- modeller_usage - salilab.org

Retain residue IDS when mutating and writing PDB
by Pedro Guillem 05 May '20

05 May '20

I'm using Modeller 9.24 to induce a couple of mutations into a PDB. I noticed that when I execute model.mutate() and export the PDB, the residue indexes are completely different from the original file... ebery residue looses its original position in the sequence and gets renumbered to therever it lands. Is there a way I can force modeller to stick to the original numbering? Best Pedro

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Threading sequence onto template with missing residues
by Ahmad Khalifa 04 May '20

04 May '20

Hello, I have a template with lots of missing residues. I want to thread my target sequence onto the aligned parts of the template that are present without moving my target structure in these areas. In my target sequence, I also wish to know how to skip modeling the missing parts altogether, thus making the job a mere threading of aligned unknown regions onto the known ones. Is there a simple way to accomplish my task without doing too much manual alignment and residue listing? Please do post a code snippet if you can. Thanks a lot.

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Ca-Ca restraints
by Mariana GONZALEZ MEDINA 20 Apr '20

20 Apr '20

Hello, I have observed that the more templates I include in the homology modeling the least Ca-Ca distance restraints I obtain. I can't understand this since I would expect to obtain restraints from missing residues, homology, etc from more templates and therefore more restraints imposed into my model. What could an explanation to this? Thank you! Best, Mariana Gonzalez Medina

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reg: template has extra residues
by Anwesha Mohapatra 14 Apr '20

14 Apr '20

Dear Sir , I am trying to build a model where the template is a homo-6-mer. What changes do I make in the MyModel class? # Override the 'special_restraints' and 'user_after_single_model' methods: class MyModel(automodel): def special_restraints(self, aln): # Constrain the A and B chains to be identical (but only restrain # the C-alpha atoms, to reduce the number of interatomic distances# that need to be calculated): s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') '''s3 = selection(self.chains['C']).only_atom_types('CA') s4 = selection(self.chains['D']).only_atom_types('CA') s5 = selection(self.chains['E']).only_atom_types('CA') s6 = selection(self.chains['F']).only_atom_types('CA')''' self.restraints.symmetry.append(symmetry(s1, s2,1.0)) def user_after_single_model(self): *Should I add restraint for each chain ??* *KIndly help me* *Thanks and Regards* *Anwesha*

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Modeller 9.24 release
by Modeller Caretaker 09 Apr '20

09 Apr '20

A new version of Modeller, 9.24, is now available for download! Please see the download page at https://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9.24 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.24 adds bug fixes, including updated handling of the MEX and ABU residue types, and adds an option to assign IDs to single chain models. See the Modeller manual for a full change log: https://salilab.org/modeller/9.24/manual/node40.html If you encounter bugs in Modeller 9.24, please see https://salilab.org/modeller/9.24/manual/node10.html for information on how to report them. Note: you are receiving this email either because you subscribed to the modeller_usage mailing list, or you provided this address when you requested a Modeller license and you ticked the "notify me of new releases" box. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply reply to this email and let us know. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

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Design a linker for two-domain chimeric protein
by Чугунов Антон 06 Apr '20

06 Apr '20

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Loop refinement problem
by Vicente Pires 04 Apr '20

04 Apr '20

I’m having porblems trying to model a structure and using the loop refinement tool. I was given the nohup_mod.out as output and the error prevented the loop refinement, although models were made. Can somebody help me with this error? Vicente Pires.

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Fwd: reg: issue in importing modeller
by Anwesha Mohapatra 01 Apr '20

