[ccp4bb] mutation and minimization - SUMMARY

2011-05-13 Thread Andreas Förster
First off, thanks to all those who sent me their suggestions, a great variety indeed. Here's the summary: - turbo-frodo can do local rotamer optimization based on environment. - SCRWL and WHAT-IF are servers for homology modeling - Swiss PDB viewer/DeepView can also do homology modeling, but

Re: [ccp4bb] mutation and minimization

2011-05-13 Thread Eric Pettersen
On May 12, 2011, at 4:00 PM, CCP4BB automatic digest system wrote: Hey all, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple approaches that don't

Re: [ccp4bb] mutation and minimization

2011-05-13 Thread Brett, Thomas
[CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eric Pettersen [p...@cgl.ucsf.edu] Sent: Friday, May 13, 2011 2:59 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] mutation and minimization On May 12, 2011, at 4:00 PM, CCP4BB automatic digest system wrote: Hey all, I would like to introduce point mutations

Re: [ccp4bb] mutation and minimization

2011-05-13 Thread Eric Pettersen
On May 13, 2011, at 4:00 PM, Tom J. Brett wrote: On a similar extension to this topic, is there a good software out there for doing these kinds of modifications and minimizations for protein structures with chemicals entities (i.e., protein/inhibitor complexes). What I am looking to do is

[ccp4bb] mutation and minimization

2011-05-12 Thread Andreas Förster
Hey all, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple approaches that don't involve VMD/NAMD or some such overkill. Thanks. Andreas --

Re: [ccp4bb] mutation and minimization

2011-05-12 Thread Thomas Holder
Hi Andreas, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple approaches that don't involve VMD/NAMD or some such overkill. PyMOL has a Mutagenesis wizard but

Re: [ccp4bb] mutation and minimization

2011-05-12 Thread gauri misra
You can try Swiss-PDB viewer.. 2011/5/12 Thomas Holder thomas.hol...@tuebingen.mpg.de Hi Andreas, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple

Re: [ccp4bb] mutation and minimization

2011-05-12 Thread Bjørn Panyella Pedersen
Hi Andreas Without the x-ray data, phenix.pdbtools might do this (http://www.phenix-online.org/version_docs/dev-712/pdbtools.htm) From the website: [phenix.pdbtools can] Perform model geometry regularization. Minimize geometry target to idealize bond lenghths, bond angles, planarities,

Re: [ccp4bb] mutation and minimization

2011-05-12 Thread Daniel Fernandez
Or try SCWRL from Dunbrack's lab... --- On Thu, 5/12/11, gauri misra kamga...@gmail.com wrote: From: gauri misra kamga...@gmail.com Subject: Re: [ccp4bb] mutation and minimization To: CCP4BB@JISCMAIL.AC.UK Date: Thursday, May 12, 2011, 12:52 PM You can try Swiss-PDB viewer.. 2011/5/12 Thomas

Re: [ccp4bb] mutation and minimization

2011-05-12 Thread Luthra,Amit
@JISCMAIL.AC.UK] On Behalf Of Andreas Förster [docandr...@gmail.com] Sent: Thursday, May 12, 2011 11:35 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] mutation and minimization Hey all, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer