- modeller_usage - salilab.org

Re: [modeller_usage] Installation problem?
by Steve Seibold 17 Nov '09

17 Nov '09

Hello Yes. It seems to be working fine now. I just thought the error message I was getting ( "Could not find platform independent libraries" etc.) was DUE to the KEY ID problem. But they are evidently two separate issues and neither is a *Fatal* error. I am now attempting to run sample scripts to verify installation. Thanks, Steve _____ From: Forlemu, Neville [mailto:neville.forlemu@mssm.edu] Sent: Tuesday, November 17, 2009 1:33 PM To: Steve Seibold Subject: RE: [modeller_usage] Installation problem? Hi Steve, I guess it installed fine. Just locate the executable file and you are good to go -----Original Message----- From: modeller_usage-bounces(a)salilab.org on behalf of Steve Seibold Sent: Tue 11/17/2009 11:28 AM To: modeller_usage(a)salilab.org Subject: [modeller_usage] Installation problem? Hi Paul I installed "Modeller" using the info on http://salilab.org/modeller/9v7/release.html#rpm. However I get the error message "warning modeller9v7-1.x86_64.rmp: Header V4 DSA signature: NOKEY, Key ID" . I have obtain a license key and attempted the install as follows: "env KEY_MODELLER9v7=licensekey -Uvh modeller-9v7-1.x86_64.rpm". I have also tried, as suggested by web site: "env KEY_MODELLER9v7=licensekeyx86_64 -Uvh modeller-9v7-1.x86_64.rpm". And "env KEY_MODELLER9v7=licensekey x86_64 -Uvh modeller-9v7-1.x86_64.rpm". However, nothing seems to be working. I must be doing something incorrect? I did check my machine using "uname -m" to verify by system's specs. Can you help me? Thanks Steve

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modelling with ligands (FAD FMN and NADP)
by Yerko Escalona 17 Nov '09

17 Nov '09

Hi I have a problem when i model the structure of proteins with ligands (hetatm = NADP, FAD and FMN), because some residues have improper bond, like the Asparagine make bond between the N and C(gamma), or Phenyalanine with wrong position of aromatic carbon. I try resolve this with the optimization of models with VTFM and MD&SA but the error in the bonds of residues is the same. Also try without ligands and that's work. I think the problem is of the ligands that make incorrect restriction to the protein and make that errors. I hope that you can help me. Bye (My native language is the Spanish, so sorry for the mistakes)

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Installation problem?
by Steve Seibold 17 Nov '09

17 Nov '09

Hi Paul I installed "Modeller" using the info on http://salilab.org/modeller/9v7/release.html#rpm. However I get the error message "warning modeller9v7-1.x86_64.rmp: Header V4 DSA signature: NOKEY, Key ID" . I have obtain a license key and attempted the install as follows: "env KEY_MODELLER9v7=licensekey -Uvh modeller-9v7-1.x86_64.rpm". I have also tried, as suggested by web site: "env KEY_MODELLER9v7=licensekeyx86_64 -Uvh modeller-9v7-1.x86_64.rpm". And "env KEY_MODELLER9v7=licensekey x86_64 -Uvh modeller-9v7-1.x86_64.rpm". However, nothing seems to be working. I must be doing something incorrect? I did check my machine using "uname -m" to verify by system's specs. Can you help me? Thanks Steve

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rotation!!!
by Cool Hunk 13 Nov '09

13 Nov '09

Dear Ben n all, i have got an issue about the side chain of some of the aminoacids that are part of some beta-strands in my predicted model.. is there any way that i can rotate specific amino acids so that their side chains orientation can flip outward which is inward in my predicted model... or can i rotate the whole strand to fix that issue.. second question regarding some loops in my model is that one loop kind of intersect the other or you can say passes in between/ thru the other and that makes my model unreal.. can you tell me, how can i resolve this issue???? Also can you suggest some tools, web or any way to validate my structure and look for the bad contacts if any, so that i could use this model for futher work.... Thanking in advance... Muhammad

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Installation in Ubuntu
by Dinesh 13 Nov '09

13 Nov '09

*I am trying to install Modeller in in Ubuntu 9.10 with the alien command and I get the below errors:* $ sudo env KEY_MODELLER9v7=<My Educational License Key> alien -ic modeller-9v7-1.i386.rpm warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 error: incorrect format: unknown tag warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 chown: cannot access `modeller-9v7//usr/lib/modeller9v7/modlib/modeller/config.py': No such file or directory failed chowning /usr/lib/modeller9v7/modlib/modeller/config.py to 0:0: Illegal seek at /usr/share/perl5/Alien/Package/Rpm.pm line 265, <GETPERMS> line 104 *I tried importing the public key of Ben Webb and still its the same... Any help will be appreciated* -- Dinesh Cyanam

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Residue renumbering
by Liam Browne 13 Nov '09

13 Nov '09

Hi all, Does anyone know a an easy way to renumber a pdb file? The residue numbers are not correct after generating a pdb with modeller - and I'm not keen on changing them manually! Many thanks, Liam _________________________________________________________________ Got more than one Hotmail account? Save time by linking them together http://clk.atdmt.com/UKM/go/186394591/direct/01/

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Alignmnet format conversion
by Raghu Bhagavat 11 Nov '09

11 Nov '09

Hello, i have some 200 alignments (for 200 proteins) in Blast output format....as i have to model the query proteins, i want the alignment in PIR format.....Is there any converter that does this?? that does this from command line and not manual submission...... i tried using many tools, but ended in no result or no command line version..... I also want to know Aln to Pir converter for linux machine.....i wanna use command line for the conversion Please suggest for both the doubts

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...disulfide and loops
by Joel Tyndall 09 Nov '09

09 Nov '09

Thanks guys. That's a great help. Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Pukenga Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034

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More than one Proline in helix!
by Raghu Bhagavat 09 Nov '09

09 Nov '09

hello.... I modeled a protein using 2 templates in Modeller9...1-312 residues w.r.t one protein and the next 65 resdiues w.r.t another protein....The template selection is done carefully and both the templates share a good homology with my query sequnce.... But, i have got prolines in helix which i doubt about its existence.....Its a pretty long helix in which 3 prolines are present and 2 of them are in the middle of long helix.....There is an immediate loop following this and then another helix having 2 Prolines.... Can anybody suggsest how modeler came up with such a model having Prolines in helix?? Is it valid ?? how stable is it?? has anybody encountered with the same Proline issue with any other protein? Please post in your views......

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Including a Thioester linkage
by João Rodrigues 09 Nov '09

09 Nov '09

Dear All, I'm currently trying to model a protein that has a thioester linkage between two residues. I've searched archives and Google and there's no mention on how to include such a linkage in the model. So the question is: is it possible? If so, how? If not, how can I overcome this? Best regards to all and thanks for the answers, João [ .. ] Rodrigues (Blog) http://doeidoei.wordpress.com (MSN) always_asleep_(a)hotmail.com (Skype) rodrigues.jglm

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