Please note the corrections below:

Best regards,

Walid > > Today's Topics: > > 1. Re: modeller_usage Digest, Vol 5, Issue 2 (Mohsen, Al-Walid) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 03 Jan 2006 11:09:35 -0500 > From: "Mohsen, Al-Walid" mohsaw@chp.edu > Subject: [modeller_usage] Re: modeller_usage Digest, Vol 5, Issue 2 > To: modeller_usage@salilab.org > Message-ID: BFE00BEF.2014%mohsaw@chp.edu > Content-Type: text/plain; charset="US-ASCII" > > If you're only trying to include 3 water molecules that you know are > important, try the following: > > 1- Edit the pdb file of your template to only include these specific ones, > i.e, delete all other water molecules. Number these three water molecules 515 > 516, and 517. > 2- Edit your .top file deleting the WATER_IO = on command and leave the > HETATM_IO = on command. > 3- I usually use .pir and not .ali but this may still be applicable. Edit > your .ali file as follows: > (a) Change the second line in the paragraph so it will be: > structureX:Bamu:1 : :517H : :unknown:unknown:-1.00:-1.00 > > (b) Remove the /w* at the end of the molecule from both template and > your sequence (model) lines. > (c) After the last residue in the template, add XXX* that would > correspond to the 3 water molecules in the pdb file. > (d) After the last residue in the Sequence (model) lines add ...* > (e) Make sure that the XXX* in the template and the model ...* align exactly > right. It seems you will not have a problem with this since the alignment is > rather simple. > (f) Change the second line in the template paragraph to: > sequence:CcHh1:1 : :523 : :unknown:unknown:-1.00:-1.00 > > I might be wrong but it seems like Modeler is confused about what is "w". > > I hope it works!! > > Best regards, > > Walid Mohsen > > Al-Walid A. Mohsen, Ph.D. > Research Assistant Professor > Department of Pediatrics > School of Medicine > University of Pittsburgh > 3460 Fifth Ave, Rangos 2113 > Pittsburgh, PA 15213 > U.S.A. > Phone: (412) 692-7928 > > > >> From: modeller_usage-request@salilab.org >> Reply-To: modeller_usage@salilab.org >> Date: Tue, 3 Jan 2006 02:52:59 -0800 >> To: modeller_usage@salilab.org >> Subject: modeller_usage Digest, Vol 5, Issue 2 >> >> Send modeller_usage mailing list submissions to >> modeller_usage@salilab.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://salilab.org/mailman/listinfo/modeller_usage >> or, via email, send a message with subject or body 'help' to >> modeller_usage-request@salilab.org >> >> You can reach the person managing the list at >> modeller_usage-owner@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. modelling with ligands again! mainly water issues (jo hanna) >> 2. Modelling with ligands - Not Working! (Joanne Hanna) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 3 Jan 2006 10:21:12 +0000 >> From: jo hanna jfhanna@gmail.com >> Subject: [modeller_usage] modelling with ligands again! mainly water >> issues >> To: modeller_usage@salilab.org >> Message-ID: >> 4b21263d0601030221y59eef18eo9a8fc712b6fe89d6@mail.gmail.com >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hello again >> >> In follow up to my own question I have found that the issue only really >> occurs when i try to include the water, either with the other ligand or even >> without (after re ordering of the pdb file) Does the water in the pdb file >> have to have H atoms attached or is a crystallographic O sufficient? >> >> My log with the hetatms only no water, is: >> delete__442E> One or more atoms absent from MODEL: O: 522: C: 522: N: 523: >> CA: 523: >> delete__442E> One or more atoms absent from MODEL: O: 523: C: 523: N: 524: >> CA: 524: >> delete__443_> Restraints marked for deletion were removed. >> Total number of restraints before, now: 51172 47475 >> >> which still shows these atoms absent errors which i don't understand. >> >> When adding just the water and no other ligand my top and aln files are >> appended and my log error is an out of bounds as before. SO it aapears that >> the water is the problem, I have also tried in my log file with only the >> water changing the line SET HETATM_IO = on, WATER_IO = on to just SET >> WATER_IO = on but this maks no difference. >> >> delete__442E> One or more atoms absent from MODEL: O: 522: C: 522: N: 523: >> CA: 523: >> delete__443_> Restraints marked for deletion were removed. >> Total number of restraints before, now: 48782 45085 >> nselat__596E> Atom index is out of range (iatm,natm): 4009 4008 >> recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 >> >> TOP >> INCLUDE >> SET ALNFILE = 'CcHh1-Bamu.ali' >> SET KNOWNS = 'Bamu' >> SET SEQUENCE = 'CcHh1' >> SET STARTING_MODEL = 1 >> SET ENDING_MODEL = 1 >> SET HETATM_IO = on, WATER_IO = on >> CALL ROUTINE = 'model'\ >> >> ALIGNMENT >>> P1;Bamu >> structureX:Bamu:1::515::undefined:undefined:-1.00:-1.00 >> GTHEEEQYLFAVNNTKAEYPRDKTIHQLFEEQVSKRPNNVAIVCENEQLTYHELNVKANQLARIFIEKGIGKDTL >> VGIMMEKSIDLFIGILAVLKAGGAYVPIDIEYPKERIQYILDDSQARMLLTQKHLVHLIHNIQFNGQVEIFEEDT >> IKIREGTNLHVPSKSTDLAYVIYTSGTTGNPKGTMLEHKGISNLKVFFEN-SLNVTEKDRIGQFASISFDASVWE >> MFMALLTGASLYIILKDTINDFVKFEQYINQKEITVITLPPTYVVHL-----DPERILSIQTLITAGSATSPSLV >> NKWKE--KVTYINAYGPTETTICATTWVATKETIGHSVPIGAPIQNTQIYIVDENLQLKSVGEAGELCIGGEGLA >> RGYWKRPELTSQKFVDNPFVP-GEKLYKTGDQARWLSDGNIEYLGRIDNQVKIRGHRVELEEVESILLKHMYISE >> TAVSVHKDHQEQPYLCAYFVSE---KHIPLEQLRQFSSEELPTYMIPSYFIQLDKMPLTSNGKIDRKQLPEPDLT >> F/w* >> >>> P1;CcHh1 >> sequence:CcHh1:1::523::::0.00: 0.00 >> GPAERLELLAGWNDTDADRAR-PGLVEMFREQARARPDAVAVVDERRTLTYRQVEKLSAQLAHQLLARGLAVEDV >> VGISLERSAEMVIGLLAVLRAGGAFVPLDPHWPAERRAVVIEDAGVVVQLDASGEPAPG---EPEAVAVDLGDWR >> FGDRPTEDTGVTVPGDALAYVIFTSGSTGRPKGAMIRHEAISERLLWQIHEILGFGHDDASLFKAPLSFDISINE >> IFLPLVSGGRLVVLRPGGERDPHHLLSVIDEQRVTFTYLVSSMLDVLLEMAGDSGRLDSLRHVWCGGEVLTPELY >> ERFRTRLDIPLYHGYGPAETTIGVSHVVYRGAAERLSTSIGRANPNTRLYVLDDELRPVPVGVGGELYAGGLLLG >> RGYVNAPGLTASRFVANPFADDGSRLYRTGDLARFAPDGSLDFLGRADNQVKIRGMRLEIEDVEVGLAEHPRVRH >> TCVVARKNTAGGTYLVGYVIPAAGHEDLRADEVKAWAGEHMVEYMVPTHVVVMTEFPLTANGKLDRNALPEPVIP >> A/w* >> >> Sorry to post so many mails, I'm really struggling to figure this out! >> >> Jo >>