Re: [PyMOL] How to automate RMSD calculation for large no of structures
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: PyMOLrun 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.orgwrote: 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.orgwrote: 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
Re: [PyMOL] How to automate RMSD calculation for large no of structures
Hi Om, asides from the usual list of suspects like access permissions try double backslashes or a raw string in your path-filenames. Python on Windows is a bit peculiar in that respect. Read up on raw strings in the Python docs. Try wt_file = D:\\STUDY\\STRUCTURE_PPT\\RMSD\\Pymol\\Original\\1APS.pdb or wt_file = rD:\STUDY\STRUCTURE_PPT\RMSD\Pymol\Original\1APS.pdb note the 'r' at the beginning of the string indicating a raw string. HTH Carsten From: Om Shiv [mailto:harhaalmekhu...@gmail.com] Sent: Thursday, January 09, 2014 6:26 AM To: Sampson, Jared Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] How to automate RMSD calculation for large no of structures 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: PyMOLrun 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.commailto:harhaalmekhu...@gmail.com wrote: Thanks Jared On Thu, Jan 9, 2014 at 12:03 AM, Sampson, Jared jared.samp...@nyumc.orgmailto: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.orgmailto: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
Re: [PyMOL] How to automate RMSD calculation for large no of structures
Thanks, Carsten. I thought it would turn out to be something related to the paths, but couldn't put my finger on it. (I was able to run the script fine without either of those fixes on Incentive PyMOL 1.5.0 32-bit on a Win XP VirtualBox VM guest on a Mac OS 10.8 host. Not sure why that might be.) Relatedly, I decided to try out Robert's align_allfiles.py (which is super handy--it prints all the RMSDs in block form at the end, sorted both alphabetically by filename AND by RMSD...very nice, Robert!), and found that the regular expression for the extension doesn't compile as desired on Windows, due to the same issue. For example, I was getting values for the `obj_name1` variable with backslashes (e.g. mut\3opl.pdb), which turned into underscores (mut_3opl) in the object names. The selections were wrong and the script couldn't delete the objects, because the names didn't match, and it printed out a list of rmsds of 0.000. That line (line 36) should read as follows: extension = re.compile( r'(^.*[\\/]|\.(pdb|ent|brk))' ) Note the raw string r as well as the double-backslash inside the brackets. Robert, perhaps you could update the script on your website? 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 9, 2014, at 2:33 PM, Schubert, Carsten [JRDUS] cschu...@its.jnj.commailto:cschu...@its.jnj.com wrote: Hi Om, asides from the usual list of suspects like access permissions try double backslashes or a raw string in your path-filenames. Python on Windows is a bit peculiar in that respect. Read up on raw strings in the Python docs. Try wt_file = D:\\STUDY\\STRUCTURE_PPT\\RMSD\\Pymol\\Original\\1APS.pdbsmb://STUDY//STRUCTURE_PPT//RMSD//Pymol//Original//1APS.pdb or wt_file = rD:\STUDY\STRUCTURE_PPT\RMSD\Pymol\Original\1APS.pdb note the ‘r’ at the beginning of the string indicating a raw string. HTH Carsten 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. = -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/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
Re: [PyMOL] How to automate RMSD calculation for large no of structures
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'smb://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.orgmailto: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.commailto: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=84349831iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.netmailto: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
[PyMOL] How to automate RMSD calculation for large no of structures
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=84349831iu=/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
Re: [PyMOL] How to automate RMSD calculation for large no of structures
Check out Robert Campbell's Pymol script repository. I think align_all_to_all.py should do what you want, including exporting RMSD values. http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ Jed On 1/7/2014 11:58 AM, Om Shiv 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=84349831iu=/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 -- Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 Phone: 508-289-4823 -- 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=84349831iu=/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
Re: [PyMOL] How to automate RMSD calculation for large no of structures
On Tue, 2014-01-07 12:05 EST, Jed Goldstone jgoldst...@whoi.edu wrote:
Check out Robert Campbell's Pymol script repository.
