Hello
I am using the following script file:
### begin script ###
from pymol import cmd
from glob import glob
# Edit these two variables with the paths to your files
wt_file = "D:\STUDY\STRUCTURE_PPT\RMSD\Pymol\Original\1APS.pdb"
mut_glob = "D:\STUDY\STRUCTURE_PPT\RMSD\Pymol\models\1APS\1APS_*.pdb"
# load the wild-type pdb
cmd.load(wt_file,"wt")
# loop through the mutants
for file in glob(mut_glob):
print file
cmd.load(file,"mut")
rms = cmd.align("wt","mut")[0]
print " %s rmsd: %s" % (file,rms)
cmd.delete("mut")
### end script ###
I ran the above script using Pymol. But I am receiving the following error:
PyMOL>run D:/STUDY/STRUCTURE_PPT/RMSD/Pymol/mut_rmsd.py
ExecutiveProcessPDBFile-Error: Unable to open file
'D:\STUDY\STRUCTURE_PPT\RMSD\Pymol\OriginalAPS.pdb'.
Traceback (most recent call last):
File "C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parsing.py", line
455, in run_file
execfile(file,global_ns,local_ns)
File "D:/STUDY/STRUCTURE_PPT/RMSD/Pymol/mut_rmsd.py", line 11, in <module>
cmd.load(wt_file,"wt")
File "C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\importing.py", line
878, in load
if _self._raising(r,_self): raise pymol.CmdException
CmdException: <pymol.CmdException instance at 0x06FF1580>
Can anyone help please.
On Thu, Jan 9, 2014 at 4:48 PM, Om Shiv <harhaalmekhu...@gmail.com> wrote:
> Thanks Jared
>
>
> On Thu, Jan 9, 2014 at 12:03 AM, Sampson, Jared
> <jared.samp...@nyumc.org>wrote:
>
>> Hi Om -
>>
>> I hope you don't mind me posting your questions back to the list.
>> (When replying to this list, you have to use Reply All, otherwise it just
>> goes to the sender.)
>>
>> Also, a quick disclaimer: I haven't used PyMOL on Windows in over 5
>> years, so what I'm saying may not be entirely accurate. (Others, please
>> correct me if there's anything incorrect here.)
>>
>>
>> Hi I have installed Pymol in windows 7 platform. Why does it not
>> allow me to save the script in the Pymol folder ?
>>
>> Is there any way to save it in Pymol working directory ?
>>
>>
>> I don't think you really want to save it to the folder where PyMOL is
>> installed (if that's what you mean by "the Pymol folder"). The working
>> directory is the directory from which PyMOL is launched. You can see where
>> this is by typing `pwd` at the PyMOL command prompt. Some other shell
>> commands work as well, such as `cd` and `ls`.
>>
>>
>> Thanks for your guidance.
>>
>> I have modified your script as follows:
>>
>> ### begin script ###
>>
>> from pymol import cmd
>> from glob import glob
>>
>> # Edit these two variables with the paths to your files
>> wt_file = "D:\STUDY\STRUCTURE_PPT\RMSD\Pymol\Original\1APS.pdb"
>> mut_glob = "D:\STUDY\STRUCTURE_PPT\RMSD\Pymol\models\1APS\1APS_*.pdb"
>>
>> # load the wild-type pdb
>> cmd.load(wt_file,"wt")
>>
>> # loop through the mutants
>> for file in glob(mut_glob):
>> print file
>> cmd.load(file,"mut")
>> rms = cmd.align("wt","mut")[0]
>> print " %s rmsd: %s" % (file,rms)
>> cmd.delete("mut")
>>
>> ### end script ###
>>
>> Used the following command from the command line: run
>> D:\STUDY\STRUCTURE_PPT\RMSD\mut-rmsd.py
>>
>> But I am receiving the following error:
>>
>> IOError: [Errno 2] No such file or directory: 'D:
>> \\STUDY\\STRUCTURE_PPT\\RMSD\\mut-rmsd.py'
>>
>> Please help.
>> thanks
>>
>>
>> Maybe try using the GUI:
>>
>> 1. File > Log... - create a log file (I usually call mine "log.pml"),
>> which will be useful later.
>> 2. File > Run... - navigate to your mut-rmsd.py file and run it.
>> 3. Go back and open your log file to see what the command looked like
>> when you ran the script.
>>
>> PyMOL log files are very widely useful for finding out how to translate
>> GUI actions into scriptable commands.
>>
>> Hope that helps!
>>
>> Cheers,
>> Jared
>>
>>
>>
>> On Wed, Jan 8, 2014 at 1:13 AM, Sampson, Jared
>> <jared.samp...@nyumc.org>wrote:
>>
>>> Hi Om -
>>>
>>> Here is another option that loads only one mutant at a time. You can
>>> save the following as a Python script (e.g., "mut-rmsd.py") and run it from
>>> the PyMOL command line by typing `run mut-rmsd.py` (with a full or relative
>>> path if it's not in PyMOL's working directory).
