pymol-users Mailing List for PyMOL Molecular Graphics System

Hello everyone,

Two years ago I used CAVER 2.1.2 for calculation of intra-molecular
tunnels. I know that the current version of CAVER allows us to view and
change the configuration file (for default tunnel calculation settings). I
couldn't find such a configuration file for CAVER 2.1.2. Does anybody know
the default tunnel calculation settings for bottleneck radius, shell radius
and shell depth for CAVER 2.1.2? Are they the same as the default settings
of CAVER 3.0?

Thank you very much

Sajeewa Dewage

Dear Arnaud,

we do parallel builds, that's why it doesn't always stop at the same file. You didn't even include the error in your example output, only (irrelevant) warnings. To find the error, do this:

export JOBS=1
python setup.py build install ...

Cheers,
  Thomas

On 30 Jan 2015, at 04:13, Arnaud Basle <arn...@ne...> wrote:

> Dear all,
> 
> I am trying to compile pymol from source following the instructions 
> here: http://www.pymolwiki.org/index.php/Linux_Install
> 
> It used to work for me a while ago but now the compilation hangs without 
> error. Pressing return give me back the terminal prompt. The compiling 
> process does not stop always at the same point.
> 
> I am using Linux Mint 17 64 bits (based on Ubuntu).
> 
> Anyone has seen such behaviour?
> 
> Cheers,
> Arnaud
> PS: see below example of output
> 
> layer3/Selector.cpp:11037:36: warning: comparison between signed and 
> unsigned integer expressions [-Wsign-compare]
>        for(a = cNDummyAtoms; a < I->NAtom; a++)
>                                     ^
> layer3/Selector.cpp: In function ‘int* SelectorEvaluate(PyMOLGlobals*, 
> char (*)[1024], int, int)’:
> layer3/Selector.cpp:11107:15: warning: variable ‘opFlag2’ set but not 
> used [-Wunused-but-set-variable]
>    int opFlag, opFlag2, maxLevel;
>                ^
> layer3/Selector.cpp:11108:19: warning: variable ‘cc2’ set but not used 
> [-Wunused-but-set-variable]
>    char *q, *cc1, *cc2;
>                    ^
> layer3/Selector.cpp: In function ‘char (* SelectorParse(PyMOLGlobals*, 
> char*))[1024]’:
> layer3/Selector.cpp:11562:51: warning: comparison between signed and 
> unsigned integer expressions [-Wsign-compare]
>          if((q - q_base) >= sizeof(SelectorWordType)) {
>                                                    ^
> layer3/Selector.cpp: In function ‘DistSet* 
> SelectorGetDistSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, 
> float, float*)’:
> layer3/Selector.cpp:11845:32: warning: comparison between signed and 
> unsigned integer expressions [-Wsign-compare]
>    for(a = cNDummyAtoms; a < I->NAtom; a++) {
>                                 ^
> layer3/Selector.cpp:11859:34: warning: comparison between signed and 
> unsigned integer expressions [-Wsign-compare]
>      for(a = cNDummyAtoms; a < I->NAtom; a++) {
>                                   ^
> layer3/Selector.cpp: In function ‘DistSet* 
> SelectorGetAngleSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, 
> int, int, float*, int*)’:
> layer3/Selector.cpp:12102:34: warning: comparison between signed and 
> unsigned integer expressions [-Wsign-compare]
>      for(a = cNDummyAtoms; a < I->NAtom; a++) {
>                                   ^
> layer3/Selector.cpp:12118:34: warning: comparison between signed and 
> unsigned integer expressions [-Wsign-compare]
>      for(a = cNDummyAtoms; a < I->NAtom; a++) {
>                                   ^
> layer3/Selector.cpp:12146:36: warning: comparison between signed and 
> unsigned integer expressions [-Wsign-compare]
>        for(a = cNDummyAtoms; a < I->NAtom; a++) {
>                                     ^
> layer3/Selector.cpp: In function ‘DistSet* 
> SelectorGetDihedralSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, 
> int, int, int, int, float*, int*)’:
> layer3/Selector.cpp:12378:34: warning: comparison between signed and 
> unsigned integer expressions [-Wsign-compare]
>      for(a = cNDummyAtoms; a < I->NAtom; a++) {
>                                   ^
> layer3/Selector.cpp:12428:34: warning: comparison between signed and 
> unsigned integer expressions [-Wsign-compare]
>      for(a = cNDummyAtoms; a < I->NAtom; a++) {
>                                   ^
> layer3/Selector.cpp:12474:38: warning: comparison between signed and 
> unsigned integer expressions [-Wsign-compare]
>          for(a = cNDummyAtoms; a < I->NAtom; a++) {
>                                       ^
> layer3/Selector.cpp: In function ‘int SelectorLoadCoords(PyMOLGlobals*, 
> PyObject*, int, int)’:
> layer3/Selector.cpp:6705:9: warning: ‘itemsize’ may be used 
> uninitialized in this function [-Wmaybe-uninitialized]
>          switch(itemsize) {
>          ^
> 
> 
> ... and then nothing
> 
> -- 
> Dr Arnaud Basle                     X-ray facilities manager
> Newcastle Structural Biology Laboratory
> University of Newcastle
> Medical School
> ICAMB
> Framlington place
> NE2 4HH Newcastle upon tyne
> Phone 0191 208 8931

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Christian,

the pymol.session variable is not really part of the API -- means, not intended to be modified or accessed by the user. However, it's all Python and obviously not hidden, so you can mess around with it, if you do it right. Short answer is: Always access it as "pymol.session", don't do "from pymol import session". This works:

--- script.py ---
import pymol
from pymol import cmd

@cmd.extend
def print_session_id():
    print id(pymol.session)

@cmd.extend
def set_foo(value):
    pymol.session.foo = value

@cmd.extend
def print_foo():
    print pymol.session.foo
--- end script.py ---

Cheers,
  Thomas

On 29 Jan 2015, at 20:20, Christian Becke <chr...@fu...> wrote:

