tag:blogger.com,1999:blog-3599722177679860131.post1064850547547015155..comments2024-01-03T10:01:29.738+01:00Comments on Chemical Quantum Images: Glucocorticoid receptorFelixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.comBlogger9125tag:blogger.com,1999:blog-3599722177679860131.post-78710065362778286612008-06-16T03:51:00.000+01:002008-06-16T03:51:00.000+01:00I would like to thank you for putting my mind in m...I would like to thank you for putting my mind in motion. The partial surface thing couldn't let me sleep for a long time... but then I came up with some ideas.<BR/><BR/>I think <A HREF="http://lightnir.blogspot.com/2008/06/cutting-binding-site-apple.html" REL="nofollow">this</A> could be of some interest to you.<BR/><BR/>Regards<BR/>DawidLightnirhttps://www.blogger.com/profile/16789348893952913132noreply@blogger.comtag:blogger.com,1999:blog-3599722177679860131.post-32287517473775151852008-06-05T18:47:00.000+01:002008-06-05T18:47:00.000+01:00sure, I am glad that you like itsure, I am glad that you like itFelixhttps://www.blogger.com/profile/05138335803929997277noreply@blogger.comtag:blogger.com,1999:blog-3599722177679860131.post-5853175634199468582008-06-05T16:21:00.000+01:002008-06-05T16:21:00.000+01:00Wow, it's really gorgeous. Thanks.PollyWow, it's really gorgeous. Thanks.<BR/>PollyAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-3599722177679860131.post-12879686505881816812008-06-02T18:46:00.000+01:002008-06-02T18:46:00.000+01:00oh, I understand. I did two things, one was "slabb...oh, I understand. I did two things, one was "slabbing". actually I did not know that Ctrl+MouseWheel command, so I zoomed on the ligand and then just used the mouse wheel<BR/><BR/>but there were things in the way. So I duplicated the protein and erased part of it, just by clicking on the amino acids and removing them. then I showed the original protein as cartoon and the duplicated protein as surface<BR/><BR/>aside from this figure I have never done it like this but I think manually erasing things that are in the way is the easiest thing, probably not the fastest thoughFelixhttps://www.blogger.com/profile/05138335803929997277noreply@blogger.comtag:blogger.com,1999:blog-3599722177679860131.post-15364936758795815502008-06-02T16:47:00.000+01:002008-06-02T16:47:00.000+01:00I was wondering how did you do the last two images...I was wondering how did you do the last two images. By "slab" I mean moving the two clipping planes. You can move them ether by the <EM><A HREF="http://www.pymolwiki.org/index.php/Clip" REL="nofollow">clip </A></EM>command or by scrolling the mouse wheel and holding Shift/Ctrl(Strg)/Shift+Ctrl keys. That's easy to work with, but some times it's hard to remove all the obstacles without hiding parts of the ligand.<BR/><BR/>I know there's a way for showing in pymol only a partial surface like on this <A HREF="http://www.pharmchem.tu-bs.de/forschung/baumann/images/sars_bp3.jpg" REL="nofollow">image</A>. After some searching I've found <A HREF="http://www.pymolwiki.org/index.php/Surface#Calculating_a_partial_surface" REL="nofollow">how to</A> do that on the PyMolWiki. I was just curious if you did it this way or had some experience with this method.Lightnirhttps://www.blogger.com/profile/16789348893952913132noreply@blogger.comtag:blogger.com,1999:blog-3599722177679860131.post-78588423442863693912008-06-02T09:35:00.000+01:002008-06-02T09:35:00.000+01:00this was just the surface of the protein without l...this was just the surface of the protein without ligand, I did not calculate anything<BR/>I don't understand what you mean by slabFelixhttps://www.blogger.com/profile/05138335803929997277noreply@blogger.comtag:blogger.com,1999:blog-3599722177679860131.post-39038168233438231092008-06-01T23:49:00.000+01:002008-06-01T23:49:00.000+01:00Did you calculate a partial surface for the bindin...Did you calculate a partial surface for the binding pocket or just moved the slab around?Lightnirhttps://www.blogger.com/profile/16789348893952913132noreply@blogger.comtag:blogger.com,1999:blog-3599722177679860131.post-1496707672070172442008-06-01T16:48:00.000+01:002008-06-01T16:48:00.000+01:00yes, I did not mean to say that the molecule slipp...yes, I did not mean to say that the molecule slipped through this small hole. but I think it is very interesting how it is caught in thereFelixhttps://www.blogger.com/profile/05138335803929997277noreply@blogger.comtag:blogger.com,1999:blog-3599722177679860131.post-72397020170383510762008-06-01T14:48:00.000+01:002008-06-01T14:48:00.000+01:00"you notice that there is a small opening which is..."you notice that there is a small opening which is probably the place where the ligand entered the binding pocket."<BR/><BR/>You've been seduced by the beauty and staticness of the crystal structure. When Kendrew first solved sperm myoglobin 50 years ago, they noted that there seemed to be no way for oxygen to get inside to bind to the iron contained in the porphyrin ring. The molecule had to breathe (e.g. change conformations). <BR/><BR/>Almost certainly the glucocorticoid receptor must as well, in addition to further changing its shape once the ligand is bound to it and the receptor begins to cooperate with other proteins (cofactors) and the megaDalton RNA polymerase II complex to turn on the gene downstream from its binding site on DNA. <BR/><BR/>RetreadAnonymousnoreply@blogger.com