From: Eric Z. <zo...@ca...> - 2003-12-03 20:54:09
|
All- I have been attempting to add atoms to proteins that are missing electron density, mostly surface positions. In most cases I have been able to just add an atom or two (Build->Fragment->group); sometimes adding a whole rotamer is required. I have been unable to add a planar guanidino group or the planar oxygens to Asp or Glu. How would I change hybridization of atoms to get the correct geometry? Also, where are the rotamers in pymol from? Are they backbone dependent or independent? How hard would it be to use a different set of rotamers? Thanks. Eric |
From: sankari t. <san...@ya...> - 2005-04-12 11:44:02
|
Hi all, I'm trying to see the effect of SNP on the protein structure. I tried to change the amino acid residue with the menu wizard mutagenesis. But unfortunately it doesn't work. I think it doesn't work with mouse clicks. I could select the residue and change the color and shape (in command mode) but i don't know how to change one amino acid residue to another. When i clikc mutagenesis,change the amino acid, change the shape , apply , done Nothing works. for example change Valine to glycine. what is the command for this. Is there any way to see the different effects of mutation ont he protein structure. Plese do suggest me. your reply will be highly appreciated. sankari --------------------------------- Do you Yahoo!? Yahoo! Small Business - Try our new resources site! |
From: Jamaine S. C. D. <jam...@gm...> - 2007-01-02 15:41:05
|
When making mutations using the mutagenesis wizard, what are the percentages that are displayed in the toggle/selection area? Is there a way to do an energy minimization after creating mutations? Thanks, Jamaine |
From: DeLano S. <de...@de...> - 2007-01-04 02:09:54
|
Jamaine, That is the percentage of structures with that particular rotamer out of the population sampled (either the backbone bin or for the residue type as a whole). PyMOL presents the rotamers in order of decreasing prevalence. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:de...@de... Not yet a PyMOL Subscriber, but want to support the project? Email sa...@de... to quote your lab, school, or employer. Thank you for participating! _____ From: pym...@li... [mailto:pym...@li...] On Behalf Of Jamaine Saydu C. Davis Sent: Tuesday, January 02, 2007 7:41 AM To: pym...@li... Subject: [PyMOL] mutagenesis When making mutations using the mutagenesis wizard, what are the percentages that are displayed in the toggle/selection area? Is there a way to do an energy minimization after creating mutations? Thanks, Jamaine |
From: Nalam, M. <Mad...@um...> - 2007-05-01 20:38:57
|
Hello: I am trying to mutate ALA to VAL in PyMOL. I would like to see possible rotamers for Val. Is it possible to do this in PyMOL? I am using mutagenesis option in PyMOL. Once I select the Val residue, it asks to select a conformational state. I assume this is for various rotamers. But how do I choose a conformational state? Thanks in advance, Madhavi |
From: Noinaj <no...@uk...> - 2007-05-02 04:53:36
|
Madhavi, Not sure if anyone has replied to your post. i think there are at least two ways to scan the available rotamers (at least with Windows XP). Once you have made the mutation... 1- use the arrow keys to change rotamers 2- use the forward (>) and back (<) arrows on the frame selection control panel (similar to DVD controls) at the bottom-right of the PyMol Viewer Window. from my experience, either one will work and allow you to scan the rotamers. the various rotamers usually have a number associated, which describes the variance of each rotamer documented thus far (i think). If you aren't happy with any of the rotamers, just cancel everything by hitting [Clear] and then [Done]. Hope some of this helps, best of luck! Cheers, Nick ----- Original Message ----- From: "Nalam, Madhavi" <Mad...@um...> To: <pym...@li...> Sent: Tuesday, May 01, 2007 4:38 PM Subject: [PyMOL] mutagenesis > Hello: > I am trying to mutate ALA to VAL in PyMOL. I would like to see possible > rotamers for Val. Is it possible to do this in PyMOL? > I am using mutagenesis option in PyMOL. Once I select the Val residue, > it asks to select a conformational state. I assume this is for various > rotamers. But how do I choose a conformational state? > Thanks in advance, > Madhavi > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |