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From: Len B. <ban...@um...> - 2019-03-16 20:04:49
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From: Chao C. <bio...@gm...> - 2019-03-13 19:55:43
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Hello PyMOL-users, Previously I used older version of Pymol, and found it was very slow to respond when I tried to click residues/chains in the software. I thought updating the software would solve the problem. Now I have the latest version of PyMOL 2.3.0 (Python 3.7.2 64-bit), unfortunately it still runs slowly. Any suggestions are very welcome. Kind regards, Chao |
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From: Jarrett J. <jar...@sc...> - 2019-03-13 18:53:12
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Hello, We do not yet have an official full release of PyMOL 2.4. After official releases, we increment the version number (into its alpha/pre-alpha stage) for ongoing development changes and additions. Latest full releases are always announced on the PyMOL website <https://pymol.org/> . Jarrett Johnson On Wed, Mar 13, 2019 at 9:16 AM ikehata akihisa <sci...@ho...> wrote: > Hello PyMOL users, > > Recently, the open source PyMOL 2.4 is seemingly released. I want to > know where I can get it. > > Thank you very much, > > Akihisa, an independent researcher in Yokohama, Japan > > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > -- Jarrett Johnson PyMOL Developer Schrödinger, Inc. |
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From: ikehata a. <sci...@ho...> - 2019-03-13 05:32:50
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Hello PyMOL users, Recently, the open source PyMOL 2.4 is seemingly released. I want to know where I can get it. Thank you very much, Akihisa, an independent researcher in Yokohama, Japan |
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From: Markus H. <mh...@cd...> - 2019-03-12 21:57:02
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Agreed, Thomas. Thanks for your help! > -----Original Message----- > From: Thomas Holder <tho...@sc...> > Sent: Tuesday, March 12, 2019 12:14 PM > To: Markus Heller <mh...@cd...> > Cc: pym...@li... > Subject: Re: [PyMOL] Compiling open source pymol 2.4 > > Hi Markus, > > I recommend to use Python 3. The PyMOLWiki has updated versions of those > two failing scripts: > > https://pymolwiki.org/index.php/Pairwise_distances > https://pymolwiki.org/index.php/Polarpairs > > I don't know why there would be no menu bar with Python 2.7. But if Python 3 > works for you, I think there is no need to figure that out. > > Cheers, > Thomas > > > On Mar 12, 2019, at 7:34 PM, Markus Heller <mh...@cd...> wrote: > > > > Hi all, > > > > I'm having trouble compiling open source Pymol 2.4. > > > > If I compile with python 2.7, the compilation finishes without errors or > warnings, but when I start Pymol, I don't see the menu bar at the top of the > window, and I don't see any errors. > > > > If, on the other hand, I compile with python 3, Pymol starts and I see the menu > bar, but I get warnings in the Pymol console that are related to a version conflict > of python 3 used for compilation and python 2 used in some scripts, e.g. the > ones shown below. > > > > What's the python version to use for compiling, and how do I best proceed? > > > > Thanks > > Markus > > > > This is part of the output shown in the Pymol console on startup: > > > > PyMOL>run /home/mheller/.pymol/show_bumps.py > > PyMOL>run /home/mheller/.pymol/pairwisedistances.py > > Traceback (most recent call last): > > File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 483, in run > > run_(path, ns_pymol, ns_pymol) > > File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 532, in > run_file > > execfile(file,global_ns,local_ns) > > File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 526, in > execfile > > co = compile(pi.file_read(filename), filename, 'exec') File > > "/home/mheller/.pymol/pairwisedistances.py", line 13 > > print "" > > ^ > > SyntaxError: Missing parentheses in call to 'print'. Did you mean print("")? > > PyMOL>run /home/mheller/.pymol/supercell.py run > > PyMOL>/home/mheller/.pymol/get_raw_distances.py > > PyMOL>run /home/mheller/.pymol/polarpairs.py > > Traceback (most recent call last): > > File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 483, in run > > run_(path, ns_pymol, ns_pymol) > > File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 532, in > run_file > > execfile(file,global_ns,local_ns) > > File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 526, in > execfile > > co = compile(pi.file_read(filename), filename, 'exec') File > > "/home/mheller/.pymol/polarpairs.py", line 39 > > print 'Settings: cutoff=%.1fangstrom angle=%.1fdegree' % (cutoff, angle) > > ^ > > SyntaxError: invalid syntax > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. |
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From: Thomas H. <tho...@sc...> - 2019-03-12 19:14:38
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Hi Markus, I recommend to use Python 3. The PyMOLWiki has updated versions of those two failing scripts: https://pymolwiki.org/index.php/Pairwise_distances https://pymolwiki.org/index.php/Polarpairs I don't know why there would be no menu bar with Python 2.7. But if Python 3 works for you, I think there is no need to figure that out. Cheers, Thomas > On Mar 12, 2019, at 7:34 PM, Markus Heller <mh...@cd...