> Dear pymol experts,
> 
> I found some odd behaviour when trying to use pymol.session in my 
> script. I'm using open source pymol 1.7.4.0 (built from svn) on linux. 
> Here comes a minimal example:
> 
> 1) Create a directory, containing the following 2 files:
> 
> --- script.py ---
> from pymol import cmd, session
> 
> def print_session_id():
>     print id(session)
> cmd.extend("print_session_id", print_session_id)
> 
> def set_foo(value):
>     session.foo = value
> cmd.extend("set_foo", set_foo)
> 
> def print_foo():
>     print session.foo
> cmd.extend("print_foo", print_foo)
> --- end script.py ---
> 
> --- .pymolrc.py ---
> import script
> --- end .pymolrc.py ---
> 
> 2) Change to this directory and start pymol.
> 
> 3) In the pymol CLI, do:
> 
> script_set_foo bar
> script_print_foo
> script_session_id
> python
> print id(session)
> print session.foo
> session.foo = "foo"
> python end
> script_print_foo
> save test.pse
> 
> This produces the output given below. Note that the id of the session 
> object is the same when printed from the script and from within the 
> pymol session, and how the script reflects changes made to the 
> session.foo variable from the pymol CLI and vice versa.
> 
> --- pymol log ---
> PyMOL>script_set_foo bar
> PyMOL>script_print_foo
> bar
> PyMOL>script_session_id
> 139958033268464
> PyMOL>python
> PyMOL>print id(session)
>     1:print id(session)
> PyMOL>print session.foo
>     2:print session.foo
> PyMOL>session.foo = "foo"
>     3:session.foo = "foo"
> PyMOL>python end
> PyMOL>python end
> 139958033268464
> bar
> PyMOL>script_print_foo
> foo
> PyMOL>save test.pse
>  Save: Please wait -- writing session file...
>  Save: wrote "test.pse".
> PyMOL>quit
>  PyMOL: normal program termination.
> --- end pymol log ---
> 
> 4) If I now start pymol, load test.pse and run the following commands in 
> the pymol CLI:
> 
> script_print_foo
> script_session_id
> script_set_foo bar
> python
> print id(session)
> print session.foo
> python end
> 
> I get the following results:
> 
> --- pymol log ---
>  Executive: Loading version 1.740 session...
> PyMOL>script_print_foo
> Traceback (most recent call last):
>   File "/usr/lib64/python2.7/site-packages/pymol/parser.py", line 256, 
> in parse
>     self.result=apply(layer.kw[0],layer.args,layer.kw_args)
>   File "script.py", line 12, in script_print_foo
>     print session.foo
> AttributeError: Session_Storage instance has no attribute 'foo'
> PyMOL>script_session_id
> 139950852452080
> PyMOL>script_set_foo bar
> PyMOL>python
> PyMOL>print id(session)
>     1:print id(session)
> PyMOL>print session.foo
>     2:print session.foo
> PyMOL>python end
> PyMOL>python end
> 139950603504528
> foo
> PyMOL>script_print_foo
> bar
> --- end pymol log ---
> 
> Note that the ids of the session objects differ when printed from the 
> script or from the pymol CLI, and the contents of the variable 
> session.foo differs between pymol CLI and script.
> 
> If I do not import script.py from .pymolrc.py, everything works as expected.
> 
> Apparently, loading of a new session file creates a new instance of the 
> pymol.session object. Shouldn't the pymol.session instance be created 
> once upon startup, so it can be shared between all scripts? And only 
> values assigned to this instance upon loading a session from file?
> 
> Is there a way to import scripts from .pymolrc.py, load a session file 
> *and* get the correct pymol.session object within the script?
> Or is there an alternative way to get custom data saved in session files 
> that can be used in scripts?
> 
> 
> Best,
> 
> Christian

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Works perfectly, thanks a lot!

On 30.01.2015 21:31, Thomas Holder wrote:
> Hi Christian,
>
> the pymol.session variable is not really part of the API -- means,
> not intended to be modified or accessed by the user. However, it's
> all Python and obviously not hidden, so you can mess around with it,
> if you do it right. Short answer is: Always access it as
> "pymol.session", don't do "from pymol import session". This works:
>
> --- script.py --- import pymol from pymol import cmd
>
> @cmd.extend def print_session_id(): print id(pymol.session)
>
> @cmd.extend def set_foo(value): pymol.session.foo = value
>
> @cmd.extend def print_foo(): print pymol.session.foo --- end
> script.py ---
>
> Cheers, Thomas
>
> On 29 Jan 2015, at 20:20, Christian Becke
> <chr...@fu...> wrote:
>
>> Dear pymol experts,
>>
>> I found some odd behaviour when trying to use pymol.session in my
>> script. I'm using open source pymol 1.7.4.0 (built from svn) on
>> linux. Here comes a minimal example:
>>
>> 1) Create a directory, containing the following 2 files:
>>
>> --- script.py --- from pymol import cmd, session
>>
>> def print_session_id(): print id(session)
>> cmd.extend("print_session_id", print_session_id)
>>
>> def set_foo(value): session.foo = value cmd.extend("set_foo",
>> set_foo)
>>
>> def print_foo(): print session.foo cmd.extend("print_foo",
>> print_foo) --- end script.py ---
>>
>> --- .pymolrc.py --- import script --- end .pymolrc.py ---
>>
>> 2) Change to this directory and start pymol.
>>
>> 3) In the pymol CLI, do:
>>
>> script_set_foo bar script_print_foo script_session_id python print
>> id(session) print session.foo session.foo = "foo" python end
>> script_print_foo save test.pse
>>
>> This produces the output given below. Note that the id of the
>> session object is the same when printed from the script and from
>> within the pymol session, and how the script reflects changes made
>> to the session.foo variable from the pymol CLI and vice versa.
>>
>> --- pymol log --- PyMOL>script_set_foo bar PyMOL>script_print_foo
>> bar PyMOL>script_session_id 139958033268464 PyMOL>python
>> PyMOL>print id(session) 1:print id(session) PyMOL>print
>> session.foo 2:print session.foo PyMOL>session.foo = "foo"
>> 3:session.foo = "foo" PyMOL>python end PyMOL>python end
>> 139958033268464 bar PyMOL>script_print_foo foo PyMOL>save test.pse
>> Save: Please wait -- writing session file... Save: wrote
>> "test.pse". PyMOL>quit PyMOL: normal program termination. --- end
>> pymol log ---
>>
>> 4) If I now start pymol, load test.pse and run the following
>> commands in the pymol CLI:
>>
>> script_print_foo script_session_id script_set_foo bar python print
>> id(session) print session.foo python end
>>
>> I get the following results:
>>
>> --- pymol log --- Executive: Loading version 1.740 session...
>> PyMOL>script_print_foo Traceback (most recent call last): File
>> "/usr/lib64/python2.7/site-packages/pymol/parser.py", line 256, in
>> parse self.result=apply(layer.kw[0],layer.args,layer.kw_args) File
>> "script.py", line 12, in script_print_foo print session.foo
>> AttributeError: Session_Storage instance has no attribute 'foo'
>> PyMOL>script_session_id 139950852452080 PyMOL>script_set_foo bar
>> PyMOL>python PyMOL>print id(session) 1:print id(session)
>> PyMOL>print session.foo 2:print session.foo PyMOL>python end
>> PyMOL>python end 139950603504528 foo PyMOL>script_print_foo bar ---
>> end pymol log ---
>>
>> Note that the ids of the session objects differ when printed from
>> the script or from the pymol CLI, and the contents of the variable
>> session.foo differs between pymol CLI and script.
>>
>> If I do not import script.py from .pymolrc.py, everything works as
>> expected.
>>
>> Apparently, loading of a new session file creates a new instance of
>> the pymol.session object. Shouldn't the pymol.session instance be
>> created once upon startup, so it can be shared between all scripts?
>> And only values assigned to this instance upon loading a session
>> from file?
>>
>> Is there a way to import scripts from .pymolrc.py, load a session
>> file *and* get the correct pymol.session object within the script?
>> Or is there an alternative way to get custom data saved in session
>> files that can be used in scripts?
>>
>>
>> Best,
>>
>> Christian
>

Hi Matthew,

good catch, we'll fix that.

Cheers,
  Thomas

On 28 Jan 2015, at 17:43, Matthew Baumgartner <mp...@pi...> wrote:

> Hi,
> I've discovered a (relatively minor) bug in the Save Molecule... dialog 
> box. This happened because I always have tons of windows up on multiple 
> monitors and it got lost.
> 
> To reproduce:
> Go to File > Save Molecule...
> Don't close the window, and do it again
> Go to File > Save Molecule...
> 
> Now you can close one of the dialogs by hitting Cancel as usual. Now if 
> you hit Cancel or Ok or the X in the corner on the other dialog, it 
> throw an error, and you can't get it to close without closing the parent 
> pymol session.
> 
> Error: 2
> <type 'exceptions.AttributeError'> Exception in Tk callback
>   Function: <function <lambda> at 0x7fc557515848> (type: <type 'function'>)
>   Args: ()
> Traceback (innermost last):
>   File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", 
> line 1747, in __call__
>     return apply(self.func, args)
>   File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py", 
> line 153, in <lambda>
>     command=lambda self=self, name=name: self._doCommand(name))
>   File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py", 
> line 132, in _doCommand
>     return command(name)
>   File 
> "/usr/local/lib/python2.7/dist-packages/pmg_tk/skins/normal/__init__.py", line 
> 792, in file_save2
>     self.my_withdraw(self.dialog)
> <type 'exceptions.AttributeError'>: Normal instance has no attribute 
> 'dialog'
> 
> 
> 
> Most of the errors appear to be in the Pwm code, which you obviously 
> don't control. I haven't dived into the code myself, but I think that 
> you can catch this by detecting when the dialog is open and if another 
> one tries to open, call raise() on the original one.
> 
> I'm running pymol 1.7.4.0, revision 4107 from the SVN built from source 
> on Ubuntu 14.04.

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear Matic,

the only option to permanently store those paths is to edit the plugin file. Look for "apbs_tools.py" in the PyMOL installation directory and there for "Global config variables".

Cheers,
  Thomas

On 30 Jan 2015, at 00:33, Matic Kisovec <Mat...@ki...> wrote:

> Dear Thomas,
> 
> thank you for your quick reply. 
> I can confirm that now APBS tools2.1 plugin inside Pymol 1.7.4 works as expected.
> 
> I do have one more issue. Every time I execute Pymol I get two lines saying:
> Could not find default location for file: psize.py
> Could not find default location for file: pdb2pqr.py
> I manually set up the paths but they get lost when I exit pymol.
> Is there a way to permanently store this information?
> 
> Kind regards,
> Matic
> 
> On 28. 01. 2015 16:58, Thomas Holder wrote:
>> Dear Matic,
>> 
>> this was fixed for 1.7.4: 
>> https://sourceforge.net/p/pymol/code/4099/
>> 
>> 
>> Please install the latest version.
>> 
>> Cheers,
>>   Thomas
>> 
>> On 28 Jan 2015, at 10:04, Matic Kisovec 
>> <Mat...@ki...>
>>  wrote:
>> 
>> 
>>> Dear Pymol users,
>>> 
>>> I have recieved the same error as mentioned in the email ate bottom that was sent by DE FALCO JR LOUIS in September 2014 to this list. There was one reply that is a known bug and a link was provided. The bug was filed in March 2013.
>>> 
>>> The difference is this time this happened on Ubuntu 14.04.1 OS. So I tried a quick and fresh install inside Virtualbox and after the OS installation finished I installed Pymol and its dependencies. Pymol version in Ubuntu repositories is 1.7.0. When I select Plugin>APBS Tools2.1 I get a popup with the following error that is almost identical to the one from DE FALCO JR LOUIS:
>>> Error: 1
>>> <class '_tkinter.TclError'> Exception in Tk callback
>>>   Function: <function <lambda> at 0x7faa60852578> (type: <type 'function'>)
>>>   Args: ()
>>> Traceback (innermost last):
>>>   File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__
>>>     return apply(self.func, args)
>>>   File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line 314, in <lambda>
>>>     command = lambda s=self: APBSTools2(s))
>>>   File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line 680, in __init__
>>>     group.pack(fill='both',expand=1, padx=4, pady=5)
>>>   File "<string>", line 1, in pack
>>>     None
>>>   File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 1890, in pack_configure
>>>     + self._options(cnf, kw))
>>> <class '_tkinter.TclError'>: cannot use geometry manager pack inside .140369735891136.140369735892288.140369735980600.140369614990728 which already has slaves managed by grid
>>> I am wondering though if this is some problem on my side since it has not been mentioned very often online. That is why I tried a fresh installation inside Virtualbox and the issue was the same.
>>> 
>>> Any help would be greatly appreciated.
>>> 
>>> Kind regards,
>>> Matic
>>> 
>>> 
>>> 
>>> Hello, 
>>> 
>>>      I just updated PyMol Open Source to version 1.7.2.0-2 via the fink package manager.  Now, when I initiate the APBS Tools.1 plugin the following error occurs:
>>> 
>>> Error in background function
>>> 
>>> Error: 1
>>> <class '_tkinter.TclError'> Exception in Tk callback
>>>   Function: <function <lambda> at 0x10cc75230> (type: <type 'function'>)
>>>   Args: ()
>>> Traceback (innermost last):
>>>   File "/sw/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py", line 1753, in __call__
>>>     return apply(self.func, args)
>>>   File "/sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py", line 314, in <lambda>
>>>     command = lambda s=self: APBSTools2(s))
>>>   File "/sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py", line 680, in __init__
>>>     group.pack(fill='both',expand=1, padx=4, pady=5)
>>>   File "<string>", line 1, in pack
>>>     None
>>>   File "/sw/lib/python2.7/lib-tk/Tkinter.py", line 1887, in pack_configure
>>>     + self._options(cnf, kw))
>>> <class '_tkinter.TclError'>: cannot use geometry manager pack inside .4509565296.4509566808.4509809840.4510083120 which already has slaves managed by grid
>>> 
>>> I brought this to the attention of apbs developers who suggested I post this error here as it seems related to PyMol and not apbs.  Not a very savvy user here so this may be entirely my fault.
>>> 
>>> Thank you!

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Monica and Andreas,

you can also do this with the builder.

1) http://pymolwiki.org/index.php/Builder
2) Click "P=O3" (Phosphite)
3) Click the Serine OG atom

Cheers,
  Thomas

On 30 Jan 2015, at 12:14, Andreas Warnecke <4nd...@gm...> wrote:

> Hi Monica,
> 
> You can check out the plugin PyTMs, which allows you to introduce PTMs into protein models within PyMOL:
> http://www.pymolwiki.org/index.php/Pytms
> 
> Let me know should you need any assistance with this plugin.
> 
> Cheers,
> 
> Andreas
> 
> On Fri, Jan 30, 2015 at 4:59 PM, Monica Mittal <mon...@gm...> wrote:
> Hi,
> Does any one know if there is a simple way to mutate a serine to a phosphoserine using pymol? Or what would be the best way to achieve this?
> Thanks
> Monica

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Monica,

You can check out the plugin PyTMs, which allows you to introduce PTMs into
protein models within PyMOL:
http://www.pymolwiki.org/index.php/Pytms

Let me know should you need any assistance with this plugin.

Cheers,

Andreas



On Fri, Jan 30, 2015 at 4:59 PM, Monica Mittal <mon...@gm...>
wrote:

> Hi,
>
> Does any one know if there is a simple way to mutate a serine to a phosphoserine using pymol? Or what would be the best way to achieve this?
>
> Thanks
>
> Monica
>
>
>
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Hi,

Does any one know if there is a simple way to mutate a serine to a
phosphoserine using pymol? Or what would be the best way to achieve
this?

Thanks

Monica

Dear PyMol,  I am doing now one of the Open3D QSAR tutorials and have the problem that I need to remove the colored surfaces.
http://open3dqsar.sourceforge.net/?Tutorials
I can't find how to do it. Can you please recommend me how can I remove the colored isosurface (isosurf command)?

Best regards,
Andrey

Dear all,

I am trying to compile pymol from source following the instructions 
here: http://www.pymolwiki.org/index.php/Linux_Install

It used to work for me a while ago but now the compilation hangs without 
error. Pressing return give me back the terminal prompt. The compiling 
process does not stop always at the same point.

I am using Linux Mint 17 64 bits (based on Ubuntu).

Anyone has seen such behaviour?

Cheers,
Arnaud
PS: see below example of output

layer3/Selector.cpp:11037:36: warning: comparison between signed and 
unsigned integer expressions [-Wsign-compare]
        for(a = cNDummyAtoms; a < I->NAtom; a++)
                                     ^
layer3/Selector.cpp: In function ‘int* SelectorEvaluate(PyMOLGlobals*, 
char (*)[1024], int, int)’:
layer3/Selector.cpp:11107:15: warning: variable ‘opFlag2’ set but not 
used [-Wunused-but-set-variable]
    int opFlag, opFlag2, maxLevel;
                ^
layer3/Selector.cpp:11108:19: warning: variable ‘cc2’ set but not used 
[-Wunused-but-set-variable]
    char *q, *cc1, *cc2;
                    ^
layer3/Selector.cpp: In function ‘char (* SelectorParse(PyMOLGlobals*, 
char*))[1024]’:
layer3/Selector.cpp:11562:51: warning: comparison between signed and 
unsigned integer expressions [-Wsign-compare]
          if((q - q_base) >= sizeof(SelectorWordType)) {
                                                    ^
layer3/Selector.cpp: In function ‘DistSet* 
SelectorGetDistSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, 
float, float*)’:
layer3/Selector.cpp:11845:32: warning: comparison between signed and 
unsigned integer expressions [-Wsign-compare]
    for(a = cNDummyAtoms; a < I->NAtom; a++) {
                                 ^
layer3/Selector.cpp:11859:34: warning: comparison between signed and 
unsigned integer expressions [-Wsign-compare]
      for(a = cNDummyAtoms; a < I->NAtom; a++) {
                                   ^
layer3/Selector.cpp: In function ‘DistSet* 
SelectorGetAngleSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, 
int, int, float*, int*)’:
layer3/Selector.cpp:12102:34: warning: comparison between signed and 
unsigned integer expressions [-Wsign-compare]
      for(a = cNDummyAtoms; a < I->NAtom; a++) {
                                   ^
layer3/Selector.cpp:12118:34: warning: comparison between signed and 
unsigned integer expressions [-Wsign-compare]
      for(a = cNDummyAtoms; a < I->NAtom; a++) {
                                   ^
layer3/Selector.cpp:12146:36: warning: comparison between signed and 
unsigned integer expressions [-Wsign-compare]
        for(a = cNDummyAtoms; a < I->NAtom; a++) {
                                     ^
layer3/Selector.cpp: In function ‘DistSet* 
SelectorGetDihedralSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, 
int, int, int, int, float*, int*)’:
layer3/Selector.cpp:12378:34: warning: comparison between signed and 
unsigned integer expressions [-Wsign-compare]
      for(a = cNDummyAtoms; a < I->NAtom; a++) {
                                   ^
layer3/Selector.cpp:12428:34: warning: comparison between signed and 
unsigned integer expressions [-Wsign-compare]
      for(a = cNDummyAtoms; a < I->NAtom; a++) {
                                   ^
layer3/Selector.cpp:12474:38: warning: comparison between signed and 
unsigned integer expressions [-Wsign-compare]
          for(a = cNDummyAtoms; a < I->NAtom; a++) {
                                       ^
layer3/Selector.cpp: In function ‘int SelectorLoadCoords(PyMOLGlobals*, 
PyObject*, int, int)’:
layer3/Selector.cpp:6705:9: warning: ‘itemsize’ may be used 
uninitialized in this function [-Wmaybe-uninitialized]
          switch(itemsize) {
          ^


... and then nothing

-- 
Dr Arnaud Basle                     X-ray facilities manager
Newcastle Structural Biology Laboratory
University of Newcastle
Medical School
ICAMB
Framlington place
NE2 4HH Newcastle upon tyne
Phone 0191 208 8931
                        

Dear Thomas,

thank you for your quick reply.
I can confirm that now APBS tools2.1 plugin inside Pymol 1.7.4 works as expected.

I do have one more issue. Every time I execute Pymol I get two lines saying:
Could not find default location for file: psize.py
Could not find default location for file: pdb2pqr.py
I manually set up the paths but they get lost when I exit pymol.
Is there a way to permanently store this information?

Kind regards,
Matic



On 28. 01. 2015 16:58, Thomas Holder wrote:

Dear Matic,

this was fixed for 1.7.4: https://sourceforge.net/p/pymol/code/4099/

Please install the latest version.

Cheers,
  Thomas

On 28 Jan 2015, at 10:04, Matic Kisovec <Mat...@ki...><mailto:Mat...@ki...> wrote:



Dear Pymol users,

I have recieved the same error as mentioned in the email ate bottom that was sent by DE FALCO JR LOUIS in September 2014 to this list. There was one reply that is a known bug and a link was provided. The bug was filed in March 2013.

The difference is this time this happened on Ubuntu 14.04.1 OS. So I tried a quick and fresh install inside Virtualbox and after the OS installation finished I installed Pymol and its dependencies. Pymol version in Ubuntu repositories is 1.7.0. When I select Plugin>APBS Tools2.1 I get a popup with the following error that is almost identical to the one from DE FALCO JR LOUIS:
Error: 1
<class '_tkinter.TclError'> Exception in Tk callback
  Function: <function <lambda> at 0x7faa60852578> (type: <type 'function'>)
  Args: ()
Traceback (innermost last):
  File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__
    return apply(self.func, args)
  File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line 314, in <lambda>
    command = lambda s=self: APBSTools2(s))
  File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line 680, in __init__
    group.pack(fill='both',expand=1, padx=4, pady=5)
  File "<string>", line 1, in pack
    None
  File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 1890, in pack_configure
    + self._options(cnf, kw))
<class '_tkinter.TclError'>: cannot use geometry manager pack inside .140369735891136.140369735892288.140369735980600.140369614990728 which already has slaves managed by grid
I am wondering though if this is some problem on my side since it has not been mentioned very often online. That is why I tried a fresh installation inside Virtualbox and the issue was the same.

Any help would be greatly appreciated.

Kind regards,
Matic



Hello,

     I just updated PyMol Open Source to version 1.7.2.0-2 via the fink package manager.  Now, when I initiate the APBS Tools.1 plugin the following error occurs:

Error in background function

Error: 1
<class '_tkinter.TclError'> Exception in Tk callback
  Function: <function <lambda> at 0x10cc75230> (type: <type 'function'>)
  Args: ()
Traceback (innermost last):
  File "/sw/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py", line 1753, in __call__
    return apply(self.func, args)
  File "/sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py", line 314, in <lambda>
    command = lambda s=self: APBSTools2(s))
  File "/sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py", line 680, in __init__
    group.pack(fill='both',expand=1, padx=4, pady=5)
  File "<string>", line 1, in pack
    None
  File "/sw/lib/python2.7/lib-tk/Tkinter.py", line 1887, in pack_configure
    + self._options(cnf, kw))
<class '_tkinter.TclError'>: cannot use geometry manager pack inside .4509565296.4509566808.4509809840.4510083120 which already has slaves managed by grid

I brought this to the attention of apbs developers who suggested I post this error here as it seems related to PyMol and not apbs.  Not a very savvy user here so this may be entirely my fault.