01 Apr '20

---------- Forwarded message --------- From: Anwesha Mohapatra <anwesha.mohapatra11(a)gmail.com> Date: Tue, Mar 31, 2020 at 11:58 PM Subject: Re: [modeller_usage] reg: issue in importing modeller To: Modeller Caretaker <modeller-care(a)salilab.org> Dear Sir, I read the modeller forum for multichain proteins however I am not sure whether I have understood correctly. I am a novice in the area of structural biology and hence have lots of queries. *1) In case of a homomeric protein.* For example protein with id *1sv6 *is my template which has 5 chains (A-E). In order to align my target protein with this template, I copied and pasted the sequence of my target 5 times separated by the delimiter '/'. The alignment of the template (1SV6) with my target gene ABM40476.1 gave the following result. * Is this the right way to proceed in case of homomeric proteins? * >P1;1sv6.pdb structureX:1sv6.pdb: 1 :A:+1305:E:MOL_ID 1; MOLECULE 2-KETO-4-PENTENOATE HYDRATASE; CHAIN A, B, C, D, E; SYNONYM 2-HYDROXYPENTADIENOIC ACID HYDRATASE; EC 4.2.1.-; ENGINEERED YES:MOL_ID 1; ORGANISM_SCIENTIFIC ESCHERICHIA COLI; ORGANISM_TAXID 562; GENE MHPD, B0350; EXPRESSION_SYSTEM ESCHERICHIA COLI; EXPRESSION_SYSTEM_TAXID 562: 2.90: 0.24 MT--KHTLEQLAADLRRAAEQGEAIAPLRDLIGIDNAEAAYAIQHINVQHDVAQGRRVVGRKVGLTHPKVQQQLG VDQPDFGTLFADMCYGDNEIIPFSRVLQPRIEAEIALVLNRDLPATDITFDELYNAIEWVLPALEVVGSRIRDWS IQFVDTVADNASCGVYVIGGPAQRPAGLDLKNCAMKMTRNNEEVSSGRGSECLGHPLNAAVWLARKMASLGEPLR TGDIILTGALGPMVAVNAGDRFEAHIEGIGSVAATFSS/ MT--KHTLEQLAADLRRAAEQGEAIAPLRDLIGIDNAEAAYAIQHINVQHDVAQGRRVVGRKVGLTHPKVQQQLGVD QPDFGTLFADMCYGDNEIIPFSRVLQPRIEAEIALVLNRDLPATDITFDELYNAIEWVLPALEVVGSRIRDWSIQFVDT VADNASCGVYVIGGPAQRPAGLDLKNCAMKMTRNNEEVSSGRGSECLGHPLNAAVWLARKMASLGEPLRTGDIILT-G ALGPMVAVNAGDRFEAHIEGIGSVAATFSS/ MTKHTLEQLAADLRRAAEQGEAIAPLRD XXXXXXXXXXX repetition of the chain XXXXXXXXXXXXX* >P1;ABM40476.1_-_Acidovorax_sp._JS42 sequence:ABM40476.1_-_Acidovorax_sp._JS42: : : : ::: 0.00: 0.00 MTMTPALIEQLGDELYQALTQRRMLEPLTNRHADITIDDAYAIQQKMLARRLAAGEKVVGKKIGVTSKAVMDMLG VFQPDFGWLTDGMVFNEGQAVQANTLIQPKAEGEIAFVLKKTLKGPGITAADVLAATEGVMACFEIVDSRIRDWK IKIQDTVADNASCGVFVLGDRLVDPRDVDLGTCGMVLEKNGDIVATGAGAA------------------------ --------ALGH-PA-NA-------------------V/ MTMTPALIEQLGDELYQALTQRRMLEPLTNRHADIT IDDAYAIQQKMLARRLAAGEKVVGKKIGVTSKAVMDMLGVFQPDFGWLTDGMVFNEGQAVQANTLIQPKAEGEIA FVLKKTLKGPGITAADVLAATEGVMACFEIVDSRIRDWKIKIQDTVADNASCGVFVLGDRLVDPRDVDLGTCGMV LEKNGDIVATGAGAAALGHPANA----------------------V/ MTMTPALIEQLGDE-------------LYQA-LTQR---RMLEPLTNR------HADIT----IDD---AYAIQQKMLARRLAAGEKVVGK KIGVTSKAVMDMLGVFQPDFGWLTDGMVFNEGQAVQANTLIQPKAEGEIAFVLKKTLKGPGITAADVLAATEGVM ACFEIVDSRIRDWKIKIQDTVADNASCGVFVLGDRLVDPRDVDLGTCGMVLEKNGDIVATGAGAAALGHPANA-------------- --------V/ (XXXX and so on )--------* *2.) In order to further model this protein should I be using MyModel instead of automodel?* *If so do I need to make changes in this part of the code as per the number of chains in the template (highlighted below)?* s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') *#Should the C,D,E chains be appended to self.restraints.symmetry?* self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) *3). I also have a heteromeric protein such as 1O7G which has a large and small subunit as chain A and B. The target gene that I want to model shows sequence similarity only with chain A. How should my alignment file be in this case?* *for example if the template is* >P1;1o7g structure:::: MNOPTHSWYRTY....XXXXXXXXX...../ MRSF...........