Re: [ccp4bb] Building peptide in density using coot.
If your peptide has less than 400 atoms, you can also try and use the 'Fit Ligand' option under the Calculate menu of the main window: read in the coordinates of a peptide of the same length as the one you wish and use Simple Mutate from the Model/Fit/Refine menu to adjust to the desired sequence. Then choose fit ligand and click flexible. That often works amazingly well with decent density. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Tue, 2 Sep 2008, Tarique wrote: Hi, Can any body tell me how to build peptide fragment of 5-6 residues using coot,if the sequence is known.I am working at 2.1 angstroms resolution map. Tarique Khan Research scholar Structural Bilogy Unit, National institute of Immunology, Aruna Asaf Ali marg, new Delhi 110067 India Open WebMail Project (http://openwebmail.org)
Re: [ccp4bb] Building peptide in density using coot.
Hi - If you could compromise to do it outside coot you could also: a. Use ARP/wARP Ligand Build and treat the peptide as a ligand (if its not too big) b. Use ARP/wARP Loops if its a missing loop (a part of a bigger chain). Both should also work well at 2.1 A. Tassos On Sep 3, 2008, at 7:34, Chavas Leo wrote: Dear Tarique -- On 2 Sep 2008, at 12:58, Tarique wrote: Can any body tell me how to build peptide fragment of 5-6 residues using coot,if the sequence is known.I am working at 2.1 angstroms resolution map. If the peptide you're trying to build is a loop, and the density is visible, you can use the Fit Loop option, straight forward to understand. Now, if you're trying to build a peptide not related to your protein, e.g. a ligand, I would start by importing a single alanine.pdb file that would contain the coordinates for an alanine, place the alanine in the density you can see, and start to build from it. You can still mutate with the proper amino acids later on. Please note that I'm still working on an hold version of Coot, without any fancy additional options :) HTH Kind regards. -- Leo -- Chavas Leonard, Ph.D. @ home Research Associate Marie Curie Actions Fellow Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED] http://personalpages.manchester.ac.uk/staff/leonard.chavas/
Re: [ccp4bb] Building peptide in density using coot.
Dear Tarique -- On 2 Sep 2008, at 12:58, Tarique wrote: Can any body tell me how to build peptide fragment of 5-6 residues using coot,if the sequence is known.I am working at 2.1 angstroms resolution map. If the peptide you're trying to build is a loop, and the density is visible, you can use the Fit Loop option, straight forward to understand. Now, if you're trying to build a peptide not related to your protein, e.g. a ligand, I would start by importing a single alanine.pdb file that would contain the coordinates for an alanine, place the alanine in the density you can see, and start to build from it. You can still mutate with the proper amino acids later on. Please note that I'm still working on an hold version of Coot, without any fancy additional options :) HTH Kind regards. -- Leo -- Chavas Leonard, Ph.D. @ home Research Associate Marie Curie Actions Fellow Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED] http://personalpages.manchester.ac.uk/staff/leonard.chavas/