> wrote: > > Hi all, > > I'm having trouble compiling open source Pymol 2.4. > > If I compile with python 2.7, the compilation finishes without errors or warnings, but when I start Pymol, I don't see the menu bar at the top of the window, and I don't see any errors. > > If, on the other hand, I compile with python 3, Pymol starts and I see the menu bar, but I get warnings in the Pymol console that are related to a version conflict of python 3 used for compilation and python 2 used in some scripts, e.g. the ones shown below. > > What's the python version to use for compiling, and how do I best proceed? > > Thanks > Markus > > This is part of the output shown in the Pymol console on startup: > > PyMOL>run /home/mheller/.pymol/show_bumps.py > PyMOL>run /home/mheller/.pymol/pairwisedistances.py > Traceback (most recent call last): > File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 483, in run > run_(path, ns_pymol, ns_pymol) > File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 532, in run_file > execfile(file,global_ns,local_ns) > File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 526, in execfile > co = compile(pi.file_read(filename), filename, 'exec') > File "/home/mheller/.pymol/pairwisedistances.py", line 13 > print "" > ^ > SyntaxError: Missing parentheses in call to 'print'. Did you mean print("")? > PyMOL>run /home/mheller/.pymol/supercell.py > PyMOL>run /home/mheller/.pymol/get_raw_distances.py > PyMOL>run /home/mheller/.pymol/polarpairs.py > Traceback (most recent call last): > File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 483, in run > run_(path, ns_pymol, ns_pymol) > File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 532, in run_file > execfile(file,global_ns,local_ns) > File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 526, in execfile > co = compile(pi.file_read(filename), filename, 'exec') > File "/home/mheller/.pymol/polarpairs.py", line 39 > print 'Settings: cutoff=%.1fangstrom angle=%.1fdegree' % (cutoff, angle) > ^ > SyntaxError: invalid syntax -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. |
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From: Markus H. <mh...@cd...> - 2019-03-12 18:35:01
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Hi all,
I'm having trouble compiling open source Pymol 2.4.
If I compile with python 2.7, the compilation finishes without errors or warnings, but when I start Pymol, I don't see the menu bar at the top of the window, and I don't see any errors.
If, on the other hand, I compile with python 3, Pymol starts and I see the menu bar, but I get warnings in the Pymol console that are related to a version conflict of python 3 used for compilation and python 2 used in some scripts, e.g. the ones shown below.
What's the python version to use for compiling, and how do I best proceed?
Thanks
Markus
This is part of the output shown in the Pymol console on startup:
PyMOL>run /home/mheller/.pymol/show_bumps.py
PyMOL>run /home/mheller/.pymol/pairwisedistances.py
Traceback (most recent call last):
File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 483, in run
run_(path, ns_pymol, ns_pymol)
File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 532, in run_file
execfile(file,global_ns,local_ns)
File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 526, in execfile
co = compile(pi.file_read(filename), filename, 'exec')
File "/home/mheller/.pymol/pairwisedistances.py", line 13
print ""
^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print("")?
PyMOL>run /home/mheller/.pymol/supercell.py
PyMOL>run /home/mheller/.pymol/get_raw_distances.py
PyMOL>run /home/mheller/.pymol/polarpairs.py
Traceback (most recent call last):
File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 483, in run
run_(path, ns_pymol, ns_pymol)
File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 532, in run_file
execfile(file,global_ns,local_ns)
File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 526, in execfile
co = compile(pi.file_read(filename), filename, 'exec')
File "/home/mheller/.pymol/polarpairs.py", line 39
print 'Settings: cutoff=%.1fangstrom angle=%.1fdegree' % (cutoff, angle)
^
SyntaxError: invalid syntax
|
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From: William T. <ywt...@gm...> - 2019-03-06 21:57:22
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Hi Dr. Holder, Thank you for your detailed explanation. Your answer is very helpful. Best, William Thomas Holder <tho...@sc...> 于2019年3月6日周三 上午4:04写道： > Hi William, > > You can use any version of PyMOL, the plugin API is the same in all of > them (Open-Source, Incentive with edu/academic/commercial license). > > Your own code, if open-sourced, needs a GPL-compatible license. You're in > the same situation as the person asking "can I release my SW under the MIT > license in situation 3?" (answer: Yes) here: > https://riverbankcomputing.com/pipermail/pyqt/2016-September/038129.html > > Only if you are going to sell your plugin, you need to purchase a > commercial PyQt license. See > https://riverbankcomputing.com/commercial/license-faq > > Hope that helps. > > Cheers, > Thomas > > > On Mar 4, 2019, at 7:03 PM, William Tao <ywt...@gm...> wrote: > > > > Hi PyMOL community, > > > > I am planning to develop a PyMOL plugin based on PyMOL 2.x versions with > PyQt. > > > > However, I am not quite clear about the legal implications and copyright > issues if I would like to make my plugin open-source in future. > > > > First, PyMOL has incentive version and open-source version. I have an > educational license for incentive version and open-source version. If I am > going to describe my plugin in a scientific article or website, which > version of PyMOL version am I allowed to use? > > > > Second, the PyQt requires the code based on it must also be open-source > according to GPL. > > > > These two factors make me confused about the possibility of publishing a > plugin for PyMOL in future. > > > > If anybody has experience in this aspect, please feel free to advise. > > > > Many thanks. > > > > William > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > > |
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From: Thomas H. <tho...@sc...> - 2019-03-06 10:13:33
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Hi Michael,
Use mode="a" to append to the log file:
cmd.log_open('/tmp/log.pml', 'a')
Cheers,
Thomas
> On Mar 6, 2019, at 5:47 AM, Michael Morgan <mic...@gm...> wrote:
>
> Dear all,
>
> I hope my log file can keep recording operations.