Thank you!

Dear pymol experts,

I found some odd behaviour when trying to use pymol.session in my 
script. I'm using open source pymol 1.7.4.0 (built from svn) on linux. 
Here comes a minimal example:

1) Create a directory, containing the following 2 files:

--- script.py ---
from pymol import cmd, session

def print_session_id():
     print id(session)
cmd.extend("print_session_id", print_session_id)

def set_foo(value):
     session.foo = value
cmd.extend("set_foo", set_foo)

def print_foo():
     print session.foo
cmd.extend("print_foo", print_foo)
--- end script.py ---

--- .pymolrc.py ---
import script
--- end .pymolrc.py ---

2) Change to this directory and start pymol.

3) In the pymol CLI, do:

script_set_foo bar
script_print_foo
script_session_id
python
print id(session)
print session.foo
session.foo = "foo"
python end
script_print_foo
save test.pse

This produces the output given below. Note that the id of the session 
object is the same when printed from the script and from within the 
pymol session, and how the script reflects changes made to the 
session.foo variable from the pymol CLI and vice versa.

--- pymol log ---
PyMOL>script_set_foo bar
PyMOL>script_print_foo
bar
PyMOL>script_session_id
139958033268464
PyMOL>python
PyMOL>print id(session)
     1:print id(session)
PyMOL>print session.foo
     2:print session.foo
PyMOL>session.foo = "foo"
     3:session.foo = "foo"
PyMOL>python end
PyMOL>python end
139958033268464
bar
PyMOL>script_print_foo
foo
PyMOL>save test.pse
  Save: Please wait -- writing session file...
  Save: wrote "test.pse".
PyMOL>quit
  PyMOL: normal program termination.
--- end pymol log ---

4) If I now start pymol, load test.pse and run the following commands in 
the pymol CLI:

script_print_foo
script_session_id
script_set_foo bar
python
print id(session)
print session.foo
python end

I get the following results:

--- pymol log ---
  Executive: Loading version 1.740 session...
PyMOL>script_print_foo
Traceback (most recent call last):
   File "/usr/lib64/python2.7/site-packages/pymol/parser.py", line 256, 
in parse
     self.result=apply(layer.kw[0],layer.args,layer.kw_args)
   File "script.py", line 12, in script_print_foo
     print session.foo
AttributeError: Session_Storage instance has no attribute 'foo'
PyMOL>script_session_id
139950852452080
PyMOL>script_set_foo bar
PyMOL>python
PyMOL>print id(session)
     1:print id(session)
PyMOL>print session.foo
     2:print session.foo
PyMOL>python end
PyMOL>python end
139950603504528
foo
PyMOL>script_print_foo
bar
--- end pymol log ---

Note that the ids of the session objects differ when printed from the 
script or from the pymol CLI, and the contents of the variable 
session.foo differs between pymol CLI and script.

If I do not import script.py from .pymolrc.py, everything works as expected.

Apparently, loading of a new session file creates a new instance of the 
pymol.session object. Shouldn't the pymol.session instance be created 
once upon startup, so it can be shared between all scripts? And only 
values assigned to this instance upon loading a session from file?

Is there a way to import scripts from .pymolrc.py, load a session file 
*and* get the correct pymol.session object within the script?
Or is there an alternative way to get custom data saved in session files 
that can be used in scripts?


Best,

Christian

Hi,
I've discovered a (relatively minor) bug in the Save Molecule... dialog 
box. This happened because I always have tons of windows up on multiple 
monitors and it got lost.

To reproduce:
Go to File > Save Molecule...
Don't close the window, and do it again
Go to File > Save Molecule...

Now you can close one of the dialogs by hitting Cancel as usual. Now if 
you hit Cancel or Ok or the X in the corner on the other dialog, it 
throw an error, and you can't get it to close without closing the parent 
pymol session.

Error: 2
<type 'exceptions.AttributeError'> Exception in Tk callback
   Function: <function <lambda> at 0x7fc557515848> (type: <type 'function'>)
   Args: ()
Traceback (innermost last):
   File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", 
line 1747, in __call__
     return apply(self.func, args)
   File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py", 
line 153, in <lambda>
     command=lambda self=self, name=name: self._doCommand(name))
   File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py", 
line 132, in _doCommand
     return command(name)
   File 
"/usr/local/lib/python2.7/dist-packages/pmg_tk/skins/normal/__init__.py", line 
792, in file_save2
     self.my_withdraw(self.dialog)
<type 'exceptions.AttributeError'>: Normal instance has no attribute 
'dialog'



Most of the errors appear to be in the Pwm code, which you obviously 
don't control. I haven't dived into the code myself, but I think that 
you can catch this by detecting when the dialog is open and if another 
one tries to open, call raise() on the original one.

I'm running pymol 1.7.4.0, revision 4107 from the SVN built from source 
on Ubuntu 14.04.

Dear Matic,

this was fixed for 1.7.4: https://sourceforge.net/p/pymol/code/4099/

Please install the latest version.

