- modeller_usage - salilab.org

modeller error; " ValueError: too many arguments to unpack"
by Sourav Pal 19 Jan '18

19 Jan '18

I am going to generate a monomer from one single Template (tseq1) by modeller. But there one problem is arised. I have a only one template. According to the basic tutorial of modeller.. I made alignment file like this, (where tseq1 is single template file)from modeller import *env = environ()aln = alignment(env)for (pdb, chain) in (('tseq1', 'A')):m = model(env, file=pdb, model_segment=('FIRST:'+chain, 'LAST:'+chain))aln.append_model(m, atom_files=pdb, align_codes=pdb+chain)aln.malign()aln.malign3d()aln.compare_structures()aln.id_table(matrix_file='family.mat')env.dendrogram(matrix_file='family.mat', cluster_cut=-1.0)That time it was failed to run by showing the following error"ValueError:too many values to unpack" .can anyone tell me where is the problem? Thank you.Best Regards. Sourav Pal JRF

2 1

Modelling of Homotrimeric protein without biological assembly
by Sourav Pal 17 Jan '18

17 Jan '18

Actually I want to build a homology model of a human homotrimeric protein from a FASTA sequences. After BLAST I got a template which is 91% identical but it is originated from Mouse organism. and it is cryo EM structure.From there, I build a single monomeric chain of that human protein by Homology modelling. But it doesn't contain any biological assembly or asymmetric unit. So that, i am unable to build its trimeric structure. so, can you help me in two sections;1) how to build its homotrimeric structure?2) is there any way to generate the biological assembly coordinates from homology protein?Thanks in advance.Best regards.

1 0

Optimization of an existing loop model
by Claire Marks 17 Jan '18

17 Jan '18

Hi! I would like to use MODELLER to optimize some models that I have generated as part of a loop prediction protocol. The loop conformations were built onto crystal structures downloaded onto the PDB; ideally I only want the loop region to be optimized. I thought the code given on the following web page would be what I should use, however it doesn't seem to do what I want: https://salilab.org/modeller/manual/node36.html This still generates the initial 'straight' conformation that the MODELLER loop modelling algorithm starts from; it doesn't start from the loop conformation in the file I provided. Is anyone able to shed some light on this for me? Claire

2 1

Fw: Builing of homotrimer from a homology structure
by Sourav Pal 16 Jan '18

16 Jan '18

Hello, Actually I want to build a homology model of a human homotrimeric protein from a FASTA sequences. After BLAST I got a template which is 91% identical but it is originated from Mouse organism. And it is the Cryo-EM structure. >From there, I build a single monomeric chain of that human protein by Homology modelling. But it doesn't contain any biological assembly or asymmetric unit. So that, i am unable to build its trimeric structure. so, can you help me in two sections; 1) how to build its homotrimeric structure? 2) is there any way to generate the biological assembly coordinates from homology protein? Thanks in advance. Best regards. Sourav PalSenior Project FellowResearch Group of Dr. Arindam TalukdarCSIR-Indian Institute of Chemical BiologyJadavpur, Kolkata, India

1 0

read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file
by Andrea Spinelli 16 Jan '18

16 Jan '18

Hello everybody! I am new to Modeller, so please excuse me if my question seems stupid. I build a model from multiple templates following your tutorial (https://salilab.org/modeller/tutorial/advanced.html) It's working. When I try to develop a module function with scripts, the 'align2d_mult.py' give me the following error: ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 3) = P02489 I can't understand because my sequence.ali file is built in the right way: >P1;P02489 sequence:P02489:::::::0.00: 0.00 MDVTIQHPWFKRTLGPFYPSRLFDQFFGEGLFEYDLLPFLSSTISPYYRQSLFRTVLDSGISEVRSDRDKFVIFLDVKHFSPEDLTVKVQDDFVEIHGKHNERQDDHGYISREFHRRYRLPSNVDQSALSCSLSADGMLTFCGPKIQTGLDATHAERAIPVSREEKPTSAPSS* In attached you can find the python module with the function of script Thank you. Andrea

