- modeller_usage - salilab.org

Socket modules and Chimera
by Casey Becker 31 Aug '20

31 Aug '20

Hello, I'm working with parallel jobs, and I can run them fine directly through IDLE, but when I try to run them through Chimera, I get an error that I lack the socket module necessary to make them work - hence me using IDLE instead. However, I would really like to be able to run my scripts directly through Chimera, but I'm having trouble finding a fix to make this happen. I've attached the two scripts I'm currently using, as well as the reply log message. Thank you.

2 1

Query related modeller script
by Aanila Ghazala 31 Aug '20

31 Aug '20

Hello, I am unable to run the script in modeller 9.24 ,i am getting log files while running the script ,please help me solve this issue . Regards, Ghazala Masood

2 1

Question automodel from NMR
by Brian Wiley 14 Aug '20

14 Aug '20

Hi Ben/Team, I can't seem to find documentation on this. If I am modelling a sequence through a PDB file that was an NMR experiment with 10 or 20 models, how does Modeller handle this? Does it just chose the first model list in PDB? Thanks, Brian

2 2

Modeller Model Building Inquiry using existing PDB cooridnates
by Joel Subach 13 Aug '20

13 Aug '20

Hi I want to build a C and N tail and one cytoplasmic loop that are missing from the PDB Cryo-EM 3-D coordinate file of a transmembrane protein. These regions were too dynamic during their Cryo-EM process and therefore are left out of the structural file that the investigators input into the PDB. Is there a way to model just these missing tails and one loop WITH the rest of the protein meaning not modeling the regions separately and then stitching them into the existing PDB coordinate file subsequently? I did not see this methodology amongst the Modeller tutorials but think it is best to maintain the fidelity of the protein as a whole i.e. non-stitching. Thanks:) Joel

2 1

Change ROOT_NAME for automodel.make()
by Brian Wiley 07 Aug '20

07 Aug '20

Hi, I thought this would be extremely easy to find if you can do, but I guess not. I would like to be able to change the ROOT_NAME of the model from automodel.make(). For instance: a = automodel(env, alnfile = 'TSC2_6ssh.ali', knowns = ('6ssh'), sequence = 'TSC2_HUMAN') a.make() # Here I want the prefix to be 'TSC2_6ssh' and not 'TSC2_HUMAN' so all files and pdb file at end would be TSC2_6ssh.B99990001.pdb Is this possible? Brian Wiley JHU

3 5

Re: [modeller_usage] modeller_usage Digest, Vol 19, Issue 52
by Brian Wiley 07 Aug '20

07 Aug '20

Nevermind. I just created a new function reset_defaults() to rewrite self.set_defaults() in automodel and I can get it. Thanks for your help. -----Original Message----- From: modeller_usage <modeller_usage-bounces(a)salilab.org> On Behalf Of modeller_usage-request(a)salilab.org Sent: Friday, August 7, 2020 6:47 PM To: modeller_usage(a)salilab.org Subject: modeller_usage Digest, Vol 19, Issue 52 External Email - Use Caution Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsalilab.o… 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. Re: Change ROOT_NAME for automodel.make() (Modeller Caretaker) 2. Re: Change ROOT_NAME for automodel.make() (Brian Wiley) ---------------------------------------------------------------------- Message: 1 Date: Fri, 7 Aug 2020 15:33:39 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> To: Brian Wiley <bwiley4(a)jhu.edu>, "modeller_usage(a)salilab.org" <modeller_usage(a)salilab.org> Subject: Re: [modeller_usage] Change ROOT_NAME for automodel.make() Message-ID: <9ffc2904-4103-32e6-3c62-a4f8fd11a4f7(a)salilab.org> Content-Type: text/plain; charset=windows-1252; format=flowed On 8/7/20 2:21 PM, Brian Wiley wrote: > a = automodel(env, > alnfile = 'TSC2_6ssh.ali', > knowns = ('6ssh'), > sequence = 'TSC2_HUMAN') > > a.make() # Here I want the prefix to be 'TSC2_6ssh' and not > 'TSC2_HUMAN' so all files and pdb file at end would be > TSC2_6ssh.B99990001.pdb automodel is written under the assumption that files are named for the sequence. If you want to name the output PDB files differently, that's straightforward; just override get_model_filename() as per https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsalilab.o… If you want to name the other output files differently, there isn't currently a mechanism for that, but it would be easy enough to modify the Python code to do so. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsalilab.o… Modeller mail list: https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsalilab.o… ------------------------------ Message: 2 Date: Fri, 7 Aug 2020 22:47:13 +0000 From: Brian Wiley <bwiley4(a)jhu.edu> To: Modeller Caretaker <modeller-care(a)salilab.org>, "modeller_usage(a)salilab.org" <modeller_usage(a)salilab.org> Subject: Re: [modeller_usage] Change ROOT_NAME for automodel.make() Message-ID: <BYAPR01MB3622652122731C17B45282EAEF490(a)BYAPR01MB3622.prod.exchangelabs.com> Content-Type: text/plain; charset="us-ascii" Thanks, I would like to change the root_name for all the output file. It's kind of silly there is not class root_name attribute in automodel. Then you could just name that. I am having trouble overriding the __init__ in automodel because it calls self.set_defaults(). Brian -----Original Message----- From: Modeller Caretaker <modeller-care(a)salilab.org> Sent: Friday, August 7, 2020 6:34 PM To: Brian Wiley <bwiley4(a)jhu.edu>; modeller_usage(a)salilab.org Subject: Re: [modeller_usage] Change ROOT_NAME for automodel.make() External Email - Use Caution On 8/7/20 2:21 PM, Brian Wiley wrote: > a = automodel(env, > alnfile = 'TSC2_6ssh.ali', > knowns = ('6ssh'), > sequence = 'TSC2_HUMAN') > > a.make() # Here I want the prefix to be 'TSC2_6ssh' and not > 'TSC2_HUMAN' so all files and pdb file at end would be > TSC2_6ssh.B99990001.pdb automodel is written under the assumption that files are named for the sequence. If you want to name the output PDB files differently, that's straightforward; just override get_model_filename() as per https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsalilab.o… If you want to name the other output files differently, there isn't currently a mechanism for that, but it would be easy enough to modify the Python code to do so. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsalilab.o… Modeller mail list: https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsalilab.o…