>
> I put “log_open” in the pymolrc.pml file. However, it seems it creates a new file. All operations from last time are wiped out.
>
> “Append…” from “File -> Log File” menu seems work. But how can I make it automatically for every time pymol is open? It seems there is no “log_append” command.
>
> Thanks.
>
> Michael
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
|
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From: Thomas H. <tho...@sc...> - 2019-03-06 10:04:39
|
Hi William, You can use any version of PyMOL, the plugin API is the same in all of them (Open-Source, Incentive with edu/academic/commercial license). Your own code, if open-sourced, needs a GPL-compatible license. You're in the same situation as the person asking "can I release my SW under the MIT license in situation 3?" (answer: Yes) here: https://riverbankcomputing.com/pipermail/pyqt/2016-September/038129.html Only if you are going to sell your plugin, you need to purchase a commercial PyQt license. See https://riverbankcomputing.com/commercial/license-faq Hope that helps. Cheers, Thomas > On Mar 4, 2019, at 7:03 PM, William Tao <ywt...@gm...> wrote: > > Hi PyMOL community, > > I am planning to develop a PyMOL plugin based on PyMOL 2.x versions with PyQt. > > However, I am not quite clear about the legal implications and copyright issues if I would like to make my plugin open-source in future. > > First, PyMOL has incentive version and open-source version. I have an educational license for incentive version and open-source version. If I am going to describe my plugin in a scientific article or website, which version of PyMOL version am I allowed to use? > > Second, the PyQt requires the code based on it must also be open-source according to GPL. > > These two factors make me confused about the possibility of publishing a plugin for PyMOL in future. > > If anybody has experience in this aspect, please feel free to advise. > > Many thanks. > > William -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. |
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From: Michael M. <mic...@gm...> - 2019-03-06 04:48:06
|
Dear all, I hope my log file can keep recording operations. I put "log_open" in the pymolrc.pml file. However, it seems it creates a new file. All operations from last time are wiped out. "Append." from "File -> Log File" menu seems work. But how can I make it automatically for every time pymol is open? It seems there is no "log_append" command. Thanks. Michael |
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From: William T. <ywt...@gm...> - 2019-03-04 18:04:06
|
Hi PyMOL community, I am planning to develop a PyMOL plugin based on PyMOL 2.x versions with PyQt. However, I am not quite clear about the legal implications and copyright issues if I would like to make my plugin open-source in future. First, PyMOL has incentive version and open-source version. I have an educational license for incentive version and open-source version. If I am going to describe my plugin in a scientific article or website, which version of PyMOL version am I allowed to use? Second, the PyQt requires the code based on it must also be open-source according to GPL. These two factors make me confused about the possibility of publishing a plugin for PyMOL in future. If anybody has experience in this aspect, please feel free to advise. Many thanks. William |
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From: Thomas H. <tho...@sc...> - 2019-03-02 22:42:05
|
Hi Seán, This issue is fixed in PyMOL 2.3.0, please download the new version from https://pymol.org/#download Cheers, Thomas > On Mar 2, 2019, at 8:45 PM, sean downey <sea...@gm...> wrote: > > Hi, > > I'm having an issue with a UnicodeDecodeError. I have an academic licence for the proprietary version of Pymol, however, when I go to install the licence file, I get the below error message. > I'm very new to Pymol and I don't really have any coding experience (I'm from a biology background). I'm just looking for a quick fix for this problem. Is there some way to change the codec, which is what I see suggested online, but I don't honestly understand them. > > Thanks in advance, > > Seán > > > PyMOL(TM) 2.2.3 - Incentive Product > Copyright (C) Schrodinger, LLC > > This Executable Build integrates and extends Open-Source PyMOL. > Detected OpenGL version 4.5. Shaders available. > Detected GLSL version 4.50. > OpenGL graphics engine: > GL_VENDOR: Intel > GL_RENDERER: Intel(R) HD Graphics 515 > GL_VERSION: 4.5.0 - Build 24.20.100.6286 > Setting: precomputed_lighting set to on. > Detected 4 CPU cores. Enabled multithreaded rendering. > > > Traceback (most recent call last): > File "C:\ProgramData\PyMOL\lib\site-packages\pmg_qt\lic_dialog.py", line 38, in browse > licensing.install_license_file(fname) > File "C:\ProgramData\PyMOL\lib\site-packages\pymol\licensing.py", line 128, in install_license_file > return install_license_key(open(filename, 'rb').read()) > File "C:\ProgramData\PyMOL\lib\site-packages\pymol\licensing.py", line 92, in install_license_key > licfile = get_license_filename_user() > File "C:\ProgramData\PyMOL\lib\site-packages\pymol\licensing.py", line 75, in get_license_filename_user > filename = os.path.expanduser(filename) > File "C:\ProgramData\PyMOL\lib\ntpath.py", line 311, in expanduser > return userhome + path[i:] > : 'utf8' codec can't decode byte 0xe1 in position 11: invalid continuation byte -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. |
