May 1998 - modeller_usage

problem!
by Paola D'Alessio 15 Jun '01

15 Jun '01

Dear users, I am trying to produce a chimeric model for my protein. The first thing I want to do is to check the alignment I have. When I tell Modeller to execute the "check_alignment" command, I get the following message: rdpir___E> alignment sequence not found in PDB file: 1 ./pXXXX.pdb ####################################################################################################################################### The alignment I have is: >P1;pXXXX structureX:pXXXX:.::.::::: CKPMSNFRF-GENHAIMGVAFTWVMALACAAPPLVGWS--RYIPEGMQC-SCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTH--------QGSDFGPIFMTIPAFFAKTSAVYNPVIYIMM* >P1;pAveM structure:pAveM:2::211::::: -----------VRWAKLYSLVIWGCTLLLSSPMLV-----------------------------EVFTNMLLNVVGFLLPLSVITFCTMQ---------------------ERRATVLVLVVLLLFIICWLPFQISTFLDTL----------------VITQIASFMAYSNSCLNPLVYVIV* >P1;Ali2 sequence:Ali2:::::::: VKTMSMGRMRGVRWAKLYSLVIWGCTLLLSSPMLVFRTMKEYSDEGHNVTACVISYPSL---IWEVFTNMLLNVVGFLLPLSVITFCTMQIMQVLRNNEMQKFKEIQT---ERRATVLVLVVLLLFIICWLPFQISTFLDTLHRLGILSSCQDERIIDVITQIASFMAYSNSCLNPLVYVIV* ####################################################################################################################################### Perhaps, something is wrong with file names or PDB codes.(I stored the pdb files as pXXXX.pdb) Can somebody help me? Thank you very much, Paola -- dott. Paola D'Alessio (PhD student) Universita' degli Studi di Salerno Dipartimento Scienze Farmaceutiche via Ponte Don Melillo, 84084 Fisciano (Sa), Italy tel.+39 089 962822; e-mail: pdalessio(a)unisa.it

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two questions
by Christian Barrett 12 May '98

12 May '98

Hi, I've recently built a homology model and have two questions that I can't find answers to in the documentation. Question 1: My template structure has hetero atoms in it. Can I 1) make these carry over into the homology model and 2) use them as restraints in building the homology model. (The hetero atoms are in contact with the template structure just as I expect them to be with the homology model. I would like this to be realized in the homology model.) Question 2: This is more a request for advice on analyzing my homology model. What is the best way to see if it makes sense? For instance, I would like to know if the core is suspiciously populated with energetically unfavorable residues, if one face of the protein is too hydrophobic, implying that it ought to be in hydrophobic contact with (in my case) the other half of the protein for which I cannot built a homology model, etc. I could do something like color hydrophobics and hydrophilics different colors and visually inspect the model, but I'm interested in something a little bit more convincing and principled. What would you do to convince yourself that the protein could be physically realizable? Thanks for any suggestions, Christian Barrett

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Energy minimization
by zaidi＠prochem.khi.sdnpk.undp.org 06 May '98

06 May '98

Hi Andrej We have docked a small peptide on the active site of protease molecule, now want to perform structural refinement and energy minimization. Can OPTIMIZE command of modeller do that or implementation of any energy minimizer is needed. Kindly note, OPTIMIZE successfully eliminate all short non-bonded contacts and improved stereochemical parameters of the initial enz-inhibitor complex.. Secondly, is it obligatory to use minimizer during these type of work. Advise please. Regards Kamran Azim

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[Fwd: About MODELLER 4 key ...]
by Andrej Sali 06 May '98

06 May '98

-- Andrej Sali, Assistant Professor The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 e-mail sali(a)rockvax.rockefeller.edu; http://salilab.org

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Re: All H in MODELER
by sali＠piano 06 May '98