1 0

Re: [modeller_usage] Treading onto known PDB template
by Modeller Caretaker 20 Jul '20

20 Jul '20

On 7/6/20 2:49 PM, Geoffrey Woollard wrote: > Can I do the modelling in the context of the tetramer? Otherwise I would > have to just do it with the protomer, and then delete out parts that > were clashing. > > Are there options for applying symmetry during modelling? Sure, this is also covered in the manual: https://salilab.org/modeller/9.24/manual/node29.html Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

2 5

Re: [modeller_usage] reg: modeling against docked protein-ligand complex
by Anwesha Mohapatra 16 Jul '20

16 Jul '20

Hello Sir, Could you tell me where am going wrong? On Wed, Jul 15, 2020, 2:10 PM Anwesha Mohapatra < anwesha.mohapatra11(a)gmail.com> wrote: > > > <https://mail.google.com/mail/u/0?ui=2&ik=2650c6341a&attid=0.1&permmsgid=msg…> > Hello Sir, > > I have a protein (6eqe.pdb) which I have docked to a ligand using autodock > vina. I want to model my query gene taking this receptor-ligand complex as > the template. The ligand is identified as UNK in the pdb file. On modeling > I am not getting all the atoms of the ligand in the modelled output (Only 1 > carbon and 1 oxygen).Attached to this mail are the template file which has > been docked to the ligand *(6eqe_bhet.pdb) , *the modelled protein with > incomplete/erroneous ligand > *(ARN19002.1_Rhizobacter_gummiphilus_NS21.B99990001.pdb)* and the > alignment file for the same* > (ARN19002.1_Rhizobacter_gummiphilus_NS21.ali) . * > Could you please look into the files? > > Kindly let me know where I am going wrong. > > Thanks and regards > Anwesha >

1 0

Multiple CPUs
by Casey Becker 06 Jul '20

06 Jul '20

Hello again, I'm trying to use modeller directly through python's IDLE interface to run a parallel job. I've attached my script and also the python core file that's created up to a point, because it stops before it actually makes the models. Three files with .slave0, .slave1, and .slave2 are created, but when edited with notepad, show an error. I've attached one of them as well. Thanks.

2 1

Treading onto known PDB template
by Geoffrey Woollard 06 Jul '20

06 Jul '20

I'm studying a transmembrane ion channel (protein 1). There are structures of protein 1 in a closed conformation, and I am interested in the open conformation. There is a very similar protein in an open conformation (protein 2). So I am trying to thread the sequence of protein 1 onto the atomic model of protein 2. I know the template. I tried robetta and swiss prot for this. How should I do things with modeller? Could someone point me to a tutorial? The sequences are quite similar, except for some insertions. I know my protein very well and am looking for a protein modelling approach where I can have low level control, and manual manipulation at the sequence alignment and structure level. I don't need something that does everything automagically. -- Geoffrey Woollard, MSc PhD student Department of Medical Biophysics, University of Toronto Princess Margaret Cancer Centre, University Health Network

2 2