I think align_all_to_all.py should do what you want, including exporting
RMSD values.
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
Actually, I think Om only wants to align the individual mutants to the
wild-type not all 500 mutants against each other which is what the above
script does. Also, I think for 500 structure you probably don't want to
load all 500 in at one time, so it would be better to have a script that
only loads each mutant one at a time, calculates its RMSD to the wild-type
and then deletes it.
I have modified my align_all.py script to create a new one called
align_allfiles.py and added that to the above website. It is also attached
here. To specify the use of all atoms simply add that to the mobile and
target selections. You can also specify PyMOL's cutoff and cycles
arguments to the align function (defaults to cycles=5, cutoff=2)
align_allfiles target_model, files=mutants*.pdb, mobile_selection=all,
target_selection=all
It will print out a list of RMSD values for each mutant in order read in as
well as sorted by RMSD.
Cheers,
Rob
Jed
On 1/7/2014 11:58 AM, Om Shiv 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.
--
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical Molecular Sciences
Botterell Hall Rm 644
Queen's University,
Kingston, ON K7L 3N6 Canada
Tel: 613-533-6821
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc
#! /usr/bin/env python
# original Written by Jules Jacobsen (jacob...@ebi.ac.uk). Feel free to do whatever you like with this code.
# extensively modified by Robert L. Campbell (r...@queensu.ca)
from pymol import cmd
import glob, re
def align_allfiles(target=None,files=None,mobile_selection='name ca',target_selection='name ca',cutoff=2, cycles=5,cgo_object=0):
Aligns all models in a list of files to one target
usage:
align_allfiles [target][files=filenames][target_selection=name ca][mobile_selection=name ca]
[cutoff=2][cycles=5][cgo_object=0]
where target specifies the model id you want to align all others against,
and target_selection, mobile_selection, cutoff and cycles are options
passed to the align command. You can specify the files to load and align
using a wildcard.
By default the selection is all C-alpha atoms and the cutoff is 2 and the
number of cycles is 5.
Setting cgo_object to 1, will cause the generation of an alignment object for
each object. They will be named like object_on_target, where object and
target will be replaced by the real object and target names.
Example:
align_allfiles target=name1, files=model.B*.pdb, mobile_selection=c. b n. n+ca+c+o,target_selection=c. a n. n+ca+c+o
cutoff = int(cutoff)
cycles = int(cycles)
cgo_object = int(cgo_object)
file_list = glob.glob(files)
file_list.sort()
extension = re.compile( '(^.*[\/]|\.(pdb|ent|brk))' )
object_list = []
rmsd = {}
rmsd_list = []
for i in range(len(file_list)):
obj_name1 = extension.sub('',file_list[i])
object_list.append(extension.sub('',file_list[i]))
cmd.load(file_list[i],obj_name1)
if cgo_object:
objectname = 'align_%s_on_%s' % (object_list[i],target)
rms = cmd.align('%s %s'%(object_list[i],mobile_selection),'%s %s'%(target,target_selection),cutoff=cutoff,cycles=cycles,object=objectname)
else:
rms = cmd.align('%s %s'%(object_list[i],mobile_selection),'%s %s'%(target,target_selection),cutoff=cutoff,cycles=cycles)
rmsd[object_list[i]] = (rms[0],rms[1])
rmsd_list.append((object_list[i],rms[0],rms[1]))
cmd.delete(obj_name1)
rmsd_list.sort(lambda x,y: cmp(x[1],y[1]))
# loop over dictionary and print out matrix of final rms values
print Aligning against:,target
for object_name in object_list:
print %s: %6.3f using %d atoms % (object_name,rmsd[object_name][0],rmsd[object_name][1])
print \nSorted from best match to worst:
for r in rmsd_list:
print %s: %6.3f using %d atoms % r
cmd.extend('align_allfiles',align_allfiles)
--
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
Re: [PyMOL] How to automate RMSD calculation for large no of structures
