absences, the space group is P6222. >We are refin

[ccp4bb] good phasing, bad R-factors

Hi all, I have run into an unusual problem and am looking for some help. I am working with a small protein that is 76 amino acids in length. I have collected anomalous data and have located the 4/5 selenomethionine sites using SHELX C/D and SHARP. The map that is produced from SHARP after dm is

[ccp4bb] Rotation angle and translation distance

Hi all I am working with a multidomain protein whcih binds to a ligand. This protein exist in two different states, a) apo form of the protein is closed state and b) holo protein is an open state. One of the domain is mobile and have different conformation compared to its closed conformation. Thi

Re: [ccp4bb] structure alignment based on the ligand

Hi, To complete the responses you already have got, I recommend to use LSQMAN ( http://xray.bmc.uu.se/usf/lsqman_man.html ) for your alignment task. It can only compare two structures at a time but LSQMAN can easily be run script-based (using one structure as the reference). Select either all atom

Re: [ccp4bb] cad gives a fortran runtime error in line 869 : comparing phase sets

For the first part of your question, I usually use sftools from the command line to combine things from different MTZ files, so you could give that a try if cad is giving you trouble. For the second part of the question, if you're staying within CCP4, then cphasematch is probably the program y

Re: [ccp4bb] structure alignment based on the ligand

Coot can do that. You can use lsq to overlap the whole atoms of ligands. Another way is using LigAlign in Pymol. Good luck! leo rui wrote: Hi, All I have dozens of complex structures ( protein + ligand ) and want to align the structures based on the ligand. Does anyone know such kind of progr

Re: [ccp4bb] structure alignment based on the ligand

Mon., April. 13th 2009 EBI On Sun, 12 Apr 2009, rui wrote: Hi, All I have dozens of complex structures ( protein + ligand ) and want to align the structures based on the ligand. Does anyone know such kind of program? Or if can get the information around the ligand site, that would be even bette