>>>
>>> For more information about these functions, you can also check out a
>>> few things on the PyMOL Wiki:
>>>
>>> http://pymolwiki.org/index.php/Process_All_Files_In_Directory
>>> http://pymolwiki.org/index.php/Align
>>>
>>> ### begin script ###
>>>
>>> from pymol import cmd
>>> from glob import glob
>>>
>>> # Edit these two variables with the paths to your files
>>> wt_file = "wt.pdb"
>>> mut_glob = "mut/*.pdb"
>>>
>>> # load the wild-type pdb
>>> cmd.load(wt_file,"wt")
>>>
>>> # loop through the mutants
>>> for file in glob(mut_glob):
>>> print file
>>> cmd.load(file,"mut")
>>> rms = cmd.align("wt","mut")[0]
>>> print " %s rmsd: %s" % (file,rms)
>>> cmd.delete("mut")
>>>
>>> ### end script ###
>>>
>>> Hope that helps.
>>>
>>> Cheers,
>>> Jared
>>>
>>> --
>>> Jared Sampson
>>> Xiangpeng Kong Lab
>>> NYU Langone Medical Center
>>> 550 First Avenue
>>> New York, NY 10016
>>> 212-263-7898
>>> http://kong.med.nyu.edu/
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Jan 7, 2014, at 11:58 AM, Om Shiv <harhaalmekhu...@gmail.com> wrote:
>>>
>>> Hello All
>>>
>>> I am a new user to Pymol and Python.
>>>
>>> I have a PDB Structure with single chain (A) and I have modeled 500
>>> single point mutants of this wild structure.
>>>
>>> Now for each such 500 modeled structures, I would like to calculate
>>> RMSD (ALL ATOMS) with the wild type PDB structure.
>>>
>>> Can anybody help me with the script to automate calculation of 500 RMSD
>>> calculations using PYMOL ?
>>>
>>> Secondly, what threshold value of RMSD can be considered above which we
>>> can say that the mutant structure is considerably different than the wild
>>> type ?
>>>
>>> Thanks in advance.
>>>
>>> ------------------------------------------------------------------------------
>>> Rapidly troubleshoot problems before they affect your business. Most IT
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>>
>>
>> ------------------------------------------------------------
>> This email message, including any attachments, is for the sole use of the
>> intended recipient(s) and may contain information that is proprietary,
>> confidential, and exempt from disclosure under applicable law. Any
>> unauthorized review, use, disclosure, or distribution is prohibited. If you
>> have received this email in error please notify the sender by return email
>> and delete the original message. Please note, the recipient should check
>> this email and any attachments for the presence of viruses. The
>> organization accepts no liability for any damage caused by any virus
>> transmitted by this email.
>> =================================
>>
>
>
On Wed, Jan 8, 2014 at 1:13 AM, Sampson, Jared <jared.samp...@nyumc.org>wrote:
> Hi Om -
>
> Here is another option that loads only one mutant at a time. You can
> save the following as a Python script (e.g., "mut-rmsd.py") and run it from
> the PyMOL command line by typing `run mut-rmsd.py` (with a full or relative
> path if it's not in PyMOL's working directory).
>
> For more information about these functions, you can also check out a few
> things on the PyMOL Wiki:
>
> http://pymolwiki.org/index.php/Process_All_Files_In_Directory
> http://pymolwiki.org/index.php/Align
>
> ### begin script ###
>
> from pymol import cmd
> from glob import glob
>
> # Edit these two variables with the paths to your files
> wt_file = "wt.pdb"
> mut_glob = "mut/*.pdb"
>
> # load the wild-type pdb
> cmd.load(wt_file,"wt")
>
> # loop through the mutants
> for file in glob(mut_glob):
> print file
> cmd.load(file,"mut")
> rms = cmd.align("wt","mut")[0]
> print " %s rmsd: %s" % (file,rms)
> cmd.delete("mut")
>
> ### end script ###
>
> Hope that helps.
>
> Cheers,
> Jared
>
> --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> 550 First Avenue
> New York, NY 10016
> 212-263-7898
> http://kong.med.nyu.edu/
>
>
>
>
>
>
> On Jan 7, 2014, at 11:58 AM, Om Shiv <harhaalmekhu...@gmail.com> wrote:
>
> Hello All
>
> I am a new user to Pymol and Python.
>
> I have a PDB Structure with single chain (A) and I have modeled 500
> single point mutants of this wild structure.
>
> Now for each such 500 modeled structures, I would like to calculate RMSD
> (ALL ATOMS) with the wild type PDB structure.
>
> Can anybody help me with the script to automate calculation of 500 RMSD
> calculations using PYMOL ?
>
> Secondly, what threshold value of RMSD can be considered above which we
> can say that the mutant structure is considerably different than the wild
> type ?
>
> Thanks in advance.
>
> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics
> Pro!
>
> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk_______________________________________________
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
> ------------------------------------------------------------
> This email message, including any attachments, is for the sole use of the
> intended recipient(s) and may contain information that is proprietary,
> confidential, and exempt from disclosure under applicable law. Any
> unauthorized review, use, disclosure, or distribution is prohibited. If you
> have received this email in error please notify the sender by return email
> and delete the original message. Please note, the recipient should check
> this email and any attachments for the presence of viruses. The
> organization accepts no liability for any damage caused by any virus
> transmitted by this email.
> =================================
>
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