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From: sean d. <sea...@gm...> - 2019-03-02 19:46:00
|
Hi,
I'm having an issue with a UnicodeDecodeError. I have an academic licence
for the proprietary version of Pymol, however, when I go to install the
licence file, I get the below error message.
I'm very new to Pymol and I don't really have any coding experience (I'm
from a biology background). I'm just looking for a quick fix for this
problem. Is there some way to change the codec, which is what I see
suggested online, but I don't honestly understand them.
Thanks in advance,
Seán
PyMOL(TM) 2.2.3 - Incentive Product
Copyright (C) Schrodinger, LLC
This Executable Build integrates and extends Open-Source PyMOL.
Detected OpenGL version 4.5. Shaders available.
Detected GLSL version 4.50.
OpenGL graphics engine:
GL_VENDOR: Intel
GL_RENDERER: Intel(R) HD Graphics 515
GL_VERSION: 4.5.0 - Build 24.20.100.6286
Setting: precomputed_lighting set to on.
Detected 4 CPU cores. Enabled multithreaded rendering.
Traceback (most recent call last):
File "C:\ProgramData\PyMOL\lib\site-packages\pmg_qt\lic_dialog.py",
line 38, in browse
licensing.install_license_file(fname)
File "C:\ProgramData\PyMOL\lib\site-packages\pymol\licensing.py",
line 128, in install_license_file
return install_license_key(open(filename, 'rb').read())
File "C:\ProgramData\PyMOL\lib\site-packages\pymol\licensing.py",
line 92, in install_license_key
licfile = get_license_filename_user()
File "C:\ProgramData\PyMOL\lib\site-packages\pymol\licensing.py",
line 75, in get_license_filename_user
filename = os.path.expanduser(filename)
File "C:\ProgramData\PyMOL\lib\ntpath.py", line 311, in expanduser
return userhome + path[i:]
: 'utf8' codec can't decode byte 0xe1 in position 11: invalid continuation byte
|
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From: Thomas H. <tho...@sc...> - 2019-02-25 08:40:17
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Hi Pedro, There is a command logging option: From the menu: File > Log File > Open... Or use the "log_open" command: https://pymol.org/d/command:log_open Decorating cmd.create like you suggested also works, but you need to update the command language as well: cmd.keyword['create'][0] = cmd.create Cheers, Thomas > On Feb 22, 2019, at 12:27 AM, Pedro Lacerda <psl...@gm...> wrote: > > Hi, > > I want to show executed commands when right before they run, so I can track my script execution. > > Something like the following for all the commands: > > orig_create = cmd.create > def create(*args, **kwargs): > print('create', repr(args), repr(kwargs)) > orig_create(*args, **kwargs) > cmd.create = create > > > I also want it to figure out what commands some GUI actions really do. Like those in presets and so on. > > There is some verbose option that does it? > > Thank you, > Pedro Lacerda -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. |
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From: Anne N. <ann...@ke...> - 2019-02-22 18:27:12
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Hi, I need to calculate the RMSD for the same residue, e.g. 131Thr, from 2 pdb files for the same target. As I need a local alignment, I use a sliding window of 5 residues (the residue of interest is in the middle.) I have adapted the script from https://pymolwiki.org/index.php/RmsdByResidue (also see below my code below) by adding a sliding window, but I need advice on the following: - I would need to check whether I am actually comparing the intended residues, e.g. 131Thr, 131Thr, or whether the same residues (e.g. His, Asp, His), with specific residue names and numbers are in the selection I have chosen from both pdb files for my sliding window. The reason: I have coded up the script below, but often it skips and doesn't compare two residues, because the atom count is different between the residue from protein A and protein B. (It is exactly double the number, I have already checked and excluded problems like occupancy and different conformations as potential causes.) - I constructed a sliding window by selecting two residues before the residue of interest and two residues which follow said residue. (I know that residues can be missing, I am working on this.) Is there a better way for constructing a sliding window? I have not found such a method in pymol. For anyone interested, I have attached a code snipplet below. I am sorry, if these seem like obvious questions, but