* *then should my target gene which has aligned to only chainA be depicted as* >P1,TargetGene sequence::::::: MNOPTYIKL--DFT--WANH--XXX--/ -----------------------------------------------* Sir , request you to please guide me in this issue as I am stuck and unable to proceed further. Thanks & Regards Anwesha On Sat, Mar 28, 2020 at 6:21 PM Anwesha Mohapatra < anwesha.mohapatra11(a)gmail.com> wrote: > Hello Sir, > > Could you please suggest how to proceed . I have attached my files and > their corresponding scenarios in the previous mail. > > Kindly guide me. > > Thanks & Regards > Anwesha > > On Fri, Mar 27, 2020, 7:25 PM Anwesha Mohapatra < > anwesha.mohapatra11(a)gmail.com> wrote: > >> Dear Sir, >> >> Firstly thank you, the previous fortran error got resolved when I used >> relative path instead of absolute and a shorter name for files. >> I have a few queries which I have mentioned below: >> ----------------------------------------------------------------------- >> 1. As per our previous discussion regarding multi-chain protein . I have >> used the template 1o7g to align against my query gene sequence. >> In the alignment I do see a chain break '/' in the sequence for the >> template however the query protein is aligned to the entire of the template >> protein (To both the chains A and B). >> But I do now this same query sequence aligns to A chain of the template >> as per my Blastp result. I can see lots of gaps added to the query gene >> when aligned to entire protein. Is this correct? >> I have attached the alignment files in the '*query.zip file'*. One file >> shows alignment of target with all chains of the template and the other >> aligned to only chain A. >> >> 2. Since the PDB file(1o7g) that I am using as a template has all the >> HETATOMS after the chains I have added the hetatms information after the >> chains in the alignment file as well. >> On modelling however I dont see the HETATMS added to the pdb file >> created. Moreoever I am unable to open the file on PyMol. (*** buffer >> overflow detected ***: python2.7 terminated). >> I have attached the file *'ModelError_Test1.zip*' which contains the >> input alignment file and the model generated in .pdb format. Could you tell >> me whether I have made any mistakes in the alignment file. >> >> 3. Since modelller only reads ATOMS and HETATOMS ,I tried to rewrite the >> PDB template file where the HETATOMS come directly after the chain. >> I have changed the alignment files accordingly. >> However, in this case modeller is not able to open the file and says its >> a corrupt pdb file. I have attached the pdb ,alignment and log files and >> shared in the attached folder named *"Query3.zip" * >> >> 4. I am unable to understand the concept of missing residues. >> If some residues are missing in the template then how should I proceed. >> Do I need to check for the presence of missing residues for each template >> file? >> >> Kindly help me with these queries. >> Thanks & Regards >> Anwesha >> >> On Tue, Mar 24, 2020 at 7:51 AM Anwesha Mohapatra < >> anwesha.mohapatra11(a)gmail.com> wrote: >> >>> Thank you Sir, I will try with shorter names and relative paths >>> >>> On Tue, Mar 24, 2020, 7:48 AM Modeller Caretaker < >>> modeller-care(a)salilab.org> wrote: >>> >>>> On 3/21/20 11:15 PM, Anwesha Mohapatra wrote: >>>> > I am sending the input files and the code I have been using . >>>> >>>> I think that what's happening here is that your alignment file names >>>> are >>>> really long, and you're hitting an internal limit inside Modeller (your >>>> input files work for me, but I can reproduce your problem if I put the >>>> files inside a directory with a very long name). This will be fixed in >>>> the next Modeller release. In the meantime you can work around it by >>>> using shorter file or directory names, or using relative rather than >>>> absolute paths to your alignment files. >>>> >>>> Ben Webb, Modeller Caretaker >>>> -- >>>> modeller-care(a)salilab.org https://salilab.org/modeller/ >>>> Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >>>> >>>