3 7

mail about an error
by vidhya sankar 02 Jan '18

02 Jan '18

Dear users I am beginner of modeller when i do basic homology modeling i got error as follows read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 1) Alignment MNQVQRSNELSQERTARLNELQRALVMMDSDFRQIALRQTRTNGEEPSKKLLHWA PDB TVGYLEQKMFAAMVADNQMAMVMLNPKNLKASNGEEELAGQTWYWKVAPVATTQP Match * Alignment residue type 11 (M, MET) does not match pdb residue type 17 (T, THR), for align code 2ret (atom file 2ret), pdb residue number "30", chain "A" Please check your alignment file header to be sure you correctly specified the starting and ending residue numbers and chains. The alignment sequence must match that from the atom file exactly. Even i searched the mailing list i got information but i am not able to understand error . Please is very useful if you point out where i have committed the mistake Thanks in advance with high regardsS.vidhyasnakr

2 1

grid_search and hetatm
by Carlo Camilloni 21 Dec '17

21 Dec '17

Dear Modellers I am fitting a protein with cofactors in a cryo-em density using grid_search. It works but the fitted structure does’t include anymore the HETATM fields with the cofactors. My input looks env = environ() env.io.hetatm = True env.libs.topology.read(file='$(LIB)/top_heav.lib') # read topology env.libs.parameters.read(file='$(LIB)/par.lib') # read parameters … den.grid_search(em_density_format='MRC', num_structures=1, em_pdb_name=struct, chains_num=[1], start_type='SPECIFIC', number_of_steps=1000, angular_step_size=30., temperature=150., best_docked_models=1, translate_type='RANDOM', em_fit_output_file='modem.log’) Is this something that is not supported or I am doing something wrong? Best, Carlo _______ Department of Biosciences University of Milano Via Celoria 26 - 20133 Milano, Italy www: sites.unimi.it/camilloni <http://sites.unimi.it/camilloni> www: bioscienze.bio <http://bioscienzebio.unimi.it/>

2 1

error in running mod9.19
by Saman Yousuf Ali 04 Dec '17

04 Dec '17

I have recently installed modeller 9.19 in my windows system with python 3.63 (64-bit). It was running perfectly fine. Even yesterday,I run basic modelling tutorial but now when I run command mod9.19 build_profile.py It gives me following error; 'md9.19' is not recognized as an internal and external command, operable program or batch file. Kindly help me to fix this issue. Regards Saman

2 1

Disulphide bonds forming with several cysteines
by Lenka 06 Nov '17

06 Nov '17

Hello everybody, I am having a problem with my model. I am new to Modeller but I googled and couldn't find an answer. I am selecting the residues I want to form the disulphide bonds but there is a one cys that gets in a way and when I visualize the disulphides in Pymol, I can see three cysteines are bonded together. How can I prevent that? Here are my patches: class MyModel(automodel): def special_patches(self, aln): self.patch(residue_type='DISU', residues=(self.residues['76'], self. residues['241'])) self.patch(residue_type='DISU', residues=(self.residues['46'], self. residues['122'])) self.patch(residue_type='DISU', residues=(self.residues['188'], self.residues['206'])) self.patch(residue_type='DISU', residues=(self.residues['105'], self.residues['202'])) self.patch(residue_type='DISU', residues=(self.residues['265'], self.residues['228'])) self.patch(residue_type='DISU', residues=(self.residues['113'], self.residues['183'])) self.patch(residue_type='DISU', residues=(self.residues['127'], self.residues['171'])) Since Modeller only reads ATOM and HETEATOM records I dont really understand why is this happening. Thank you for any help!

2 1

Help with Modelface
by Daravuth Cheam 25 Oct '17

25 Oct '17

Hi, I recently installed Modelface, and I'm having issues trying to get it set up. It first prompts me to enter the password, followed by the Modeller version and installation path of Modeller. I am able to enter the password and Modeller version (version 9.19), but I can't get the installation path of Modeller correct. I entered the default path which is C:\Program Files\Modeller9.19, but I got a message saying "Modeller executables were not found." I checked to make sure that the Modeller9.19 folder is in Program Files, and it is. The Modeller.exe file is specifically within the x86_64-w64 folder found in C:\Program Files\Modeller9.19\lib\x86_64-w64\mod9.19. I tried typing this in the command prompt, but I got the same "Modeller executables were not found" message. Any help with this would be appreciated. Thanks in advance! Sincerely, Daravuth Cheam Portland State University Biology Department The Estes Lab

2 1