I tried various approaches and I feel that I need a push in the right direction. I have the feeling that I am missing something fundamental. Many thanks for any suggestion! Anne (Newbie in Pymol) ###################################### Code snipplet (Python/Pymol interface): referenceProteinChain = cmd.fetch(pbdstructure1) targetProteinChain = cmd.fetch(pdbstructure2) sel = referenceProteinChain list_atoms = [[133, 133]] # example list, I want to calculate the rmsd between residue 133 and residue 133 of two pdb structures for j in list_atoms: # I formulate my sliding window of 5 residues, my residue of interest is in the middle ref_begin = int(j[0])-2 ref_end = int(j[0])+2 target_begin = int(j[1])-2 target_end = int(j[1])+2 # I create a selection for the reference protein and the target protein cmd.create("ref_gzt", referenceProteinChain+" and polymer and not alt B and not Alt C and not alt D and resi %s-%s" cmd.alter("ref_gzt", "chain='A'") cmd.alter("ref_gzt", "segi=''") cmd.create("target_gzt", targetProteinChain+" and polymer and not alt B and not Alt C and not alt D and resi %s-%s" %(target_begin,target_end) ) cmd.alter("target_gzt", "chain='A'") cmd.alter("target_gzt", "segi=''") # I align my selected 5 residues for a local alignment window cmd.align("target_gzt","ref_gzt",object="align", cycles =5) # select alpha carbon of in reference structure to loop over calpha=cmd.get_model(sel+" and name CA and not alt B and not Alt C and not alt D and resi %s-%s" %(ref_begin,ref_end) ) ## here I loop over all residues in the sliding window and calculte the rmsd for my residues of interest. for g in calpha.atom : I loop over the slinding window if g.resi == str(j[0]): ## we select only our residue of interest within the sliding window if cmd.count_atoms("ref_gzt and polymer and resi "+g.resi)==cmd.count_atoms("target_gzt and polymer and resi "+g.resi): ## calculte the pairwise RMSD between the residues I specified in list_atoms rmsdRes=cmd.rms_cur("ref_gzt and polymer and resi "+g.resi,"target_gzt and polymer and resi "+g.resi) |
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From: Thomas H. <tho...@sc...> - 2019-02-22 16:15:43
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Hi Thomas, If you add "and present" to the selection expression, then you'll only include atoms which have coordinates in the current state: select s1, 2hduA & present I had a quick look at 2hduA and 2r9wA and don't see any non-standard residues, but a lot of alternate coordinates. Depending on what your script exactly does, you might need: select s1, 2hduA & alt +A Another (maybe the best) approach would be to use an alignment object: align 2hduA, 2r9wA, object=aln, cycles=0, transform=0 select s1, 2hduA & aln Cheers, Thomas > On Feb 22, 2019, at 4:05 PM, Thomas Evangelidis <te...@gm...> wrote: > > Hi Thomas, > > With regard to selections, sometimes a residue has missing atoms or is non-standard amino acid. In the first case it is matched with another residue in a second structure during the alignment and then when I try to fit the two selections of atoms from the two structures I get the following error: > > Calculating RMSD between pocket of model 2hduA and 2r9wA. > ExecutiveRMS-Error: Atom counts between selections don't match (799 vs 797) > Executive: Error -- no atoms left after refinement! > RMSD = -1.000000 > > Can you think of a clever way to exclude amino acids with missing atoms or non-standard ones from pair_fit() or rms_cur()? > > Best, > Thomas > > > > > > On Fri, 22 Feb 2019 at 12:32, Thomas Holder <tho...@sc...> wrote: > Hi Thomas, > > In general, the PyMOL API should raise pymol.CmdException if things go wrong. But in case of cmd.pair_fit() this wasn't happening (see my fix that I pushed few minutes ago: https://github.com/schrodinger/pymol-open-source/commit/b26d91c40d20344fef511ea9d6bb664a93f1bb4a ) > > cmd.select() correctly raises an exception, so if you want to make a script more robust against selection failures, you could always create a named selection first to check if it's valid. > > tmpsele1 = cmd.get_unused_name('_sele1') > try: > cmd.select(tmpsele1, someexpression, 0) > except pymol.CmdException: > print('invalid selection') > finally: > cmd.delete(tmpsele1) > > > Cheers, > Thomas > > > On Feb 22, 2019, at 12:11 PM, Thomas Evangelidis <te...@gm...> wrote: > > > > Hi Thomas, > > > > This is great! I can even include more atom types in the selection. > > Just for the record, is it possible to catch PyMOL exceptions like "Selector-Error" from within a Python script? Is there any general strategy to select which exception type to look for? In the past, I was catching exceptions from 'tmalign' with "except AssertionError:" which doesn't work for "Selector-Error". > > > > Best, > > Thomas > > -- > ====================================================================== > Dr Thomas Evangelidis > Research Scientist > IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences > Prague, Czech Republic > & > CEITEC - Central European Institute of Technology > Brno, Czech Republic > > email: te...@gm... > website: https://sites.google.com/site/thomasevangelidishomepage/ -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. |