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ModellerError: read_te_290E> Number of residues in the alignment and pdb files are differen
by Joao Sartori 01 Apr '20

01 Apr '20

Hello, i'am struggling for days, i am new with modeller, i'm a grad student in biotechnology area and i'm trying to learn how to use modeller. I'm trying for days to model this sequence but i keep getting this error "modeller.ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different: 3525 4026 For alignment entry: 1 6nzk" follows the alignment.pir file, can anyone tell what can i do to fix that? Thanks >P1;6nzk structure:6nzk.pdb:15:A:1234:A:::: VIGDLKCTSDNINDKDTGPPPISTDTVDVTNGLGTYYVLDRVYLNTTLFLNGYYPTSGST YRNMALKGSVLLSRLWFKPPFLSDFINGIFAKVKNTKVIKDRVMYSEFPAITIGSTFVNT SYSVVVQPRTINKLQGLLEVSVCQYNMCEYPQTICHPNLGNHRKELWHLDTGVVSCLYKR NFTYDVNADYLYFHFYQEGGTFYAYFTDTGVVTKFLFNVYLGMALSHYYVMPLTCNSKLT LEYWVTPLTSRQYLLAFNQDGIIFNAVDCMSDFMSEIKCKTQSIAPPTGVYELNGYTVQP IADVYRRKPNLPNCNIEAWLNDKSVPSPLNWERKTFSNCNFNMSSLMSFIQADSFTCNNI DAAKIYGMCFSSITIDKFAIPNGRKVDLQLGNLGYLQSFNYRIDTTATSCQLYYNLPAAN VSVSRFNPSTWNKRFGFIEDSVFKPRPAGVLTNHDVVYAQHCFKAPKNFCPCKLNNGIGT CPAGTNYLTCTPDPITFTGTYKCPQTKSLVGIGEHCSGLAVKSDYCGGNSCTCRPQAFLG WSADSCLQGDKCNIFANFILHDVNSGLTCSTDLQKANTDIILGVCVNYDLYGILGQGIFV EVNATYYNSWQNLLYDSNGNLYGFRDYITNRTFMIRSCYSGRVSAAFHANSSEPALLFRN IKCNYVFNNSLTRQLQPINYFDSYLGCVVNAYNSTAISVQTCDLTVGSGYCVDYSTTGYR FTNFEPFTVNSVNDSLEPVGGLYEIQIPSEFTIGNMVEFIQTSSPKVTIDCAAFVCGDYA ACKSQLVEYGSFCDNINAILTEVNELLDTTQLQVANSLMNGVTLSTKLKDGVNFNVDDIN FSPVLGCLGSASSRSAIEDLLFDKVKLSDVGFVEAYNNCTGGAEIRDLICVQSYKGIKVL PPLLSENQFSGYTLAATSASLFPPWTAAAGVPFYLNVQYRINGLGVTMDVLSQNQKLIAN AFNNALYAIQEGFDATNSALVKIQAVVNANAEALNNLLQQLSNRFGAISASLQEILSRLD ALEAEAQIDRLINGRLTALNAYVSQQLSDSTLVKFSAAQAMEKVNECVKSQSSRINFCGN GNHIISLVQNAPYGLYFIHFSYVPTKYVTARVSPGLCIAGDRGIAPKSGYFVNVNNTWMY TGSGYYYPEPITENNVVVMSTCAVNYTKAPYVMLNVIGDLKCTSDNINDKDTGPPPISTD TVDVTNGLGTYYVLDRVYLNTTLFLNGYYPTSGSTYRNMALKGSVLLSRLWFKPPFLSDF INGIFAKVKNTKVIKDRVMYSEFPAITIGSTFVNTSYSVVVQPRTIN-------KLQGLL EVSVCQYNMCEYPQTICHPNLGNHRKELWHLDTGVVSCLYKRNFTYDVNADYLYFHFYQE GGTFYAYFTDTGVVTKFLFNVYLGMALSHYYVMPLTCNSKLTLEYWVTPLTSRQYLLAFN QDGIIFNAVDCMSDFMSEIKCKTQSIAPPTGVYELNGYTVQPIADVYRRKPNLPNCNIEA WLNDKSVPSPLNWERKTFSNCNFNMSSLMSFIQADSFTCNNIDAAKIYGMCFSSITIDKF AIPNGRKVDLQLGNLGYLQSFNYRIDTTATSCQLYYNLPAANVSVSRFNPSTWNKRFGFI