- modeller_usage - salilab.org

about the installation of modeller8v1
by Shulin Zhuang 18 Jan '06

18 Jan '06

Dear All, I just install the modeller8v1 on SGI300 and I run the install script. At finally the message"Happy modeling!" "MODELLER Team, 2005" arise. At the bin directory, there are such commands as mod8v1_i386-intel8,mod8v1_iris4d..... but no mod8v1. For my machine is SGI300, the command that I should use is mod8v1_iris4d. Therefore after the installation , I set the environment at the .cshrc file: #Modeller setenv PATH $PATH\://usr/people/biomd/modeller/bin setenv KEY_MODELLER8v1 xxxx(the password) alias mod8v1 mod8v1_iris4d But when I run the examles at the automodel: run_tests It tells me that: Fatal error, MODINSTALL8v1 environment variables not set: incomplete installation. What is the error in my environment variables. How should I do. -- Shulin Zhuang Chemistry Department Zhejiang University PRC shulin.zhuang(a)gmail.com

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Advantages of manual protein sequence alignment between target and template [Very urgent please]
by rajesh rengaraj 17 Jan '06

17 Jan '06

Hello protein builders; I am new to the Homology modeling field, I have membrane protein as a target and I need to model this protein, because of less sequence identity I suppose to model this protein by manual protein sequence alignment between the target and template. Let me know the advantages of manual protein sequence alignment and by this whether it is possible to improve the structure of the target protein. I need some ideas regarding this issue. Any suggestions would be appreciated. With regards, Rajesh Rangaraj. Send instant messages to your online friends http://in.messenger.yahoo.com

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Re: modeller_usage Digest, Vol 5, Issue 7
by jo hanna 13 Jan '06