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From: Thomas E. <te...@gm...> - 2019-02-22 15:08:45
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Hi Thomas, With regard to selections, sometimes a residue has missing atoms or is non-standard amino acid. In the first case it is matched with another residue in a second structure during the alignment and then when I try to fit the two selections of atoms from the two structures I get the following error: Calculating RMSD between pocket of model 2hduA and 2r9wA. > ExecutiveRMS-Error: Atom counts between selections don't match (799 vs 797) > Executive: Error -- no atoms left after refinement! > RMSD = -1.000000 Can you think of a clever way to exclude amino acids with missing atoms or non-standard ones from pair_fit() or rms_cur()? Best, Thomas On Fri, 22 Feb 2019 at 12:32, Thomas Holder <tho...@sc...> wrote: > Hi Thomas, > > In general, the PyMOL API should raise pymol.CmdException if things go > wrong. But in case of cmd.pair_fit() this wasn't happening (see my fix that > I pushed few minutes ago: > https://github.com/schrodinger/pymol-open-source/commit/b26d91c40d20344fef511ea9d6bb664a93f1bb4a > ) > > cmd.select() correctly raises an exception, so if you want to make a > script more robust against selection failures, you could always create a > named selection first to check if it's valid. > > tmpsele1 = cmd.get_unused_name('_sele1') > try: > cmd.select(tmpsele1, someexpression, 0) > except pymol.CmdException: > print('invalid selection') > finally: > cmd.delete(tmpsele1) > > > Cheers, > Thomas > > > On Feb 22, 2019, at 12:11 PM, Thomas Evangelidis <te...@gm...> > wrote: > > > > Hi Thomas, > > > > This is great! I can even include more atom types in the selection. > > Just for the record, is it possible to catch PyMOL exceptions like > "Selector-Error" from within a Python script? Is there any general strategy > to select which exception type to look for? In the past, I was catching > exceptions from 'tmalign' with "except AssertionError:" which doesn't work > for "Selector-Error". > > > > Best, > > Thomas > > > > > > -- > > ====================================================================== > > Dr Thomas Evangelidis > > Research Scientist > > IOCB - Institute of Organic Chemistry and Biochemistry of the Czech > Academy of Sciences > > Prague, Czech Republic > > & > > CEITEC - Central European Institute of Technology > > Brno, Czech Republic > > > > email: te...@gm... > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > > -- ====================================================================== Dr Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en> Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/> Brno, Czech Republic email: te...@gm... website: https://sites.google.com/site/thomasevangelidishomepage/ |
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From: Thomas H. <tho...@sc...> - 2019-02-22 11:32:56
|
Hi Thomas, In general, the PyMOL API should raise pymol.CmdException if things go wrong. But in case of cmd.pair_fit() this wasn't happening (see my fix that I pushed few minutes ago: https://github.com/schrodinger/pymol-open-source/commit/b26d91c40d20344fef511ea9d6bb664a93f1bb4a ) cmd.select() correctly raises an exception, so if you want to make a script more robust against selection failures, you could always create a named selection first to check if it's valid. tmpsele1 = cmd.get_unused_name('_sele1') try: cmd.select(tmpsele1, someexpression, 0) except pymol.CmdException: print('invalid selection') finally: cmd.delete(tmpsele1) Cheers, Thomas > On Feb 22, 2019, at 12:11 PM, Thomas Evangelidis <te...@gm...> wrote: > > Hi Thomas, > > This is great! I can even include more atom types in the selection. > Just for the record, is it possible to catch PyMOL exceptions like "Selector-Error" from within a Python script? Is there any general strategy to select which exception type to look for? In the past, I was catching exceptions from 'tmalign' with "except AssertionError:" which doesn't work for "Selector-Error". > > Best, > Thomas > > > -- > ====================================================================== > Dr Thomas Evangelidis > Research Scientist > IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences > Prague, Czech Republic > & > CEITEC - Central European Institute of Technology > Brno, Czech Republic > > email: te...@gm... > website: https://sites.google.com/site/thomasevangelidishomepage/ -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. |
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From: Thomas E. <te...@gm...> - 2019-02-22 11:14:43
|
Hi Thomas,
This is great! I can even include more atom types in the selection.
