Thanks for kind reply. Here I found this script:
But it just contains one PDB file for rank. However, I contains 1000 structures, how can I rank them in one time?
On Tue, 2011-03-01 at 13:53 +0530, Ashish Runthala wrote: > Dear Knut J, > Please don't use DOPE as such to evaluate model. > NEVER USE DOPE ALONE TO RANK MODELS. ONLY DOPE IS NOT A GOOD SELECTION MEASURE. > Use normalized_dope or GDT to rank models/Clusters/Hybrid Models. > > Ashish > > > > ----- Original Message ----- > From: "modeller usage-request" email@example.com > To: "modeller usage" firstname.lastname@example.org > Sent: Monday, February 28, 2011 5:02:41 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi > Subject: modeller_usage Digest, Vol 10, Issue 39 > > Send modeller_usage mailing list submissions to > email@example.com > > To subscribe or unsubscribe via the World Wide Web, visit > https://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > firstname.lastname@example.org > > You can reach the person managing the list at > email@example.com > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. Re: Structural alignment using iterative_structural_alignment > (Modeller Caretaker) > 2. about model rank (albert) > 3. Regarding Salign (Ashish Runthala) > 4. Re: about model rank (Knut J Bjuland) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 25 Feb 2011 16:04:47 -0800 > From: Modeller Caretaker firstname.lastname@example.org > Subject: Re: [modeller_usage] Structural alignment using > iterative_structural_alignment > To: Seungyeul Yoo email@example.com > Cc: firstname.lastname@example.org > Message-ID: 4D68439F.email@example.com > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 2/25/11 9:48 AM, Seungyeul Yoo wrote: > > I was trying to clean two pdb files and superpose them based on the > > pairwise structural alignment. > ... > > But when I replaced it to > > 'modeller.salign.iterative_structural_align(aln), I had error message like: > > My best guess is that every combination of parameters failed for the > first loop, so it has no alignment to refine. If you can send me your > full inputs (which two PDBs are you trying to align?) I'll see if it can > be fixed. > > Ben Webb, Modeller Caretaker > -- > firstname.lastname@example.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > ------------------------------ > > Message: 2 > Date: Sun, 27 Feb 2011 23:28:20 +0800 (CST) > From: albert email@example.com > Subject: [modeller_usage] about model rank > To: modeller_usage firstname.lastname@example.org > Message-ID: 2e2442cd.2c66.12e67bc0d5d.Coremail.email@example.com > Content-Type: text/plain; charset="gbk" > > Hello: > I've built 1000 models by modeller and I forgot save the log file. So I cannot obtain the DOPE or MOLPDF information for each residues. I am wondering, is it possible to rank then manually? > > Thank you very much >
On 3/1/11 11:42 PM, albert wrote: > Thanks for kind reply. Here I found this script: > > http://salilab.org/modeller/9v8/manual/node194.html > > But it just contains one PDB file for rank. However, I contains 1000 > structures, how can I rank them in one time?
Just write a Python loop in your script.
Ben Webb, Modeller Caretaker