EDSVFKPRPAGVLTNHDVVYAQHCFKAPKNFCPCKLN-----------NGIGTCPAGTNY LTCT----PDPITFTGTYKCPQTKSLVGIGEHCSGLAVKSDYCGGNSCTCRPQAFLGWSA DSCLQGDKCNIFANFILHDVNSGLTCSTDLQKANTDIILGVCVNYDLYGILGQGIFVEVN ATYYNSWQNLLYDSNGNLYGFRDYITNRTFMIRSCYSGRVSAAFHANSSEPALLFRNIKC NYVFNNSLTRQLQPINYFDSYLGCVVNAYNSTAISVQTCDLTVGSGYCVDYS-------- -TTGYRFTNFEPFTVNSVNDSLEPVGGLYEIQIPSEFTIGNMVEFIQTSSPKVTIDCAAF VCGDYAACKSQLVEYGSFCDNINAILTEVNELLDTTQLQVANSLMNGVTLSTKLKDGVNF NVDDINFSPVLGCLG----SASSRSAIEDLLFDKVKLSDVGFVEAYNNCTGGAEIRDLIC VQSYKGIKVLPPLLSENQFSGYTLAATSASLFPPWTAAAGVPFYLNVQYRINGLGVTMDV LSQNQKLIANAFNNALYAIQEGFDATNSALVKIQAVVNANAEALNNLLQQLSNRFGAISA SLQEILSRLDALEAEAQIDRLINGRLTALNAYVSQQLSDSTLVKFSAAQAMEKVNECVKS QSSRINFCGNGNHIISLVQNAPYGLYFIHFSYVPTKYVTARVSPGLCIAGDRGIAPKSGY FVNVNNTWMYTGSGYYYPEPITENNVVVMSTCAVNYTKAPYVMLNVIGDLKCTSDNINDK DTGPPPISTDTVDVTNGLGTYYVLDRVYLNTTLFLNGYYPTSGSTYRNMALKGSVLLSRL WFKPPFLSDFINGIFAKVKNTKVIKDRVMYSEFPAITIGSTFVNTSYSVVVQPRTINKLQ GLLEVSVCQYNMCEYPQTICHPNLGNHRKELWHLDTGVVSCLYKRNFTYDVNADYLYFHF YQEGGTFYAYFTDTGVVTKFLFNVYLGMALSHYYVMPLTCNSKLTLEYWVTPLTSRQYLL AFNQDGIIFNAVDCMSDFMSEIKCKTQSIAPPTGVYELNGYTVQPIADVYRRKPNLPNCN IEAWLNDKSVPSPLNWERKTFSNCNFNMSSLMSFIQADSFTCNNIDAAKIYGMCFSSITI DKFAIPNGRKVDLQLGNLGYLQSFNYRIDTTATSCQLYYNLPAANVSVSRFNPSTWNKRF GFIEDSVFKPRPAGVLTNHDVVYAQHCFKAPKNFCPCKLNNGIGTCPAGTNYLTCTPDPI TFTGTYKCPQTKSLVGIGEHCSGLAVKSDYCGGNSCTCRPQAFLGWSADSCLQGDKCNIF ANFILHDVNSGLTCSTDLQKANTDIILGVCVNYDLYGILGQGIFVEVNATYYNSWQNLLY DSNGNLYGFRDYITNRTFMIRSCYSGRVSAAFHANSSEPALLFRNIKCNYVFNNSLTRQL QPINYFDSYLGCVVNAYNSTAISVQTCDLTVGSGYCVDYSTTGYRFTNFEPFTVNSVNDS LEPVGGLYEIQIPSEFTIGNMVEFIQTSSPKVTIDCAAFVCGDYAACKSQLVEYGSFCDN INAILTEVNELLDTTQLQVANSLMNGVTLSTKLKDGVNFNVDDINFSPVLGCLGSASSRS AIEDLLFDKVKLSDVGFVEAYNNCTGGAEIRDLICVQSYKGIKVLPPLLSENQFSGYTLA ATSASLFPPWTAAAGVPFYLNVQYRINGLGVTMDVLSQNQKLIANAFNNALYAIQEGFDA TNSALVKIQAVVNANAEALNNLLQQLSNRFGAISASLQEILSRLDALEAEAQIDRLINGR LTALNAYVSQQLSDSTLVKFSAAQAMEKVNECVKSQSSRINFCGNGNHIISLVQNAPYGL YFIHFSYVPTKYVTARVSPGLCIAGDRGIAPKSGYFVNVNNTWMYTGSGYYYPEPITENN VVVMSTCAVNYTKAPYVMLN* >P1;cvd sequence:cvd:1:A:1353:A:::: ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ --------------MFLILLISLPTAFA-------------------------------- -----------------------------------VIGDLKCTSDNINDKDTGPPPISTD TVDVTNGLGTYYVLDRVYLNTTLFLNGYYPTSGSTYRNMALKGSVLLSRLWFKPPFLSDF