Cheers,
  Thomas

On 28 Jan 2015, at 10:04, Matic Kisovec <Mat...@ki...> wrote:

> Dear Pymol users,
> 
> I have recieved the same error as mentioned in the email ate bottom that was sent by DE FALCO JR LOUIS in September 2014 to this list. There was one reply that is a known bug and a link was provided. The bug was filed in March 2013.
> 
> The difference is this time this happened on Ubuntu 14.04.1 OS. So I tried a quick and fresh install inside Virtualbox and after the OS installation finished I installed Pymol and its dependencies. Pymol version in Ubuntu repositories is 1.7.0. When I select Plugin>APBS Tools2.1 I get a popup with the following error that is almost identical to the one from DE FALCO JR LOUIS:
> Error: 1
> <class '_tkinter.TclError'> Exception in Tk callback
>   Function: <function <lambda> at 0x7faa60852578> (type: <type 'function'>)
>   Args: ()
> Traceback (innermost last):
>   File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__
>     return apply(self.func, args)
>   File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line 314, in <lambda>
>     command = lambda s=self: APBSTools2(s))
>   File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line 680, in __init__
>     group.pack(fill='both',expand=1, padx=4, pady=5)
>   File "<string>", line 1, in pack
>     None
>   File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 1890, in pack_configure
>     + self._options(cnf, kw))
> <class '_tkinter.TclError'>: cannot use geometry manager pack inside .140369735891136.140369735892288.140369735980600.140369614990728 which already has slaves managed by grid
> I am wondering though if this is some problem on my side since it has not been mentioned very often online. That is why I tried a fresh installation inside Virtualbox and the issue was the same.
> 
> Any help would be greatly appreciated.
> 
> Kind regards,
> Matic
> 
> 
> 
> Hello, 
> 
>      I just updated PyMol Open Source to version 1.7.2.0-2 via the fink package manager.  Now, when I initiate the APBS Tools.1 plugin the following error occurs:
> 
> Error in background function
> 
> Error: 1
> <class '_tkinter.TclError'> Exception in Tk callback
>   Function: <function <lambda> at 0x10cc75230> (type: <type 'function'>)
>   Args: ()
> Traceback (innermost last):
>   File "/sw/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py", line 1753, in __call__
>     return apply(self.func, args)
>   File "/sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py", line 314, in <lambda>
>     command = lambda s=self: APBSTools2(s))
>   File "/sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py", line 680, in __init__
>     group.pack(fill='both',expand=1, padx=4, pady=5)
>   File "<string>", line 1, in pack
>     None
>   File "/sw/lib/python2.7/lib-tk/Tkinter.py", line 1887, in pack_configure
>     + self._options(cnf, kw))
> <class '_tkinter.TclError'>: cannot use geometry manager pack inside .4509565296.4509566808.4509809840.4510083120 which already has slaves managed by grid
> 
> I brought this to the attention of apbs developers who suggested I post this error here as it seems related to PyMol and not apbs.  Not a very savvy user here so this may be entirely my fault.
> 
> Thank you!

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear Pymol users,

I have recieved the same error as mentioned in the email ate bottom that was sent by DE FALCO JR LOUIS in September 2014 to this list. There was one reply that is a known bug and a link was provided. The bug was filed in March 2013.

The difference is this time this happened on Ubuntu 14.04.1 OS. So I tried a quick and fresh install inside Virtualbox and after the OS installation finished I installed Pymol and its dependencies. Pymol version in Ubuntu repositories is 1.7.0. When I select Plugin>APBS Tools2.1 I get a popup with the following error that is almost identical to the one from DE FALCO JR LOUIS:
Error: 1
<class '_tkinter.TclError'> Exception in Tk callback
  Function: <function <lambda> at 0x7faa60852578> (type: <type 'function'>)
  Args: ()
Traceback (innermost last):
  File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__
    return apply(self.func, args)
  File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line 314, in <lambda>
    command = lambda s=self: APBSTools2(s))
  File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line 680, in __init__
    group.pack(fill='both',expand=1, padx=4, pady=5)
  File "<string>", line 1, in pack
    None
  File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 1890, in pack_configure
    + self._options(cnf, kw))
<class '_tkinter.TclError'>: cannot use geometry manager pack inside .140369735891136.140369735892288.140369735980600.140369614990728 which already has slaves managed by grid
I am wondering though if this is some problem on my side since it has not been mentioned very often online. That is why I tried a fresh installation inside Virtualbox and the issue was the same.

Any help would be greatly appreciated.

Kind regards,
Matic




Hello,

     I just updated PyMol Open Source to version 1.7.2.0-2 via the fink package manager.  Now, when I initiate the APBS Tools.1 plugin the following error occurs:

Error in background function

Error: 1
<class '_tkinter.TclError'> Exception in Tk callback
  Function: <function <lambda> at 0x10cc75230> (type: <type 'function'>)
  Args: ()
Traceback (innermost last):
  File "/sw/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py", line 1753, in __call__
    return apply(self.func, args)
  File "/sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py", line 314, in <lambda>
    command = lambda s=self: APBSTools2(s))
  File "/sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py", line 680, in __init__
    group.pack(fill='both',expand=1, padx=4, pady=5)
  File "<string>", line 1, in pack
    None
  File "/sw/lib/python2.7/lib-tk/Tkinter.py", line 1887, in pack_configure
    + self._options(cnf, kw))
<class '_tkinter.TclError'>: cannot use geometry manager pack inside .4509565296.4509566808.4509809840.4510083120 which already has slaves managed by grid

I brought this to the attention of apbs developers who suggested I post this error here as it seems related to PyMol and not apbs.  Not a very savvy user here so this may be entirely my fault.

Thank you!

This occurs when retain_order is set before loading a protein.

You have to:
unset retain_order
Then load your protein again.

You might say: "I didn't set retain_order". This is likely true. Some very
popular pymol plugins set it when loaded, most famously the autodock plugin.

-David


On Tue, Jan 27, 2015 at 2:58 AM, Biao Ma <jac...@gm...> wrote:

> Hi, pymol users.
>
> I want to change same residues to another one.
>
> I try to do it refer to following site, I changed TRY128 to PHE128,
> http://www.pymolwiki.org/index.php/Mutagenesis
>
> But when I save the modified molecular to PDB file, the sequence of
> residue is out of turn.
>
> Who can tell me how to fix this problem?
>
> Thank a lot.
>
> Jacky
>
> The following is a part of PDB.(the original pdb file is start from 124)
>
> ATOM      1  N   GLY A 124      -9.861  12.581   5.804  1.00  1.00
>   N
> TER       2      GLY A 124
> ATOM      3  N   PHE A 128     -12.196  10.147   0.017  1.00  0.00
>   N
> TER       4      PHE A 128
> ATOM      5  CA  GLY A 124     -10.625  12.191   4.609  1.00  1.00
>   C
> TER       6      GLY A 124
> ATOM      7  CA  PHE A 128     -11.765   8.834   0.485  1.00  0.00
>   C
> TER       8      PHE A 128
> ATOM      9  C   GLY A 124      -9.855  12.324   3.299  1.00  1.00
>   C
> TER      10      GLY A 124
>
> [image: Inline image 1]
>
>
> ------------------------------------------------------------------------------
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> your
> hub for all things parallel software development, from weekly thought
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi, pymol users.