If the Wild-Type is called wildtype: rmsds = [(i,cmd.align(i,wildtype)[0]) for i in cmd.get_object_list(not wildtype)] print rmsds or, writing out the results directly open(rmsds.dat,w).writelines(%s %f\n%(i,cmd.align(i,wildtype)[0]) for i in cmd.get_object_list(not wildtype)) Cheers, Tsjerk On Tue, Jan 7, 2014 at 7:20 PM, Robert Campbell robert.campb...@queensu.cawrote: On Tue, 2014-01-07 12:05 EST, Jed Goldstone jgoldst...@whoi.edu wrote: Check out Robert Campbell's Pymol script repository. I think align_all_to_all.py should do what you want, including exporting RMSD values. http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ Actually, I think Om only wants to align the individual mutants to the wild-type not all 500 mutants against each other which is what the above script does. Also, I think for 500 structure you probably don't want to load all 500 in at one time, so it would be better to have a script that only loads each mutant one at a time, calculates its RMSD to the wild-type and then deletes it. I have modified my align_all.py script to create a new one called align_allfiles.py and added that to the above website. It is also attached here. To specify the use of all atoms simply add that to the mobile and target selections. You can also specify PyMOL's cutoff and cycles arguments to the align function (defaults to cycles=5, cutoff=2) align_allfiles target_model, files=mutants*.pdb, mobile_selection=all, target_selection=all It will print out a list of RMSD values for each mutant in order read in as well as sorted by RMSD. Cheers, Rob Jed On 1/7/2014 11:58 AM, Om Shiv 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. -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical Molecular Sciences Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- 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=84349831iu=/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 -- Tsjerk A. Wassenaar, Ph.D. -- 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=84349831iu=/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
Re: [PyMOL] How to automate RMSD calculation for large no of structures
I like to add that to get the ALL ATOMS RMSD you need to pass cycles=0 to cmd.align or to Rob's align_allfiles. Otherwise, the outlier rejection refinement might drop atoms from the alignment. Cheers, Thomas On 07 Jan 2014, at 13:58, Tsjerk Wassenaar tsje...@gmail.com wrote: If the Wild-Type is called wildtype: rmsds = [(i,cmd.align(i,wildtype)[0]) for i in cmd.get_object_list(not wildtype)] print rmsds or, writing out the results directly open(rmsds.dat,w).writelines(%s %f\n%(i,cmd.align(i,wildtype)[0]) for i in cmd.get_object_list(not wildtype)) Cheers, Tsjerk On Tue, Jan 7, 2014 at 7:20 PM, Robert Campbell robert.campb...@queensu.ca wrote: On Tue, 2014-01-07 12:05 EST, Jed Goldstone jgoldst...@whoi.edu wrote: Check out Robert Campbell's Pymol script repository. I think align_all_to_all.py should do what you want, including exporting RMSD values. http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ Actually, I think Om only wants to align the individual mutants to the wild-type not all 500 mutants against each other which is what the above script does. Also, I think for 500 structure you probably don't want to load all 500 in at one time, so it would be better to have a script that only loads each mutant one at a time, calculates its RMSD to the wild-type and then deletes it. I have modified my align_all.py script to create a new one called align_allfiles.py and added that to the above website. It is also attached here. To specify the use of all atoms simply add that to the mobile and target selections. You can also specify PyMOL's cutoff and cycles arguments to the align function (defaults to cycles=5, cutoff=2) align_allfiles target_model, files=mutants*.pdb, mobile_selection=all, target_selection=all It will print out a list of RMSD values for each mutant in order read in as well as sorted by RMSD. Cheers, Rob Jed On 1/7/2014 11:58 AM, Om Shiv 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. -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical Molecular Sciences Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- 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=84349831iu=/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
Re: [PyMOL] How to automate RMSD calculation for large no of structures
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.commailto: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=84349831iu=/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. = -- 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=84349831iu=/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
