Haddock? -----Original Message----- From: Lapolla, Suzanne M (HSC) [mailto:suzanne-lapo...@ouhsc.edu] Sent: Tuesday, 8 April 2014 7:12 a.m. To: pymol-users@lists.sourceforge.net Cc: thomas.hol...@schrodinger.com Subject: Re: [PyMOL] manual superposition with pymol--and another question
This worked--thanks. I have another ? that may have been addressed previously but do not know the answer. Is there a way to do an alignment (or maybe docking is a better word) on two structures/selections and input a constraint for that alignment? For example, i am working on generating a model RE a dimer of two molecules, and I have some data suggesting a range of distances between certain residues of the selection. Is there a way to input that data into Pymol before it completes the alignment, or do I need to use other docking programs to do that? Hope that makes sense. Thanks. ________________________________________ From: Lapolla, Suzanne M (HSC) Sent: Friday, April 04, 2014 5:11 PM To: Thomas Holder Subject: RE: [PyMOL] manual superposition with pymol Thank you! I will try this and get back to you. ________________________________________ From: Thomas Holder [thomas.hol...@schrodinger.com] Sent: Friday, April 04, 2014 3:16 PM To: Lapolla, Suzanne M (HSC) Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] manual superposition with pymol Hi Suzanne, looks like you only deprotected the CA atoms. If you have this as a named selection, try "A > modify > complete > molecules" and deprotect again. Or type: PyMOL> deprotect bymol (sele) Instead of working with one object and protecting/deprotecting of subsets of atoms, I suggest to extract the selection that you want to move to its own object. That's usually easier to handle. Cheers, Thomas On 04 Apr 2014, at 13:38, Lapolla, Suzanne M (HSC) <suzanne-lapo...@ouhsc.edu> wrote: > I am using pymol 1.3 and having trouble with doing manual > superposition with my structures. I am able to download my structures, > select the portion I want to move manually and, after deprotecting it > using the action menu move it using the shift-mouse editing command. > When I do this with my selection shown in cartoon mode, things look > great, but then when i switch to show my selected residues as sticks, > the sticks become huge --they get bigger and/or smaller as I move > the structure. Ideas on what I may be doing wrong? Hope this makes > sense. Thanks, Suzanne -- Thomas Holder PyMOL Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test & Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ------------------------------------------------------------------------------ Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test & Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
