[ccp4bb] Ligplot for active sites without any ligand
Dear BBs, I am looking for a program to plot the network of the residues in the active site of my enzyme in 2D. I want to show how the residues differ in distances to each other in several variants. A Program just like ligplot, but also for active sites without a ligand. Does anybody know such a program or can recommend one? Thank you very much, Katja __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com
[ccp4bb] Alignment of AU?
Hi everybody, I have a question concerning a sequence alignment with the sequences of my 4 molecules in the AU. Unfortunately I found out that the sequences of the 4 monomers do not match exactly. I used the program moleman and it showed me the different numbers of atoms for the monomers. I know in Coot there is a sequence view button, but I can't see the differing residues. The number of residues matches, so I think the mistakes happened when I mutated loops etc. for building and refining. Thanks in advance for any suggestions, Katja __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com
[ccp4bb] PDB Validation Report
Dear all, I just finished my first protein structure. More or less. I'm using right now the pdb validation server to check the data and the data look quite well.. The only point irretating is following line in the Adit Validation Report: The following residues have unexpected configuration of the chiral center using C(i) - N(i) - Ca(i) - Cb(i) chirality. Residue Chain SequenceImproper Details LYS A 470 22.18 Expecting L Found L OUTSIDE RANGEI am not sure what this means and what I should do. What is outside the L range? I would be thankful for any advice. Thanks, Katja __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com
[ccp4bb] off-topic: crystal optimization without buffer
Hi everybody, sorry for my off-topic question. I got small initial crystals in 200mM NaSulfat and 20% PEG 3350. There is no buffer in this condition. How can I optimize these crystals? Just vary the PEG concentration? Or should I add a buffer; or vary the pH of the buffer the proteinsolution was in? Thank you and best regards, Katja
[ccp4bb] structure validation tools
Hi everybody, I solved my first crystalstructure and now want to publish it. But how do I know the structure is ready for publication and deposition in the pdb. We can explain our theory with the structure but which factors I have to regard to publish nothing wrong or bad. Can anybody tell how many outliers are allowed as long as they are in a well defined density? I found several validation tools in coot, but I would like to be sure on what I have to emphasize. Thank you very much in advance, Katja __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com
[ccp4bb] anisotropic data
Hi everybody, is there a way to improve crystals that diffract strongly anisotropic? We got data between 2.5 and 4.0 A and scala says we should cut these data at 3.9 A. It's such a... I want to solve this structure! greetings Katja __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com
