<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><span>Hello all,</span></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><span>I am trying to build a protein-ligand model using align-ligand.ali file. . Below is the python script to generate 5 model and to calculate the Dope and GA score. </span>but I am unable to calculate the DOPE score and GA score. Plz help</div><div><span><div><br></div><div><br></div><div>from modeller import *</div><div>from modeller.automodel import *</div><div><br></div><div>log.verbose() # request verbose output</div><div>env = environ() # create a new MODELLER environment to build this model in</div><div><br></div><div># directories for input atom
files</div><div>env.io.atom_files_directory = ['.', '../atom_files']</div><div><br></div><div>env = environ()</div><div>a = automodel(env, alnfile='alignment.ali',</div><div> knowns='5fd1', sequence='1fdx',</div><div> assess_methods=(assess.DOPE, assess.GA341))</div><div>a.starting_model = 1</div><div>a.ending_model = 5</div><div>a.make()</div></span></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "> </div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><br></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">Regards,</div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><span style="color: rgb(127, 0, 63); font-family: courier, monaco, monospace, sans-serif; "
class="yui_3_2_0_2_132929193857946">Nutan Chauhan<br>Research Scholar</span></div><div style="color: rgb(127, 0, 63); font-size: 13px; background-color: transparent; font-style: normal; font-family: courier, monaco, monospace, sans-serif; "><span style="color: rgb(127, 0, 63); font-family: courier, monaco, monospace, sans-serif; ">Department of Biotechnology<br>BIT, Mesra<br>Ranchi-835215, Jharkhand</span></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><br></div> <div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "> <div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "> <div dir="ltr"> <font size="2" face="Arial"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> "modeller_usage-request@salilab.org" <modeller_usage-request@salilab.org><br> <b><span style="font-weight: bold;">To:</span></b>
modeller_usage@salilab.org <br> <b><span style="font-weight: bold;">Sent:</span></b> Tuesday, 10 April 2012 8:58 AM<br> <b><span style="font-weight: bold;">Subject:</span></b> modeller_usage Digest, Vol 11, Issue 43<br> </font> </div> <br>Send modeller_usage mailing list submissions to<br> <a ymailto="mailto:modeller_usage@salilab.org" href="mailto:modeller_usage@salilab.org">modeller_usage@salilab.org</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br> <a href="https://salilab.org/mailman/listinfo/modeller_usage" target="_blank">https://salilab.org/mailman/listinfo/modeller_usage</a><br>or, via email, send a message with subject or body 'help' to<br> <a ymailto="mailto:modeller_usage-request@salilab.org" href="mailto:modeller_usage-request@salilab.org">modeller_usage-request@salilab.org</a><br><br>You can reach the person managing the list at<br> <a
ymailto="mailto:modeller_usage-owner@salilab.org" href="mailto:modeller_usage-owner@salilab.org">modeller_usage-owner@salilab.org</a><br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of modeller_usage digest..."<br><br><br>Today's Topics:<br><br> 1. Re: In what are the initial structures different?<br> (Modeller Caretaker)<br> 2. Re: modeller_usage Digest, Vol 11, Issue 42 (Ashish Runthala)<br> 3. Re: modeller_usage Digest, Vol 11, Issue 42 (Ashish Runthala)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Mon, 09 Apr 2012 11:46:02 -0700<br>From: Modeller Caretaker <<a ymailto="mailto:modeller-care@salilab.org" href="mailto:modeller-care@salilab.org">modeller-care@salilab.org</a>><br>To: BIN ZHANG <<a ymailto="mailto:zhngbn@gmail.com" href="mailto:zhngbn@gmail.com">zhngbn@gmail.com</a>><br>Cc:
<a ymailto="mailto:modeller_usage@salilab.org" href="mailto:modeller_usage@salilab.org">modeller_usage@salilab.org</a><br>Subject: Re: [modeller_usage] In what are the initial structures<br> different?<br>Message-ID: <<a ymailto="mailto:4F832E6A.5020001@salilab.org" href="mailto:4F832E6A.5020001@salilab.org">4F832E6A.5020001@salilab.org</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>On 04/08/2012 11:58 PM, BIN ZHANG wrote:<br>> I have a question about the differences of the initial structure built<br>> for homology modeling. Can anyone tell me how exactly are these initial<br>> structures different? Do they differ in the secondary structures in<br>> uncertain regions? I cannot find this information in the manual.<br><br>See <a href="http://salilab.org/modeller/9.10/manual/node470.html" target="_blank">http://salilab.org/modeller/9.10/manual/node470.html</a>, in particular <br>step 3 and