Just for the record, is it possible to catch PyMOL exceptions like
"Selector-Error" from within a Python script? Is there any general strategy
to select which exception type to look for? In the past, I was catching
exceptions from 'tmalign' with "except AssertionError:" which doesn't work
for "Selector-Error".
Best,
Thomas
On Fri, 22 Feb 2019 at 11:28, Thomas Holder <tho...@sc...>
wrote:
> Hi Thomas,
>
> Getting rid of the string length limitations would need some major
> refactoring. There is currently no good workaround, other than avoiding
> such long selections.
>
> In this particular case, the script could use cmd.select_list() instead of
> concatenating the index list to a string:
>
> cmd.select_list('sel1', obj1, [int(i) for i in id1], mode='index')
> cmd.select_list('sel2', obj2, [int(i) for i in id2], mode='index')
> cmd.pair_fit("sel1 and aln", "sel2 and aln")
> cmd.delete('sel1')
> cmd.delete('sel2')
>
> Hope that helps.
>
> Cheers,
> Thomas
>
>
> > On Feb 22, 2019, at 9:32 AM, Thomas Evangelidis <te...@gm...>
> wrote:
> >
> > Greetings,
> >
> > I am trying to run focus_alignment command (
> https://pymolwiki.org/index.php/Focus_alignment) from within a Python
> script with my own custom selection (I include CA+CB atoms instead of only
> CA as in the default). Sometimes the selection is very large and PyMOL
> cannot hand it:
> >
> > Selector-Error: Word too long. Truncated:
> > Selector-Error:
> 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+115Selector-Error:
> Invalid selection name "730".
> > poly and 4kz6A and aln and index
> 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+1158+1175+1178+1183+1421+1424+1428+1431+1647+1650+1655+1658+
> 730<--
> > Selector-Error: Word too long. Truncated:
> > Selector-Error:
> 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+121Selector-Error:
> Invalid selection name "868".
> > poly and 2r9wA and aln and index
> 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+1212+1229+1232+1237+1491+1494+1498+1501+1747+1750+1755+1758+
> 868<--
> > ExecutiveRMS-Error: No atoms selected.
> > Selector-Error: Word too long. Truncated:
> > Selector-Error:
> 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+115Selector-Error:
> Word too long. Truncated:
> > Selector-Error:
> 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+121Selector-Error:
> Invalid selection name "730".
> > ( ( poly and 4kz6A and aln and index
> 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+1158+1175+1178+1183+1421+1424+1428+1431+1647+1650+1655+1658+
> 730 ) in ( poly and 2r9wA and aln and index
> 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+1212+1229+1232+1237+1491+1494+1498+1501+1747+1750+1755+1758+
> 868 ) )<--
> >
> > Is there a way to ask PyMOL to accept longer selection strings?
> > Alternatively, is it possible to catch this exception from within the
> script using "try: ... except <some exception>:" statement?
> >
> > Thanks in advance.
> > Thomas
> >
> > --
> > ======================================================================
> > Dr Thomas Evangelidis
> > Research Scientist
> > IOCB - Institute of Organic Chemistry and Biochemistry of the Czech
> Academy of Sciences
> > Prague, Czech Republic
> > &
> > CEITEC - Central European Institute of Technology
> > Brno, Czech Republic
> >
> > email: te...@gm...
> > website: https://sites.google.com/site/thomasevangelidishomepage/
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
--
======================================================================
Dr Thomas Evangelidis
Research Scientist
IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>
Prague, Czech Republic
&
CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>
Brno, Czech Republic
email: te...@gm...
website: https://sites.google.com/site/thomasevangelidishomepage/
|
|
From: Thomas H. <tho...@sc...> - 2019-02-22 10:28:44
|
Hi Thomas,
Getting rid of the string length limitations would need some major refactoring. There is currently no good workaround, other than avoiding such long selections.
In this particular case, the script could use cmd.select_list() instead of concatenating the index list to a string:
cmd.select_list('sel1', obj1, [int(i) for i in id1], mode='index')
cmd.select_list('sel2', obj2, [int(i) for i in id2], mode='index')
cmd.pair_fit("sel1 and aln", "sel2 and aln")
cmd.delete('sel1')
cmd.delete('sel2')
Hope that helps.