13 Jan '06

Hi I would like to ask a question re the check.py and prosa2003 analysis of my model In the model I am building the check.py script identifies a region int he modeller produced alignment where the distance is greater than 8 angstroms This region corresponds to an insertion in the sequence to be modelled which aligns with a helix region in the template. Using prosa to assess the quality of a model built with this alignment shows that the energy for this region is lower than that of the template (there is a peak in the template at this region of beta sheet of 0.7). adjusting the alignment to remove this insertion against the region of secondary structure, and to move it to a region of no secondary strcuture, provides a clean check.py result but a combined energy peak in prosa at the postion this previous insertion was which is 0.8 and matches the template. As I have mentioned in the template there is a helix located at this position, In the secondary strcuture for the sequence, thetre is no predicted helix in the corresponding region. Could anyone please give me any thoughts on this behaviour?! Thanks Jo On 1/6/06, modeller_usage-request(a)salilab.org < modeller_usage-request(a)salilab.org> wrote: > > Send modeller_usage mailing list submissions to > modeller_usage(a)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(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. FW: Ligand clues and water blues (correction) (Mohsen, Al-Walid) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 06 Jan 2006 11:59:36 -0500 > From: "Mohsen, Al-Walid" <mohsaw(a)chp.edu> > Subject: [modeller_usage] FW: Ligand clues and water blues > (correction) > To: <modeller_usage(a)salilab.org> > Message-ID: <BFE40C28.2154%mohsaw(a)chp.edu> > Content-Type: text/plain; charset="US-ASCII" > > Sorry. when the .ini file is written it means Modeler accepted the > alignment, right or wrong, and the run will not stop for the error > mentioned > in your option 1. > > Best regards, > > Walid Mohsen > > > ------ Forwarded Message > From: <Mohsen>, Al-Walid <mohsaw(a)chp.edu> > Date: Fri, 06 Jan 2006 11:54:23 -0500 > To: <modeller_usage(a)salilab.org> > Conversation: Ligand clues and water blues > Subject: Re: Ligand clues and water blues > > Hi Jo, > > You have two messages and I am not sure where you are. I mentioned earlier > in my reply to replace the /...* with XXX* for the template and ...* for > the > model in your alignment file. It seems like you're still including the '/' > character, which is unnecessary at the end of the sequence and may cause > problems (shifts). The '/' is necessary to break the peptide sequence in > the > middle of the sequence, not at the end. IF you do a dimer for example you > need it there between the monomers, but NOT at the end. > > In option one, > > > this gives this error: > > rdabrk__290E> Number of residues in the alignment and pdb files are > > different: 517 516 > > For alignment entry: 1 > > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > the error is real and you should look for where the problem is in the pdb > file vs the alignment file. As I understand it you should have the > residues > coordinates in the pdb file then two ligands AMP (515) and Mg (516), and > then one water molecule, which should be marked as HETATM with the number > 517. If this is the way it is and the second line of the template in > alignment file is: > > structureX:Bamu:1 : :517H : :unknown:unknown:-1.00:-1.00 > > RKQLPEPDLTFXXX* > > and the XXX* is aligned with the ...* AFTER the .ini is written (see > below), > then you should not get this error, unless you deleted something (a > residue) > by mistake. > > In option 2: > > You MUST check the alignment file for shifts after you exe or start the > Modeler_Run AND the .ini file is written. Modeler 7 is known for > introducing > '-' into the sequence and things get messed up. This occurs near the '/' > character. > > In option 3: > > Everyone else can correct me, if I am wrong, but I do not see the problem > with water coming up as BLK. As long as it's in the proper position in the > 3D structure, it's OK. Just replace BLK with HOH manually in the pdb file. > If you do the XXX aligned with ... then all HETATM including water are > treated as HETATM and renamed BLK. > > In option 4: > > I would leave water_IO = on out. Do not assume that all the commands work > perfectly right. As I mentioned above Modeler 7 has this shift issues that > was not present in Modeler 6. > > Best regards, > > Walid Mohsen > > > > > From: <modeller_usage-request(a)salilab.org> > > Reply-To: <modeller_usage(a)salilab.org> > > Date: Fri, 6 Jan 2006 04:21:40 -0800 > > To: <modeller_usage(a)salilab.org> > > Subject: modeller_usage Digest, Vol 5, Issue 5 > > > > Send modeller_usage mailing list submissions to > > modeller_usage(a)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(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. modelling with water again (jo hanna) > > 2. Help needed (jo hanna) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Wed, 4 Jan 2006 00:33:28 +0000 > > From: jo hanna <jfhanna(a)gmail.com> > > Subject: [modeller_usage] modelling with water again > > To: modeller_usage(a)salilab.org > > Message-ID: > > <4b21263d0601031633p52f2b0dbid0d1190a1301f952(a)mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Hello > > > > Many thanks for the advice Walid, I have done as you have suggested and > have > > made some progress but still am not seeing the behaviour that I am > > expecting. > > > > I have been using the pap format for the alignment as this has being > working > > better and have tried the following varied options in the top and align > > files, I should also mention that in my pdb i have the exact number of > > ligands(2), and single water that i would want to include in my model > > > > Option 1: > > remove water_io command from top file, > > try X for water and not w therefore at end of alignment > > structure = /..W > > and seqeunce = /... > > > > this gives this error: > > rdabrk__290E> Number of residues in the alignment and pdb files are > > different: 517 516 > > For alignment entry: 1 > > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > > > Option 2: > > water_io = on in top file, in alignment file, structure end aligmment = > /..X > > seqeunce end alignment = /... > > gives this error > > rdabrk__291E> Sequence difference between alignment and pdb : > > > > STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- > > 1 517 24 UNK 28 TIP3 LTF..X > > check_a_337E> Structure not read in: 1 > > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > > > Option 3: > > water_io = on in top file, end of alignments, strcuture = /..w seqeunce > = > > /... > > > > This combination creates a model but there is no mention in the logfile > of > > the BLK residues or of whether the water is accepted and in the final > model > > the water O is written as a BLK residue. From previoud posts i was > expecting > > a message in the log file re the TIP3 water and also for the model to > > contain a HOH or OH2 and not a BLK. > > > > Option 4: > > water_io = on in top file and end os alignments strcuture = > /..w seqeunce = > > /..w > > This once agaian produces the out of range error > > delete__443_> Restraints marked for deletion were removed. > > Total number of restraints before, now: 51247 47550 > > nselat__596E> Atom index is out of range (iatm,natm): 4033 4032 > > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > > > Any help would be greatly apprecaited. > > > > Thanks > > Jo > >

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adminaddress
by N.Arun Prasanna 12 Jan '06

12 Jan '06

Sir, Im not able to access subscribers list Admin id: prasanna(a)bits-pilani.ac.in password: modellerac Regards, Prasanna