06 May '98

Hi, Andrzej, Please try BUILD_METHOD = 'INTERNAL_COORDINATES', wherever BUILD_METHOD = '3D_INTERPOLATION' occurs in the script(s). If this does not help, please send me a sample problem. Best, Andrej > > This is a multi-part message in MIME format. > --------------D65A8975251E8BB9BC9BC0B2 > Content-Type: text/plain; charset=us-ascii > Content-Transfer-Encoding: 7bit > > Dear Andrej, > > I have again ( or additional) problems with MODELLER4. > I have added all H to short peptide from PBD using 'all_hydrogen.top' script > from examples directory but result is somehow strange. Some H's are 2.5A away > but some others only 0.5A from respective root atoms. It could be that it is problem > with my installation of MODELLER therefore I do not expect that you will work > on this (unless it is already recognized, general problem). However I will appreciate > some hints. > - What is logistic for adding hydrogens to heavy atoms? Formaly it is only > different library which I am using (top.lib instead of top_heav.lib) but what > happens in the program? > - What is the name of subroutine where H atom positions are calculated? > I think that something is going wrong in this subroutine. > Of course, if you want, I will inform you about results of my investigations. > > Kind regards, > Andrzej > > --------------D65A8975251E8BB9BC9BC0B2 > Content-Type: text/x-vcard; charset=us-ascii; name="vcard.vcf" > Content-Transfer-Encoding: 7bit > Content-Description: Card for Andrzej Sawaryn > Content-Disposition: attachment; filename="vcard.vcf" > > begin: vcard > fn: Andrzej Sawaryn > n: Sawaryn;Andrzej > org: Institute of Physics > adr: Ratzeburger Allee 160;;;Luebeck;;D-23538;Germany > email;internet: sawaryn(a)physik.mu-luebeck.de > title: Dr. > tel;work: +49-451-5004203 > tel;fax: +49-451-5004214 > tel;home: Do not ditsurb me at home! > x-mozilla-cpt: ;0 > x-mozilla-html: TRUE > version: 2.1 > end: vcard > > > --------------D65A8975251E8BB9BC9BC0B2-- > -- -- Andrej Sali, Assistant Professor The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 e-mail sali(a)rockvax.rockefeller.edu; http://salilab.org

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Re: error in installation modeller4
by sali＠piano 06 May '98