Cheers,
Thomas
> On Feb 22, 2019, at 9:32 AM, Thomas Evangelidis <te...@gm...> wrote:
>
> Greetings,
>
> I am trying to run focus_alignment command (https://pymolwiki.org/index.php/Focus_alignment) from within a Python script with my own custom selection (I include CA+CB atoms instead of only CA as in the default). Sometimes the selection is very large and PyMOL cannot hand it:
>
> Selector-Error: Word too long. Truncated:
> Selector-Error: 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+115Selector-Error: Invalid selection name "730".
> poly and 4kz6A and aln and index 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+1158+1175+1178+1183+1421+1424+1428+1431+1647+1650+1655+1658+ 730<--
> Selector-Error: Word too long. Truncated:
> Selector-Error: 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+121Selector-Error: Invalid selection name "868".
> poly and 2r9wA and aln and index 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+1212+1229+1232+1237+1491+1494+1498+1501+1747+1750+1755+1758+ 868<--
> ExecutiveRMS-Error: No atoms selected.
> Selector-Error: Word too long. Truncated:
> Selector-Error: 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+115Selector-Error: Word too long. Truncated:
> Selector-Error: 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+121Selector-Error: Invalid selection name "730".
> ( ( poly and 4kz6A and aln and index 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+1158+1175+1178+1183+1421+1424+1428+1431+1647+1650+1655+1658+ 730 ) in ( poly and 2r9wA and aln and index 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+1212+1229+1232+1237+1491+1494+1498+1501+1747+1750+1755+1758+ 868 ) )<--
>
> Is there a way to ask PyMOL to accept longer selection strings?
> Alternatively, is it possible to catch this exception from within the script using "try: ... except <some exception>:" statement?
>
> Thanks in advance.
> Thomas
>
> --
> ======================================================================
> Dr Thomas Evangelidis
> Research Scientist
> IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
> Prague, Czech Republic
> &
> CEITEC - Central European Institute of Technology
> Brno, Czech Republic
>
> email: te...@gm...
> website: https://sites.google.com/site/thomasevangelidishomepage/
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
|
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From: Thomas E. <te...@gm...> - 2019-02-22 08:35:43
|
Greetings, I am trying to run focus_alignment command ( https://pymolwiki.org/index.php/Focus_alignment) from within a Python script with my own custom selection (I include CA+CB atoms instead of only CA as in the default). Sometimes the selection is very large and PyMOL cannot hand it: Selector-Error: Word too long. Truncated: > Selector-Error: > 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+115Selector-Error: > Invalid selection name "730". > poly and 4kz6A and aln and index > 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+1158+1175+1178+1183+1421+1424+1428+1431+1647+1650+1655+1658+ > 730<-- > Selector-Error: Word too long. Truncated: > Selector-Error: > 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+121Selector-Error: > Invalid selection name "868". > poly and 2r9wA and aln and index > 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+1212+1229+1232+1237+1491+1494+1498+1501+1747+1750+1755+1758+ > 868<-- > ExecutiveRMS-Error: No atoms selected. > Selector-Error: Word too long. Truncated: > Selector-Error: > 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+115Selector-Error: > Word too long. Truncated: > Selector-Error: > 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+121Selector-Error: > Invalid selection name "730". > ( ( poly and 4kz6A and aln and index > 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+1158+1175+1178+1183+1421+1424+1428+1431+1647+1650+1655+1658+ > 730 ) in ( poly and 2r9wA and aln and index > 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+1212+1229+1232+1237+1491+1494+1498+1501+1747+1750+1755+1758+ > 868 ) )<-- Is there a way to ask PyMOL to accept longer selection strings? Alternatively, is it possible to catch this exception from within the script using "try: ... except <some exception>:" statement? Thanks in advance. Thomas -- ====================================================================== Dr Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en> Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/> Brno, Czech Republic email: te...@gm... website: https://sites.google.com/site/thomasevangelidishomepage/ |
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From: Pedro L. <psl...@gm...> - 2019-02-21 23:28:02
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Hi,
I want to show executed commands when right before they run, so I can track
my script execution.
Something like the following for all the commands:
orig_create = cmd.create
def create(*args, **kwargs):
print('create', repr(args), repr(kwargs))
orig_create(*args, **kwargs)
cmd.create = create
I also want it to figure out what commands some GUI actions really do. Like
those in presets and so on.
There is some verbose option that does it?
Thank you,
Pedro Lacerda
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From: Thomas H. <tho...@sc...> - 2019-02-19 09:20:37
|
Hi all, If you have Python scripts or plugins which aren't Python 3 compatible yet, you might find this guide useful: https://pymolwiki.org/index.php/2to3 Cheers, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. |
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