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Modeling antibody
by BiplabBose＠bits-pilani.ac.in 09 Jan '06

09 Jan '06

Hi, I am trying to model an antibody variable region using Modeller. I have two questions : 1. I have modelled the heavy chain and Light chain seperately. Now, how can I orient this two chains to generate the complete molecule? 2. CDR loops of antibodies have specific canonical structures, which depends upon loop length, hydrogen bond ladder etc. Can I modify Modeller to build the loops as per the canonical structures? With regards Biplab -- Biplab Bose, Ph. D Lecturer, Biological Sciences Group, Birla Institute of Technology & Science (BITS), Pilani, Rajasthan, INDIA PIN-333031 Ph.# 9828717874 http://www.biplabbose.wb.st http://www.bits-pilani.ac.inBITS, Pilani

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varied models
by Inbal Halperin 06 Jan '06

06 Jan '06

Hi fellow Modellers ! Does anyone know how can I create variable models? I want to get models that are different from one another (high rmsd between models). Thanks ! -Inbal

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varied models
by Inbal Halperin 06 Jan '06

06 Jan '06

Hi fellow Modellers ! Does anyone know how can I create variable models? I want to get models that are different from one another (high rmsd between models). Thanks ! -Inbal

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Re: Ligand clues and water blues
by Mohsen, Al-Walid 06 Jan '06

06 Jan '06

Hi Jo, You have two messages and I am not sure where you are. I mentioned earlier in my reply to replace the /...* with XXX* for the template and ...* for the model in your alignment file. It seems like you're still including the '/' character, which is unnecessary at the end of the sequence and may cause problems (shifts). The '/' is necessary to break the peptide sequence in the middle of the sequence, not at the end. IF you do a dimer for example you need it there between the monomers, but NOT at the end. In option one, > this gives this error: > rdabrk__290E> Number of residues in the alignment and pdb files are > different: 517 516 > For alignment entry: 1 > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 the error is real and you should look for where the problem is in the pdb file vs the alignment file. As I understand it you should have the residues coordinates in the pdb file then two ligands AMP (515) and Mg (516), and then one water molecule, which should be marked as HETATM with the number 517. If this is the way it is and the second line of the template in alignment file is: structureX:Bamu:1 : :517H : :unknown:unknown:-1.00:-1.00 RKQLPEPDLTFXXX* and the XXX* is aligned with the ...* AFTER the .ini is written (see below), then you should not get this error, unless you deleted something (a residue) by mistake. In option 2: You MUST check the alignment file for shifts after you exe or start the Modeler_Run AND the .ini file is written. Modeler 7 is known for introducing '-' into the sequence and things get messed up. This occurs near the '/' character. In option 3: Everyone else can correct me, if I am wrong, but I do not see the problem with water coming up as BLK. As long as it's in the proper position in the 3D structure, it's OK. Just replace BLK with HOH manually in the pdb file. If you do the XXX aligned with ... then all HETATM including water are treated as HETATM and renamed BLK. In option 4: I would leave water_IO = on out. Do not assume that all the commands work perfectly right. As I mentioned above Modeler 7 has this shift issues that was not present in Modeler 6. Best regards, Walid Mohsen > From: <modeller_usage-request(a)salilab.org> > Reply-To: <modeller_usage(a)salilab.org> > Date: Fri, 6 Jan 2006 04:21:40 -0800 > To: <modeller_usage(a)salilab.org> > Subject: modeller_usage Digest, Vol 5, Issue 5 > > Send modeller_usage mailing list submissions to > modeller_usage(a)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(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. modelling with water again (jo hanna) > 2. Help needed (jo hanna) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 4 Jan 2006 00:33:28 +0000 > From: jo hanna <jfhanna(a)gmail.com> > Subject: [modeller_usage] modelling with water again > To: modeller_usage(a)salilab.org > Message-ID: > <4b21263d0601031633p52f2b0dbid0d1190a1301f952(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello > > Many thanks for the advice Walid, I have done as you have suggested and have > made some progress but still am not seeing the behaviour that I am > expecting. > > I have been using the pap format for the alignment as this has being working > better and have tried the following varied options in the top and align > files, I should also mention that in my pdb i have the exact number of > ligands(2), and single water that i would want to include in my model > > Option 1: > remove water_io command from top file, > try X for water and not w therefore at end of alignment > structure = /..W > and seqeunce = /... > > this gives this error: > rdabrk__290E> Number of residues in the alignment and pdb files are > different: 517 516 > For alignment entry: 1 > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > Option 2: > water_io = on in top file, in alignment file, structure end aligmment = /..X > seqeunce end alignment = /... > gives this error > rdabrk__291E> Sequence difference between alignment and pdb : > > STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- > 1 517 24 UNK 28 TIP3 LTF..X > check_a_337E> Structure not read in: 1 > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > Option 3: > water_io = on in top file, end of alignments, strcuture = /..w seqeunce = > /... > > This combination creates a model but there is no mention in the logfile of > the BLK residues or of whether the water is accepted and in the final model > the water O is written as a BLK residue. From previoud posts i was expecting > a message in the log file re the TIP3 water and also for the model to > contain a HOH or OH2 and not a BLK. > > Option 4: > water_io = on in top file and end os alignments strcuture = /..w seqeunce = > /..w > This once agaian produces the out of range error > delete__443_> Restraints marked for deletion were removed. > Total number of restraints before, now: 51247 47550 > nselat__596E> Atom index is out of range (iatm,natm): 4033 4032 > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > Any help would be greatly apprecaited. > > Thanks > Jo >