06 May '98

The HOSTTYPE is not recognized correctly by your shell. Please set the env variable HOSTTYPE to r10000, as described in the file INSTALLATION; for example, in your .cshrc file: setenv HOSTTYPE r10000 I hope this helps. Best, Andrej > > This message is in MIME format. The first part should be readable text, > while the remaining parts are likely unreadable without MIME-aware tools. > Send mail to mime(a)docserver.cac.washington.edu for more info. > > --0-414718936-894440868=:23177 > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Dear sir, > I try to install modeller4 on SGI octane conatianing dual r10000 cpu. > I got error message as in attach file. Plase help me to solve this problem > > Best regards, > Panapat Uawithya > pu1(a)mggec.st.mahidol.ac.th > > --0-414718936-894440868=:23177 > Content-Type: TEXT/PLAIN; charset=US-ASCII; name="mod.log" > Content-Transfer-Encoding: BASE64 > Content-ID: <Pine.OSF.3.96.980506144748.23177B(a)imbg.st.mahidol.ac.th> > Content-Description: > > DQogICAgICAgICAgICAgICAgICAgICAgICAgIE1PREVMTEVSIDRoLCBKdW5l > IDE2LCAxOTk3ICAgIA0KDQogICAgIFBST1RFSU4gU1RSVUNUVVJFIE1PREVM > TElORyBCWSBTQVRJU0ZBQ1RJT04gT0YgU1BBVElBTCBSRVNUUkFJTlRTDQoN > CiAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAg > ICAgICAgICB2ICAgICAgICAgICAgDQogICAgICAgICAgICAgICAgICAgICAg > Q29weXJpZ2h0KGMpIDE5ODktMTk5NyBBbmRyZWogU2FsaSAgICAgICAgIA0K > ICAgICAgICAgICAgICAgICAgICAgICAgICAgICBBbGwgUmlnaHRzIFJlc2Vy > dmVkICAgICAgICAgICAgICAgICANCg0KICAgICAgICAgICAgICAgICAgICAg > ICAgICAgIHYgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAN > CiAgICAgICAgICAgICAgV3JpdHRlbiBieSBBLiBTYWxpLCBSLiBTYW5jaGV6 > ICYgQS4gQmFkcmV0ZGlub3YgICAgDQogICAgICAgICAgICAgICAgICAgUm9j > a2VmZWxsZXIgVW5pdmVyc2l0eSwgTmV3IFlvcmssIFVTQSAgICAgICAgIA0K > ICAgICAgICAgICAgICAgICAgICAgSGFydmFyZCBVbml2ZXJzaXR5LCBDYW1i > cmlkZ2UsIFVTQSAgICAgICAgICANCiAgICAgICAgICAgICAgICAgSW1wZXJp > YWwgQ2FuY2VyIFJlc2VhcmNoIEZ1bmQsIExvbmRvbiwgVUsgICAgICAgDQog > ICAgICAgICAgICAgQmlya2JlY2sgQ29sbGVnZSwgVW5pdmVyc2l0eSBvZiBM > b25kb24sIExvbmRvbiwgVUsgIA0KDQoNCkFycmF5IGRpbWVuc2lvbnMgKCE4 > LzkvOTYhKToNCg0KICBNYXhpbXVtIG51bWJlciBvZiByZXNpZHVlcyAgICAg > ICAgICAgICAgICAgICAgICAgOiAgICAgICAxMDAwDQogIE1heGltdW0gbnVt > YmVyIG9mIGF0b21zICAgICAgICAgICAgICAgICAgICAgICAgICA6ICAgICAg > MTYwMDANCiAgTWF4aW11bSBsZW5ndGggb2YgYWxpZ25tZW50ICAgICAgICAg > ICAgICAgICAgICAgIDogICAgICAgMTAwMA0KICBNYXhpbXVtIG51bWJlciBv > ZiBzZXF1ZW5jZXMgaW4gYWxpZ25tZW50ICAgICAgICAgOiAgICAgICAgIDQw > DQogIE1heGltdW0gbnVtYmVyIG9mIHJlc3RyYWluZWQgZmVhdHVyZXMgICAg > ICAgICAgICA6ICAgICAxNjAwMDANCiAgTWF4aW11bSBudW1iZXIgb2YgcmVz > dHJhaW50IHBhcmFtZXRlcnMgICAgICAgICAgIDogICAgMTYwMDAwMA0KICBN > YXhpbXVtIG51bWJlciBvZiByZXN0cmFpbnQgYXRvbXMgICAgICAgICAgICAg > ICAgOiAgICAgNDgwMDAwDQogIE1heGltdW0gbnVtYmVyIG9mIG5vbi1ib25k > ZWQgYXRvbSBwYWlycyAgICAgICAgICA6ICAgICAgOTAwMDANCiAgTWF4aW11 > bSBudW1iZXIgb2Ygbm9uLWJvbmRlZCByZXN0cmFpbnQgdHlwZXMgICAgIDog > ICAgICAgICAgMQ0KICBNYXhpbXVtIG51bWJlciBvZiBub24tYm9uZGVkIHJl > c3RyYWludCB0eXBlIHBhcm1zOiAgICAgICAgICAxDQogIE1heGltdW0gbnVt > YmVyIG9mIGV4cGxpY2l0bHkgZXhjbHVkZWQgcGFpcnMgICAgICA6ICAgICAg > ICAxMDANCiAgTWF4aW11bSBudW1iZXIgb2YgcHNldWRvIGF0b21zICAgICAg > ICAgICAgICAgICAgIDogICAgICAgIDIwMA0KICBNYXhpbXVtIG9wdGltaXph > dGlvbiBzY2hlZHVsZSBsZW5ndGggICAgICAgICAgICAgOiAgICAgICAgIDUw > DQoNCk1PREVMTEVSIGlzIGNvbXBpbGVkIGluIDogc2luZ2xlIHByZWNpc2lv > bg0KSm9iIHN0YXJ0aW5nIHRpbWUgICAgICAgOiAwNi1NYXktOTggMDA6Mzk6 > MzENCg0Kb3BlbmY1X19fPiBmaWxlIGRvZXMgbm90IGV4aXN0OiAvZGlzazIv > cGRiL3BkYi5lbnQvTGlzdC5lbnQNCiAgICAgICAgICAgKGRvIG5vdCB3b3Jy > eSBhYm91dCB0aGlzIG9uZSkNCmluZGFjdF9fRT4gY29tbWFuZCBub3QgcmVj > b2duaXplZDogSE9TVFRZUEUgPWBIT1NUVFlQRWANCg== > --0-414718936-894440868=:23177-- > -- -- Andrej Sali, Assistant Professor The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 e-mail sali(a)rockvax.rockefeller.edu; http://salilab.org

