Re: [PyMOL] manual superposition with pymol--and another question
Suzanne, There isn't an easy way to do this, as far as I know. `pair_fit` can be used to do a superposition based on an arbitrary alignment, but it is very tedious to specify each aligned pair individually, and it's hard to modify the alignment. I've used NCBI's Cn3D program for detailed manual alignments, as it has a good alignment editor and can show the superpositions internally after each modification. However, it doesn't output two-model pdb files like most of the structure alignment tools (eg pdb.org's structure comparison tool). Thus you still might have to write an arduous pair_fit command (or a python script to parse cn3 file) if you want to get it into pymol for nice graphics. Cn3D has a confusing interface, so if you want to try it out I can send you my notes on creating alignments off-list. -Spencer On Mon, Apr 7, 2014 at 9:11 PM, Lapolla, Suzanne M (HSC) suzanne-lapo...@ouhsc.edu wrote: 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
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
Re: [PyMOL] manual superposition with pymol--and another question
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
