modeller_usage

modeller_usage@salilab.org

3151 discussions

loop.py
by Jeff Reneker 24 Sep '20

24 Sep '20

Following the example in “Refining an existing PDB file” I want to “refine a region of an existing PDB file without comparative modeling.” The first thing I want to do is to get the loop.py script in the examples to work for any other structure. The only change I made is in this block of code from loop.py where I substitute 6aa0 for 1fdx as follows: m = MyLoop(env, inimodel='1fdx.B99990001.pdb', # initial model of the target sequence='1fdx', # code of the target loop_assess_methods=assess.DOPE) # assess loops with DOPE # loop_assess_methods=soap_loop.Scorer()) # assess with SOAP-Loop m = MyLoop(env, inimodel=‘6aa0.pdb', # initial model of the target sequence=‘6aa0', # code of the target loop_assess_methods=assess.DOPE) # assess loops with DOPE # loop_assess_methods=soap_loop.Scorer()) # assess with SOAP-Loop Then, I copy the 6aa0.pdb file to the appropriate directory. This is the error message at the tail end of the output: Traceback (most recent call last): File "loop.py", line 35, in <module> m.make() File "/usr/lib/python3.6/dist-packages/modeller/automodel/loopmodel.py", line 37, in make self.build_seq(self.inimodel, 1) File "/usr/lib/python3.6/dist-packages/modeller/automodel/loopmodel.py", line 169, in build_seq atmsel = self._check_select_loop_atoms() File "/usr/lib/python3.6/dist-packages/modeller/automodel/loopmodel.py", line 398, in _check_select_loop_atoms atmsel = self.select_loop_atoms() File "loop.py", line 18, in select_loop_atoms return selection(self.residue_range('19:', '28:')) File "/usr/lib/python3.6/dist-packages/modeller/coordinates.py", line 329, in residue_range start = self.residues[start]._num File "/usr/lib/python3.6/dist-packages/modeller/coordinates.py", line 259, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib/python3.6/dist-packages/modeller/util/modutil.py", line 23, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/lib/python3.6/dist-packages/modeller/coordinates.py", line 323, in _indxres raise KeyError("No such residue: %s" % indx) KeyError: 'No such residue: 19:' So, I’m not sure what the deal is because that’s how new I am to Modeller. Thanks, JR.

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Modeller 9.25 release
by Modeller Caretaker 09 Sep '20

09 Sep '20

A new version of Modeller, 9.25, 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 9.25 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.25 adds binaries and installation packages for Linux on both 32-bit and 64-bit ARM (e.g. on Raspberry Pi), allows overriding the prefix for automodel output file names, and fixes a number of bugs. See the Modeller manual for a full change log: https://salilab.org/modeller/9.25/manual/node40.html If you encounter bugs in Modeller 9.25, please see https://salilab.org/modeller/9.25/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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problem in anaconda
by Anas Jamshed 01 Sep '20

01 Sep '20

I successfully installed modeller through conda install modeller and also change the license key in config.py but when I try to run : from modeller import * it shows the following error : ModuleNotFoundError Traceback (most recent call last)<ipython-input-1-80c5cec1a705> in <module>()----> 1 from modeller import * ModuleNotFoundError: No module named 'modeller' plz help me

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Re: [modeller_usage] modeller_usage Digest, Vol 19, Issue 60
by Anas Jamshed 31 Aug '20

31 Aug '20

i used conda install modeller to install modeller and i dont know how to ser environment On Tue, Sep 1, 2020 at 1:20 AM <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 > https://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. Re: problem in anaconda (Ajasja Ljubeti?) > 2. Re: problem in anaconda (Eugene Radchenko) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 31 Aug 2020 12:50:54 -0700 > From: Ajasja Ljubeti? <ajasja.ljubetic(a)gmail.com> > To: Anas Jamshed <anasjamshed1994(a)gmail.com> > Cc: modeller_usage(a)salilab.org > Subject: Re: [modeller_usage] problem in anaconda > Message-ID: > < > CAEA_a5ze3PKdnxh5TKN9XO8MwoTBGLb2Lfjdz3pzd4Lb9cW-gg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Anas, > > Did you activate the conda environment into which you have installed > modeller? > > What command lines did you use to install modeller and to start ipython? > > Best, > Ajasja > > > On Mon, Aug 31, 2020 at 12:38 PM Anas Jamshed <anasjamshed1994(a)gmail.com> > wrote: > > > I successfully installed modeller through conda install modeller and also > > change the license key in config.py but when I try to run : > > > > > > from modeller import * > > > > it shows the following error : > > > > ModuleNotFoundError Traceback (most recent call > last)<ipython-input-1-80c5cec1a705> in <module>()----> 1 from modeller > import * > > ModuleNotFoundError: No module named 'modeller' > > > > > > > > plz help me > > _______________________________________________ > > modeller_usage mailing list > > modeller_usage(a)salilab.org > > https://salilab.org/mailman/listinfo/modeller_usage > > >

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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.

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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

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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

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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

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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

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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…

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