- modeller_usage - salilab.org

BIOVIA Dassault Systèmes’ North American User Conference
by Modeller Caretaker 28 Feb '20

28 Feb '20

Posting on behalf of the folks at BIOVIA: Dear Colleagues We would like to invite you to attend BIOVIA Dassault Systèmes’ North American User Conference (https://www.3dsbiovia.com/biovia-users-2020.html) April 6-8, at the Marriott Marquis San Diego Marina (https://www.marriott.com/hotels/travel/sandt-marriott-marquis-san-diego-mar…) Spring is a wonderful time to be in San Diego with sunny skies, moderate temperatures and fresh ocean breezes. This valuable user conference will feature one day of hands-on training (April 6) and two days of proven best practices and previews of the latest BIOVIA solutions (April 7-8). Our track on upstream biopharmaceutical research includes discussions on how AI and machine learning can help guide drug discovery and development as well as a deep dive into the latest modeling and simulation techniques for small and large molecule R&D. Come along and see how MODELER impacts lead design in discovery R&D. For more information on the conference, see our AGENDA at https://www.3dsbiovia.com/biovia-users-2020-agenda.html. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

1 0

restrains.make_distance function
by Mariana GONZALEZ MEDINA 27 Feb '20

27 Feb '20

Hello, I am trying to obtain the stereochemical restraints between Calphas in two of my templates. However, I am not sure how to set the parameter maximal_distance. How do I chose the right distance to set the maximal distance between Calphas that I need to use to obtain the distance restraints? Thank you! Best, Mariana

2 1

Integrate X-ray structure with missing domains using templates
by Stefano Motta 25 Feb '20

25 Feb '20

Dear Modeller users, I'm trying to build a model of a hetero-dimer starting from an X-ray structure. Each monomer have 3 domains (6 in total). An X-ray structure of part of the complex (two domains of each monomer) exist and I want to complete the model with the two missing domains (one for each monomer). I would use the X-ray of homologous proteins for which all 6 domains are available. Which would be the best approach? I want to keep the X-ray part as frozen as possible, and only model the two missing domains from the template (both structure and orientation in the complex). Thank you very much in advance for any tips Stefano -- ________________________________________________________________ Stefano Motta PhD Email: stefano.motta(a)unimib.it <s.motta17(a)campus.unimib.it> *Field of study:* Molecular Modeling, and Proteins Molecular Dynamics Università degli Studi di Milano Bicocca Department of Earth and Environmental Sciences Piazza dell'Ateneo Nuovo, 1 - 20126, Milano (Italy). _________________________________________________________________ -- ________________________________________________________________ Stefano Motta PhD Email: stefano.motta(a)unimib.it <s.motta17(a)campus.unimib.it> *Field of study:* Molecular Modeling, and Proteins Molecular Dynamics Università degli Studi di Milano Bicocca Department of Earth and Environmental Sciences Piazza dell'Ateneo Nuovo, 1 - 20126, Milano (Italy). _________________________________________________________________

3 6

Charmm error : missing residues
by Yogesh Sharma 18 Feb '20

18 Feb '20

Hi everyone I used modeller to generate structure of my membrane protein. But when I am using that structure in charmm gui to build setup. I am getting error stating missing residues or error in pdb. How can I rectify it? -- * with regards* *Yogesh Sharma*

2 1

Modeller will only read the first 4096 characters of this line.
by Yogesh Sharma 18 Feb '20

18 Feb '20

Hi iam new to modeller. readlinef__W> File: pdb_95.pir, Line: 421 Modeller will only read the first 4096 characters of this line. readlinef__W> File: pdb_95.pir, Line: 29819 Modeller will only read the first 4096 characters of this line. readlinef__W> File: pdb_95.pir, Line: 29829 Modeller will only read the first 4096 characters of this line. readlinef__W> File: pdb_95.pir, Line: 29839 Modeller will only read the first 4096 characters of this line. readlinef__W> File: pdb_95.pir, Line: 29846 Modeller will only read the first 4096 characters of this line. readlinef__W> File: pdb_95.pir, Line: 29852 No more warnings will be printed for truncated lines in this file. Are these warnings safe?

2 1

how to generate the ini file only
by Li Xue 06 Feb '20

06 Feb '20

Hello all, Does anyone know how to ask modeller to generate the ini file and stop? I tried the following but failed: a = automodel(env, alnfile='my_alignment.ali', > knowns='3mrb', sequence='query', > assess_methods=assess.DOPE) > aln = alignment(env) > aln.append(file='T3mrb_Q1duz.ali') > a.transfer_xyz(aln) Best, Li

2 3

Molecules MEX and CME
by Daniel Evans 03 Feb '20

03 Feb '20

Hi all- The MODELLER documentation at https://salilab.org/modeller/manual/node149.html#MEMB:iodata.convertmodres says the following: "Some special handling is done for certain commonly-used modified residues. The MSE residue type is mapped to the regular MET amino acid, and the SE atom in this residue is mapped to SD. The MEX and ABU residue types are both mapped to CYS." According to https://salilab.org/archives/modeller_usage/2003/msg00051.html the reason for this is that MEX is "cysteine bridged with beta-mercaptoethanol". I recently encountered PDB ID 3OW6. This structure includes a ligand labeled MEX. The ligand does not resemble CYS, and the presence of MEX causes an error. I'm reluctant to set io_data.convert_modres to False, because I'd like to handle other modified residues (ex. MSE). I was able to work around the issue, so it didn't impact me too much. But I thought I should say something in case others run into the same issue. I see that the ligand CME does resemble CYS, with beta-mercaptoethanol attached through a disulfide bond. Is it possible that MEX and CME are switched? Best, Daniel Evans

2 1

Use modeller with slurm
by Mariana GONZALEZ MEDINA 10 Jan '20

10 Jan '20

Hello, I would like to know if there is a way in which I can use parallel jobs to create 1,000 models with slurm, since I can't use the sge_qsub_job command. Thank you. Mariana

2 1

Modeller produces primary structure only
by Danilo Boskovic 03 Jan '20

03 Jan '20

Dear all, I tried to model part of my missing protein from a template but i fail to get proper structure (its just a linear line of amino acids) even though i followed the tutorial 100%. My script (it is properly spaced in my file): from modeller import * from modeller.automodel import * log.verbose() env = environ() env.io.atom_files_directory = ['.', './template_struc'] env.io.hetatm = True env.io.water = True class MyModel(automodel): def select_loop_atoms(self): return selection( self.residue_range('1154', '1298')) a = MyModel(env, alnfile = 'alignment.ali', knowns = '5xwp', sequence = 'sequence', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 1000 a.make() Alignment was proper and i checked every missing residue one by one. Dope scores are negative, GA scores 1.00). My templates are in /template_struc and this was tested to be working when i produced .ali files for my templates. So whats the problem? sincerely, D.B.

2 2

Error - Unavailable server
by CYNTHIA CHRISTINA DE OLIVEIRA 26 Dec '19

26 Dec '19

Hello, I am trying to use the “Modeller (loops/refinement)” tool present in Chimera software and the following error message is displayed: NonChimeraError: Web service appears to be down. See Reply Log for more details. Service 'opal:Modeller9v8Service' is unavailable. See Reply Log for more details. Is this a temporary server issue or is there a problem with the version of the program I am using (Modeller9v8)? In the latter case, what should I do to resolve this situation? Thanks in advance, Cynthia de Oliveira

2 1