substep 3. The initial structures are simply randomized by <br>calling selection.randomize_xyz().<br><br> Ben Webb, Modeller Caretaker<br>-- <br><a ymailto="mailto:modeller-care@salilab.org" href="mailto:modeller-care@salilab.org">modeller-care@salilab.org</a> <a href="http://www.salilab.org/modeller/" target="_blank">http://www.salilab.org/modeller/</a><br>Modeller mail list: <a href="http://salilab.org/mailman/listinfo/modeller_usage" target="_blank">http://salilab.org/mailman/listinfo/modeller_usage</a><br><br><br>------------------------------<br><br>Message: 2<br>Date: Tue, 10 Apr 2012 08:33:02 +0530 (IST)<br>From: Ashish Runthala <<a ymailto="mailto:ashishr@bits-pilani.ac.in" href="mailto:ashishr@bits-pilani.ac.in">ashishr@bits-pilani.ac.in</a>><br>To: modeller usage <<a ymailto="mailto:modeller_usage@salilab.org"
href="mailto:modeller_usage@salilab.org">modeller_usage@salilab.org</a>><br>Subject: Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 42<br>Message-ID:<br> <<a ymailto="mailto:15240798.16751334026982399.JavaMail.root@mailserver.bits-pilani.ac.in" href="mailto:15240798.16751334026982399.JavaMail.root@mailserver.bits-pilani.ac.in">15240798.16751334026982399.JavaMail.root@mailserver.bits-pilani.ac.in</a>><br> <br>Content-Type: text/plain; charset=utf-8<br><br>Focus on the statement with ALIGN_CODES, as it is inclusive of the PDB_ID and the PDB_CHAIN used in the alignment file. <br>So it could probably be '2AHNA' or '2AHNB'. <br><br><br><br>Ashish Runthala,<br>Lecturer, Structural Biology Cell,<br>Biological Sciences Group,<br>BITS, Pilani<br>Rajasthan, INDIA<br><br>------------------------------<br><br>Message: 2<br>Date: Mon, 9 Apr 2012 17:21:12 +0530<br>From: Sumedha Roy <<a
ymailto="mailto:sumedharoy@gmail.com" href="mailto:sumedharoy@gmail.com">sumedharoy@gmail.com</a>><br>To: modeller usage <<a ymailto="mailto:modeller_usage@salilab.org" href="mailto:modeller_usage@salilab.org">modeller_usage@salilab.org</a>><br>Subject: [modeller_usage] Error in ALIGN_CODES(i)<br>Message-ID:<br> <CABFmE0dNMawUwZgsh07bsRd43+-O3Yrzq6VhfkSQJOTjp=<a ymailto="mailto:NECA@mail.gmail.com" href="mailto:NECA@mail.gmail.com">NECA@mail.gmail.com</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Hello all,<br><br>When I try to model my protein-DNA complex, I get the error:<br>_modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i)<br>was not found in the alignment file; ALIGN_CODES( 2) = 2AHN<br><br>But I see no mistake either in the alignment or the format. I've attached<br>both the ALI file and model-ligand.py. Please help!!!<br><br>-- <br>Sumedha
Roy<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <<a href="http://salilab.org/archives/modeller_usage/attachments/20120409/e4ef0163/attachment.html" target="_blank">http://salilab.org/archives/modeller_usage/attachments/20120409/e4ef0163/attachment.html</a>><br>-------------- next part --------------<br>A non-text attachment was scrubbed...<br>Name: alignment-ligand.ali<br>Type: application/octet-stream<br>Size: 428 bytes<br>Desc: not available<br>URL: <<a href="http://salilab.org/archives/modeller_usage/attachments/20120409/e4ef0163/attachment.obj" target="_blank">http://salilab.org/archives/modeller_usage/attachments/20120409/e4ef0163/attachment.obj</a>><br>-------------- next part --------------<br>A non-text attachment was scrubbed...<br>Name: model-ligand.py<br>Type: text/x-python<br>Size: 981 bytes<br>Desc: not available<br>URL: <<a
href="http://salilab.org/archives/modeller_usage/attachments/20120409/e4ef0163/attachment.py" target="_blank">http://salilab.org/archives/modeller_usage/attachments/20120409/e4ef0163/attachment.py</a>><br><br>------------------------------<br><br>Message: 3<br>Date: Mon, 09 Apr 2012 11:44:11 -0700<br>From: Modeller Caretaker <<a ymailto="mailto:modeller-care@salilab.org" href="mailto:modeller-care@salilab.org">modeller-care@salilab.org</a>><br>To: Sumedha Roy <<a ymailto="mailto:sumedharoy@gmail.com" href="mailto:sumedharoy@gmail.com">sumedharoy@gmail.com</a>><br>Cc: modeller usage <<a ymailto="mailto:modeller_usage@salilab.org" href="mailto:modeller_usage@salilab.org">modeller_usage@salilab.org</a>><br>Subject: Re: [modeller_usage] Error in ALIGN_CODES(i)<br>Message-ID: <<a ymailto="mailto:4F832DFB.1020106@salilab.org" href="mailto:4F832DFB.1020106@salilab.org">4F832DFB.1020106@salilab.org</a>><br>Content-Type: text/plain;
charset=ISO-8859-1; format=flowed<br><br>On 04/09/2012 04:51 AM, Sumedha Roy wrote:<br>> When I try to model my protein-DNA complex, I get the error:<br>> _modeller.ModellerError: read_al_373E> Protein specified in<br>> ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES(<br>> 2) = 2AHN<br>><br>> But I see no mistake either in the alignment or the format. I've<br>> attached both the ALI file and model-ligand.py. Please help!!!<br><br>Your alignment file is in incorrect format. Each sequence must start <br>with a >P1; header. Your second sequence starts with >P2; instead.<br><br> Ben Webb, Modeller Caretaker<br>-- <br><a ymailto="mailto:modeller-care@salilab.org" href="mailto:modeller-care@salilab.org">modeller-care@salilab.org</a> <a href="http://www.salilab.org/modeller/" target="_blank">http://www.salilab.org/modeller/</a><br>Modeller mail list:
<a href="http://salilab.org/mailman/listinfo/modeller_usage" target="_blank">http://salilab.org/mailman/listinfo/modeller_usage</a><br><br><br>------------------------------<br><br>_______________________________________________<br>modeller_usage mailing list<br><a ymailto="mailto:modeller_usage@salilab.org" href="mailto:modeller_usage@salilab.org">modeller_usage@salilab.org</a><br><a href="https://salilab.org/mailman/listinfo/modeller_usage" target="_blank">https://salilab.org/mailman/listinfo/modeller_usage</a><br><br><br>End of modeller_usage Digest, Vol 11, Issue 42<br>**********************************************<br><br><br>------------------------------<br><br>Message: 3<br>Date: Tue, 10 Apr 2012 08:30:34 +0530 (IST)<br>From: Ashish Runthala <<a ymailto="mailto:ashishr@bits-pilani.ac.in" href="mailto:ashishr@bits-pilani.ac.in">ashishr@bits-pilani.ac.in</a>><br>To: modeller usage <<a
ymailto="mailto:modeller_usage@salilab.org" href="mailto:modeller_usage@salilab.org">modeller_usage@salilab.org</a>><br>Subject: Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 42<br>Message-ID:<br> <<a ymailto="mailto:24731645.16721334026834741.JavaMail.root@mailserver.bits-pilani.ac.in" href="mailto:24731645.16721334026834741.JavaMail.root@mailserver.bits-pilani.ac.in">24731645.16721334026834741.JavaMail.root@mailserver.bits-pilani.ac.in</a>><br> <br>Content-Type: text/plain; charset=utf-8<br><br>Dear BIN ZHANG,<br>MODELLER based on your constructed alignment file parsing the reliable template residues mapped against the target ones, constructs and fixes the average alpha carbon backbone (if you choose a single template) or an average backbone topology (for Multiple templates' local aligned chunks). Then it fits in the side chains and backbone atoms to make the model complete.
<br>However, easy saying but really a vicious circle problem, the alignment could have actually been wrong to incorrectly fit target against parsed template residues. <br>Regardless of the earlier problems, On increased sampling, MODELLER tries best to satisfy the Lennard Jones and all the energetic equations composing its DOPE energy function. The non-physical local atomic clashes are thus minimized with every such iteration. So only you see, Restraints earlier, now with end of every such iterative step. That in fact, is the trial to leap the energetic landscape, precisely focusing on the probably erroneous regions encompassing the higher local steric clashes. <br><br>The story continues until the number of iterations are over. <br><br><br>Ashish<br><br><br>Ashish Runthala,<br>Lecturer, Structural Biology Cell,<br>Biological Sciences Group,<br>BITS, Pilani<br>Rajasthan, INDIA<br><br>Message: 1<br>Date: Sun, 8 Apr 2012 23:58:13 -0700<br>From: BIN ZHANG
<<a ymailto="mailto:zhngbn@gmail.com" href="mailto:zhngbn@gmail.com">zhngbn@gmail.com</a>><br>To: <a ymailto="mailto:modeller_usage@salilab.org" href="mailto:modeller_usage@salilab.org">modeller_usage@salilab.org</a><br>Subject: [modeller_usage] In what are the initial structures<br> different?<br>Message-ID: <<a ymailto="mailto:602A5241-132A-4319-81BA-94C238A459AF@gmail.com" href="mailto:602A5241-132A-4319-81BA-94C238A459AF@gmail.com">602A5241-132A-4319-81BA-94C238A459AF@gmail.com</a>><br>Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes<br><br>Dear All:<br><br>I have a question about the differences of the initial structure built <br>for homology modeling. Can anyone tell me how exactly are these <br>initial structures different? Do they differ in the secondary <br>structures in uncertain regions? I cannot find this information in the <br>manual.<br><br>For example, by
using<br><br>a = automodel()<br>a.starting_model = 1<br>a.ending_model = 50<br><br>I can built 50 different homology models starting from different <br>initial structures, but I have want to know how these different <br>initial structures are constructed.<br><br>Thanks very much for help.<br><br>Best,<br>Bin<br><br><br>------------------------------<br><br>_______________________________________________<br>modeller_usage mailing list<br><a ymailto="mailto:modeller_usage@salilab.org" href="mailto:modeller_usage@salilab.org">modeller_usage@salilab.org</a><br><a href="https://salilab.org/mailman/listinfo/modeller_usage" target="_blank">https://salilab.org/mailman/listinfo/modeller_usage</a><br><br><br>End of modeller_usage Digest, Vol 11, Issue 43<br>**********************************************<br><br><br> </div> </div> </div></body></html>