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Help needed
by jo hanna 06 Jan '06

06 Jan '06

Hello I have been trying for some time now to model with 2 ligands and 1 water molecule and I feel that I have tried everything from the list, faq and tutorials and not got very far. I have posted a number of questions to the list but can still not get this to work, properly! I have managed to include the ligands and the water O into my output pdb by using the script and alignment below, however there is not recognition that this oxygen is a water and in the output model it is listed as BLK along with the other ligands. From reading posts in the user list I was expecting this water oxygen to be recognised as such, since i have used the w character to represent it and also HOH in the pdb file (the file has been edited to include only the protain, ligand and water that I am wishing to model around). I cannot type w at the end of the sequence alignment however as this causes modeller to fail with an out of range error. I would really appreciate some help as I have completelty exhaused all of my options now. Thanks Jo top INCLUDE SET ALNFILE = 'CcHh1-Bamu.pap', ALIGNMENT_FORMAT = 'PAP' SET KNOWNS = 'Bamu' SET SEQUENCE = 'CcHh1' SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 SET HETATM_IO = on, WATER_IO = on CALL ROUTINE = 'model' end of alignment (pap format) alignment _aln.pos 480 490 500 510 520 Bamu RKQLPEPDLTF/..w CcHh1 RNALPEPVIPA/... produce model with water included as: HETATM 4032 O BLK 525 37.988 89.184 33.629 1.00 25.09 2SG4034 END

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modelling with water again
by jo hanna 03 Jan '06

03 Jan '06

Hello Many thanks for the advice Walid, I have done as you have suggested and have made some progress but still am not seeing the behaviour that I am expecting. I have been using the pap format for the alignment as this has being working better and have tried the following varied options in the top and align files, I should also mention that in my pdb i have the exact number of ligands(2), and single water that i would want to include in my model Option 1: remove water_io command from top file, try X for water and not w therefore at end of alignment structure = /..W and seqeunce = /... this gives this error: rdabrk__290E> Number of residues in the alignment and pdb files are different: 517 516 For alignment entry: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Option 2: water_io = on in top file, in alignment file, structure end aligmment = /..X seqeunce end alignment = /... gives this error rdabrk__291E> Sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 1 517 24 UNK 28 TIP3 LTF..X check_a_337E> Structure not read in: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Option 3: water_io = on in top file, end of alignments, strcuture = /..w seqeunce = /... This combination creates a model but there is no mention in the logfile of the BLK residues or of whether the water is accepted and in the final model the water O is written as a BLK residue. From previoud posts i was expecting a message in the log file re the TIP3 water and also for the model to contain a HOH or OH2 and not a BLK. Option 4: water_io = on in top file and end os alignments strcuture = /..w seqeunce = /..w This once agaian produces the out of range error delete__443_> Restraints marked for deletion were removed. Total number of restraints before, now: 51247 47550 nselat__596E> Atom index is out of range (iatm,natm): 4033 4032 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Any help would be greatly apprecaited. Thanks Jo

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