From owner-chemistry@ccl.net Sun Apr 8 08:40:01 2012 From: "Ben Webb ben++salilab.org" To: CCL Subject: CCL: Homology modeling of protein with more than one chain Message-Id: <-46657-120408021425-32311-VbnlrxofR0lpINGtJSnhRg{:}server.ccl.net> X-Original-From: Ben Webb Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 07 Apr 2012 23:14:17 -0700 MIME-Version: 1.0 Sent to CCL by: Ben Webb [ben^^^salilab.org] On 4/7/12 7:44 AM, Richard W Harper drrwharper%gmail.com wrote: > I am attempting to build a homology model of a protein with more than > one chain. The only way I have discovered to accomplish this is to > model the two chains independently and combine them by overlaying on > the x-ray structure. Is there a better way? MODELLER can do this - it is very straightforward if your template also has multiple chains. Simply proceed as per normal but add chain break characters (/) between chains in your alignment for both template and model sequence. Ben -- ben,+,salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle From owner-chemistry@ccl.net Sun Apr 8 22:13:00 2012 From: "shamsa alina shamsa.pakistan ~ yahoo.com" To: CCL Subject: CCL: slow job Message-Id: <-46658-120408221058-22340-yrACO+cqmSAjAsNCasUOFw(!)server.ccl.net> X-Original-From: "shamsa alina" Date: Sun, 8 Apr 2012 22:10:55 -0400 Sent to CCL by: "shamsa alina" [shamsa.pakistan-x-yahoo.com] My scanning calculation are running for a X shape big molecule, share memory and nprocess =6 , it have to complete 36 steps but after 17 steps it has become so slow that since last two days yet it did not complete further a single step, If I change its assigned node(if node has problem) from pbs file directly and leave the job as it is running, would it effect my calculations ? or should I restart it from new end ? If anybody can suggest me something better about it please guide me .