But it just contains one PDB file for rank. However, I contains 1000 structures, how can I rank them in one time?
THX
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" <> > To: "modeller usage" <> > 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 > > > 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 > > > You can reach the person managing the list at > > > 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 Caretak
er <> > Subject: Re: [modeller_usage] Structural alignment using > iterative_structural_alignment > To: Seungyeul Yoo <> > Cc: > Message-ID: <> > 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 > -- > 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 <> > Subject: [modeller_usage] about model rank > To: modeller_usage <> > Message-ID: <> > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://salilab.org/archives/modeller_usage/attachments/20110227/81097b68/attachment.html <
br>> > ------------------------------ > > Message: 3 > Date: Mon, 28 Feb 2011 16:03:50 +0530 (IST) > From: Ashish Runthala <> > Subject: [modeller_usage] Regarding Salign > To: modeller <> > Message-ID: > <> > > Content-Type: text/plain; charset=utf-8 > > Dear Modellers, > How does align2d_mult actually adds the target sequence onto the aligned templates ali file. > What is the logic considered by align2d_mult to align the target sequence onto the structurally aligned templates' ali file.It just considers topology of coordinates but no structural information is known for target. So how does it considers restraints from templates to align target sequence? > > Thanks > Ashish > > Ashish Runthala, > Lecturer, Structural Biology Cell, > Biological Sciences Group, > BITS Pilani > Rajasthan - INDIA > > > > ------------------------------ > > Message: 4 > Date: Mon, 28 Feb 2011 11:32:34 +0100 > From: Knut J Bjuland <> > Subject: Re: [modeller_usage] about model rank > To: > Message-ID: <> > Content-Type: text/plain; charset="x-gbk" > > Hi > > You can use a script to evaluate dope score for each model you build and > output the dope score to a log file. Then you can use a spreeadsheet to > rank the models according to a dope score. > > Knut J > > Den 27.02.2011 16:28, skrev albert: > > 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 t
o rank then manually? > > > > Thank you very much > > > > > > _______________________________________________ > > modeller_usage mailing list > > > > https://salilab.org/mailman/listinfo/modeller_usage > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://salilab.org/archives/modeller_usage/attachments/20110228/b810859f/attachment.html > > ------------------------------ > > _______________________________________________ > modeller_usage mailing list > > https://salilab.org/mailman/listinfo/modeller_usage > > > End of modeller_usage Digest, Vol 10, Issue 39 > ********************************************** > _______________________________________________ > modeller_usage mailing list > > https://salilab.org/mailman/listinfo/modeller_usage