Using local PDB file for homology modelling
Hi Is there any way to use a pdb structure file stored locally for homology modelling using the Chimera interface to Modeller? Presently the only option seems to be an automatic association from the pdb database. I simply want to use my own structure file as a template and not the one in the pdb database. Thanks for your help.
Hi Steven, There is no restriction on what structure is used for a template; all you need is a template-target sequence alignment and the template structure both open in Chimera, with the template associated with the sequence. The second link below explains how to get to that state, starting with your own template structure. Homology modeling via Chimera: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html> ... some ways to generate the needed inputs: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 16, 2012, at 6:15 PM, Steven Bottomley wrote:
Hi Is there any way to use a pdb structure file stored locally for homology modelling using the Chimera interface to Modeller? Presently the only option seems to be an automatic association from the pdb database. I simply want to use my own structure file as a template and not the one in the pdb database. Thanks for your help.
Hi Elaine Thank you very much for your quick feedback. I had read all the web pages you referred to in your email. However, your email did help me realise I was making a very simple (and embarrassing) mistake. I was using a filename for my template structure that was different from the filename I used for the alignment of the templates's sequence to the target sequence. Consequently, when I chose 'Modeller Tools' from 'MultAlign Viewer' and tried to 'find' my template structure's filename in the 'Choose at least one template' dialog box it wasn't there. The dialog box only contained the name of the template's sequence and the 'structure ID' column was blank. Of course, I had also failed to realise that Chimera had automatically associated the sequence to the structure even though the structure's filename was not listed in the dialog box. I know this sounds a bit weird but thank you for your help! Regards Steven On 18/01/2012, at 1:24 AM, Elaine Meng wrote:
Hi Steven, There is no restriction on what structure is used for a template; all you need is a template-target sequence alignment and the template structure both open in Chimera, with the template associated with the sequence. The second link below explains how to get to that state, starting with your own template structure.
Homology modeling via Chimera: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html>
... some ways to generate the needed inputs: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 16, 2012, at 6:15 PM, Steven Bottomley wrote:
Hi Is there any way to use a pdb structure file stored locally for homology modelling using the Chimera interface to Modeller? Presently the only option seems to be an automatic association from the pdb database. I simply want to use my own structure file as a template and not the one in the pdb database. Thanks for your help.
Dr Steven Bottomley Unit Coordinator, and lecturer, for Biochemistry 233, Biochemistry 234, Structural Bioinformatics 332, and Molecular Techniques 632 | School of Biomedical Sciences | Faculty of Health Sciences Curtin University Tel | +61 8 9266 4369 Fax | +61 8 9266 2342 Email | mailto: s.bottomley@curtin.edu.au Web | http://curtin.edu.au
Hi Steven, Not to worry, there are many potentially confusing bits here and there! Better to ask than to give up and be disgruntled. As you saw, in the dialog "choose template structure" really meant "choose sequence that is associated with your template structure." I'm glad you got it sorted out - Elaine On Jan 18, 2012, at 3:47 AM, Steven Bottomley wrote:
Hi Elaine
Thank you very much for your quick feedback. I had read all the web pages you referred to in your email. However, your email did help me realise I was making a very simple (and embarrassing) mistake. I was using a filename for my template structure that was different from the filename I used for the alignment of the templates's sequence to the target sequence. Consequently, when I chose 'Modeller Tools' from 'MultAlign Viewer' and tried to 'find' my template structure's filename in the 'Choose at least one template' dialog box it wasn't there. The dialog box only contained the name of the template's sequence and the 'structure ID' column was blank. Of course, I had also failed to realise that Chimera had automatically associated the sequence to the structure even though the structure's filename was not listed in the dialog box. I know this sounds a bit weird but thank you for your help!
Regards Steven
On 18/01/2012, at 1:24 AM, Elaine Meng wrote:
Hi Steven, There is no restriction on what structure is used for a template; all you need is a template-target sequence alignment and the template structure both open in Chimera, with the template associated with the sequence. The second link below explains how to get to that state, starting with your own template structure.
Homology modeling via Chimera: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html>
... some ways to generate the needed inputs: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 16, 2012, at 6:15 PM, Steven Bottomley wrote:
Hi Is there any way to use a pdb structure file stored locally for homology modelling using the Chimera interface to Modeller? Presently the only option seems to be an automatic association from the pdb database. I simply want to use my own structure file as a template and not the one in the pdb database. Thanks for your help.
participants (2)
-
Elaine Meng -
Steven Bottomley