- modeller_usage - salilab.org

error message how to sol
by Nandha Kumar 11 Aug '12

11 Aug '12

error openf______E> Cannot open file qseq1-tseq1.ali: No such file or directory -- nandhakumar

2 1

how to download pdb_95.pir&bin file
by Nandha Kumar 11 Aug '12

11 Aug '12

questions 1.why use pdb _95.pir&bin? 2.another modelling using pdb_95 .pir&bin? -- nandhakumar

2 2

i am using windows 8 os
by Nandha Kumar 10 Aug '12

10 Aug '12

[' import site' failed; use -v for traceback cannot open logfile model-default.py: permission denied] please help me -- nandhakumar

2 1

(no subject)
by Nandha Kumar 10 Aug '12

10 Aug '12

[' import site' failed; use -v for traceback cannot open logfile model-default.py: permission denied] -- nandhakumar

2 1

Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 83
by Ashish Runthala 09 Aug '12

09 Aug '12

Dear James, You search for Salign_*.py scripts in MODELLER and then you can integrate both the templates. However, you need to include both the template to later curate the alignment file as per your fusion consideration requirement. Regards Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Wednesday, 8 August, 2012 18:57:12 GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 11, Issue 83 Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org 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 modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. Re: struggling to make structure predictions (Modeller Caretaker) 2. Template PDB files (Nanda Pandey) 3. Re: Template PDB files (Modeller Caretaker) 4. Modelling of Chimeric protein (James Starlight) ---------------------------------------------------------------------- Message: 1 Date: Mon, 06 Aug 2012 18:22:09 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> To: "Adhikari, Badri (MU-Student)" <bap54(a)mail.missouri.edu> Cc: "modeller_usage(a)salilab.org" <modeller_usage(a)salilab.org> Subject: Re: [modeller_usage] struggling to make structure predictions Message-ID: <50206DC1.10905(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 8/6/12 2:24 PM, Adhikari, Badri (MU-Student) wrote: > I am struggling to write a python program that takes protein sequence as > input and produces some conformations as the output (with no any other > input data). The scripts you've attached are IMP scripts. This is the Modeller mailing list. You'd probably have more luck on the IMP mailing list. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Tue, 7 Aug 2012 17:38:21 +0530 From: Nanda Pandey <pnanda1780(a)gmail.com> To: modeller_usage(a)salilab.org Subject: [modeller_usage] Template PDB files Message-ID: <CAPR-BHD352XAOK_w-k2aia7wyN+N8_z5q=vS_NhxYVVPDzTsOQ(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi, I am very new to modeller so a small query, Please let me know how do I compare the template sequences using compare script. Do I need to download individual template files from PDB or Is there any other possible way. Also, whta should be done in case I have too many template sequences with same e -value (e.g. 0 e -value) should i download all of them?? Thanks and Regards.

1 0

Modelling of Chimeric protein
by James Starlight 08 Aug '12

08 Aug '12

Dear Modeller's users! I want to model chimeric protein which consist of two fussed proteins ( tail to head fussion C to N termi). It's important that both of that proteins have known spatial structures which could be used as the templates. In the input I can define merged sequences of my proteins as one entry. Is there any way to use both of the templates to guide such modelling ? In the input option I've found only possibility to use one template. What extra additions should I provide for better modelling of the fussed protein? Thanks for help Gleb

2 1

Template PDB files
by Nanda Pandey 07 Aug '12

07 Aug '12

Hi, I am very new to modeller so a small query, Please let me know how do I compare the template sequences using compare script. Do I need to download individual template files from PDB or Is there any other possible way. Also, whta should be done in case I have too many template sequences with same e -value (e.g. 0 e -value) should i download all of them?? Thanks and Regards.

2 1

struggling to make structure predictions
by Adhikari, Badri (MU-Student) 06 Aug '12

06 Aug '12

Hello all, I am struggling to write a python program that takes protein sequence as input and produces some conformations as the output (with no any other input data). With the help of previous replies, I tried merging the examples: "structure_from_sequence.py", "charm_forcefield.py" and "basic_optimization.py" and wrote a script that is attached. This script runs and produces chimera python files that I can visualize through chimera. 1. Will the script that I have prepared work as an example to produce 3D structures with just sequence as input? OR have I made any fundamental/conceptual mistakes while merging them? 2. I can produce chimera python files for each of the predicted conformations. But I want pdb files. Is it possible to do that? Are there any examples? 3. Is it possible to add contacts restrain (distance between atoms as a restrain) moving forward with this approach? Sincerely, Badri Adhikari CS Graduate Student, University of Missouri-Columbia, Columbia, Missouri BAP54(a)mail.missouri.edu<mailto:BAP54@mail.missouri.edu>

2 1

Modelling of GFP
by James Starlight 06 Aug '12

06 Aug '12

Dear Modeller Users! I'm using lattest version of Modeller with the Easy Modeller GUI. I'm modelling Green fluorescent protein (GFP) which consist of chromophore heterogroup which is covalently lincked in the middle of the sequence of that protein ( so this HET group is missing in the fasta sequence of that protein- and during sequence-template alignment I obtained GAP in the place where Chromophore group should be). How I could model this protein with inclusion of the Heterogroup in the final model ? If I try to make my model based on my template ( with missing some regions) ussing of its sequence ( where Chromophore group is absent) I've obtained error like class_modeller'_sequenceMissmatchError' On other hand in some case I've used template without chromphore groups ( with the mutations for instance where this region replaced with standart amino acids ). In that case I have no problems but my final model lack for chromophore group ( as in the template). Thanks for help James

2 1

[Fwd: Re: doubt on selecting condition]
by vmahesh＠ibab.ac.in 30 Jul '12

30 Jul '12

Respected sir Could you please clarify my doubt that among these four values which one we have to more preference (RMSD(Å),Seq.Id.%)'Eq.Pos.P-value) for selecting these four Structure's(2mdh:A,2mdh:B.1b8p:A,1dbm:A) for given example of advance modelling in modeller tutorial. Really sorry for asking this same question again and again because i could not convince with your last messages and i hope this time you will clear my doubt. thanks you somuch for your reply's -----------------------------------------------------------------------------Multiple templates The structure of the Malate Dehydrogenase 1bdm has been clustered in the DBAli database within the family fm00495 of 4 members (2mdh:A, 2mdh:B. 1b8p:Aand 1dbm:A). The multiple alignment generated by the command salign() in MODELLER is used in DBAli to generate a multiple structure alignment of the family. The alignment can be downloaded from the DBAli database or you can use the file `salign.py' to calculate it on your computer. -----------------------------------------------------------------------------

2 1