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....Bugs???
by Golfredo Catalani 05 May '98

05 May '98

Hi....!!!!!!!! I intenteed running MODELLER at SP2 (RS/600), but, surprise: golfredo/MODELLER>% modeller TOP_____E> Environment variable for application directory undefined.Program probably not installed correctly. recover__> MODELLER_STATUS >= STOP_ON_ERROR: 1 0 STOP Who know how resolve this problem...????? Golfredo catalani

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Killed
by sali＠piano 05 May '98

05 May '98

This is probably caused by the lack of memory (physical and swap). See file INSTALLATION. Probably somebody changed swap space or memory on your computer, or something else is using your computer. swap -s (on an SGI) should indicate about 300MB free space available ... Best, Andrej Forwarded message: > From owner-modeller_usage@guitar Tue May 5 02:25:52 1998 > From: owner-modeller_usage@guitar > Date: Tue, 5 May 1998 02:25:50 -0400 > Message-Id: <199805050625.CAA15106(a)salilab.org> > To: owner-modeller_usage@guitar > Subject: BOUNCE modeller_usage(a)salilab.org: Admin request: /^subject:\s*help\b/i > > >From owner-modeller_usage Tue May 5 02:25:48 1998 > Received: from cmb2.saha.ernet.in by salilab.org via ESMTP (951211.SGI.8.6.12.PATCH1502/951211.SGI) > for <modeller_usage(a)salilab.org> id CAA15101; Tue, 5 May 1998 02:25:40 -0400 > Received: by cmb2.saha.ernet.in (940816.SGI.8.6.9/921111.SGI) > for modeller_usage(a)salilab.org id MAA05479; Tue, 5 May 1998 12:03:48 -0700 > Date: Tue, 5 May 1998 12:03:48 -0700 > From: deb(a)cmb2.saha.ernet.in (Debashis ) > Message-Id: <199805051903.MAA05479(a)cmb2.saha.ernet.in> > To: modeller_usage > Subject: Help > > Hi All, > > Here's a PANIC. I've been using Modeller successfully for some time > but from yesterday onwards whenever I'm trying to run it (any .top > file) it's giving the only message: > "Killed" > .....and that's all. There's no data in the .log file and no output as well. > > As I'm in the midst of my work - this is creating trouble. > What could go wrong? > > Please help. > Debashis. > ------------------------------------------------------------------------------ > ("`-''-/").___..--''"`-._ > `6_ 6 ) `-. ( ).`-.__.`) Debashis Mukhopadhyay > (_Y_.)' ._ ) `._ `. ``-..-' Research Fellow,C&MB Div., > _..`--'_..-_/ /--'_.' ,' Saha Institute Of Nuclear Physics, > (il).-'' (li).' ((!.-' 1/AF, Bidhannagar,Calcutta-700 064. > deb(a)cmb2.saha.ernet.in > ------------------------------------------------------------------------------ > -- -- Andrej Sali, Assistant Professor The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 e-mail sali(a)rockvax.rockefeller.edu; http://salilab.org

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