INGIFAKVKNTKVIKDRVMYSEFPAITIGSTFVNTSYSVVVQPRTINSTQDGDNKLQGLL EVSVCQYNMCEYPQTICHPNLGNHRKELWHLDTGVVSCLYKRNFTYDVNADYLYFHFYQE GGTFYAYFTDTGVVTKFLFNVYLGMALSHYYVMPLTCNSKLTLEYWVTPLTSRQYLLAFN QDGIIFNAEDCMSDFMSEIKCKTQSIAPPTGVYELNGYTVQPIADVYRRKPNLPNCNIEA WLNDKSVPSPLNWERKTFSNCNFNMSSLMSFIQADSFTCNNIDAAKIYGMCFSSITIDKF AIPNGRKVDLQLGNLGYLQSFNYRIDTTATSCQLYYNLPAANVSVSRFNPSTWNKRFGFI EDSVFKPRPAGVLTNHDVVYAQHCFKAPKNFCPCKLNGSCVGSGPGKNNGIGTCPAGTNY LTCDNLCTPDPITFTGTYKCPQTKSLVGIGEHCSGLAVKSDYCGGNSCTCRPQAFLGWSA DSCLQGDKCNIFANFILHDVNSGLTCSTDLQKANTDIILGVCVNYDLYGILGQGIFVEVN ATYYNSWQNLLYDSNGNLYGFRDYIINRTFMIRSCYSGRVSAAFHANSSEPALLFRNIKC NYVFNNSLTRQLQPINYFDSYLGCVVNAYNSTAISVQTCDLTVGSGYCVDYSKNRRSRGA ITTGYRFTNFEPFTVNSVNDSLEPVGGLYEIQIPSEFTIGNMVEFIQTSSPKVTIDCAAF VCGDYAACKSQLVEYGSFCDNINAILTEVNELLDTTQLQVANSLMNGVTLSTKLKDGVNF NVDDINFSPVLGCLGSECSKASSRSAIEDLLFDKVKLSDVGFVEAYNNCTGGAEIRDLIC VQSYKGIKVLPPLLSENQISGYTLAATSASLFPPWTAAAGVPFYLNVQYRINGLGVTMDV LSQNQKLIANAFNNALYAIQEGFDATNSALVKIQAVVNANAEALNNLLQQLSNRFGAISA SLQEILSRLDALEAEAQIDRLINGRLTALNAYVSQQLSDSTLVKFSAAQAMEKVNECVKS QSSRINFCGNGNHIISLVQNAPYGLYFIHFSYVPTKYVTARVSPGLCIAGDRGIAPKSGY FVNVNNTWMYTGSGYYYPEPITENNVVVMSTCAVNYTKAPYVMLNTS------------- ------------------------------------------------------------ ---IPNLPDFKEELDQWFKN---------------------------------------- ----------------QTSVAPDLS----------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ -------------LDYINVTFLDLQVEMNRLQEAIKVLNQSYINLKDIGTY--------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------------------EYYVKWP---- ---------------WYVWLLICLAG------------------------------VAML VLLFFICCCTGCGTSCFKKCG------------GCCDDY-------TGYQELVIKTSHDD ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ --------------------*

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Questions about alignment and stereo clashes
by Li,Haoxi 30 Mar '20

30 Mar '20

Dear Modeller Users, Hope this email finds you well! I’m recently working on homology modeling of Dopamine D1 receptor. Can I ask two questions? 1. Am I able to use the sequence alignment from external sources, like Blast? 2. When the model was built, I found many stereo clashes in the structure. Is this normal? Is there any way that I can fix the stereo clashes? Thank you so much, Haoxi

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