I want to change same residues to another one.

I try to do it refer to following site, I changed TRY128 to PHE128,
http://www.pymolwiki.org/index.php/Mutagenesis

But when I save the modified molecular to PDB file, the sequence of residue
is out of turn.

Who can tell me how to fix this problem?

Thank a lot.

Jacky

The following is a part of PDB.(the original pdb file is start from 124)

ATOM      1  N   GLY A 124      -9.861  12.581   5.804  1.00  1.00
  N
TER       2      GLY A 124
ATOM      3  N   PHE A 128     -12.196  10.147   0.017  1.00  0.00
  N
TER       4      PHE A 128
ATOM      5  CA  GLY A 124     -10.625  12.191   4.609  1.00  1.00
  C
TER       6      GLY A 124
ATOM      7  CA  PHE A 128     -11.765   8.834   0.485  1.00  0.00
  C
TER       8      PHE A 128
ATOM      9  C   GLY A 124      -9.855  12.324   3.299  1.00  1.00
  C
TER      10      GLY A 124

[image: Inline image 1]

Hi Albert -

Surface mode 2 outlines the mesh edges with thin cylinders, but if I remember correctly, I think PyMOL’s OBJ export doesn’t do cylinders (or spheres or cones), only triangle meshes.  You could try exporting to VRML2 (.wrl) or COLLADA (.dae) format and using something like, e.g. Blender to convert to OBJ if that’s what you really need.

Hope that helps,
Jared

P.S. Albert - sorry for the duplicate email, I forgot to CC the list last time…

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Jan 21, 2015, at 5:50 AM, Albert Solernou <a.s...@le...<mailto:a.s...@le...>> wrote:

Hi,
I am trying to get a .obj file, but fail when setting up surface_type to
2. More explicitly:
load 1ppe.pdb, 1ppe
set surface_type, 2
hide everything
show surface
shows a nice triangulated surface. However,
save myscene.obj
saves an empty file.

I've tried pymol versions 1.7.4 and 1.6.0. Saving into an obj file works
well when surface_type is set to 0, or 1. Any help?

Best,
Albert


--
---------------------------------
  Dr Albert Solernou
  EPSRC Research Fellow,
  Department of Physics and Astronomy,
  University of Leeds

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Hello,

I am using PyMOL in my senior biochemistry course. I am using a Macbook Pro with the latest version of the OS. I downloaded the educational version of PyMOL, and was able to load a PDB file, 2G47, and manipulate colors and what is seen and what is hidden. However, I attempted to use the Mutagenesis wizard for my project, in which we have to create an enzyme mutant, and I was unable to mutate the residue. I looked on the PyMOL wiki page under mutagenesis, and followed the tutorial. However, I was still not able to mutate the residue; instead I got the following message:

You clicked /2G47//D/PHE`19/CA
Traceback (most recent call last):
  File "/Applications/MacPyMOLEdu.app/pymol/modules/pymol/creating.py", line 742, in fragment
    reduce(operator.__add__,map(lambda a:a.coord[0],model.atom)),
AttributeError: 'module' object has no attribute 'reduce'
Error: unable to load fragment 'lys'.
Traceback (most recent call last):
  File "/Applications/MacPyMOLEdu.app/pymol/modules/pymol/wizard/mutagenesis.py", line 732, in do_select
    self.do_library()
  File "/Applications/MacPyMOLEdu.app/pymol/modules/pymol/wizard/mutagenesis.py", line 502, in do_library
    cmd.fragment(string.lower(frag_type),frag_name)
  File "/Applications/MacPyMOLEdu.app/pymol/modules/pymol/creating.py", line 760, in fragment
    if _self._raising(r,_self): raise pymol.CmdException
pymol.CmdException: <pymol.CmdException instance at 0xd2e39e0>

I tried multiple different residues, but got the same message each time. I need to be able to use PyMOL for my class for multiple projects, and I need to be able to create mutants and model them.

Dear Pymol users
I would like to use Pymol (1.7.4)  with 3D stereo, so I bought a nVidia Quadro K4200, an asus VG278H and nVidia vision 2 kit ( with IR emitter) and I'm using Windows 7 Pro x64. 
I installed the latest nVidia driver for Quadro card (347.25) . In the nVidia control Panel for Pymol I set '' enable stereo '' to ON. In Pymol, when I click on display - Quad buffered, the light of the IR transmitter turn green but I get flickering and no 3D effect on the molecule. What is the issue ?
Cheers
Sam 		 	   		  

> On Jan 23, 2015, at 7:32 PM, McCully, Dwayne (NIH/NIAMS) [C] <dmc...@ma...> wrote:
> 
> When running "python setup.py build" in the pymol directory of version 1.7.4.0,
> I get an error that stops pymol from compiling (see below).  Does anyone know how
> to fix this problem.
> 
> Dwayne
> 
> 
> layer3/Executive.cpp:13998: error: ‘glutLeaveFullScreen’ was not declared in this scope


This was fixed in the svn commit following 1.7.4.0 (commit 4105)

http://sourceforge.net/p/pymol/code/4107/log/?path=/trunk <" rel="nofollow">http://sourceforge.net/p/pymol/code/4107/log/?path=/trunk>

-David

When running "python setup.py build" in the pymol directory of version 1.7.4.0,
I get an error that stops pymol from compiling (see below).  Does anyone know how
to fix this problem.

Dwayne


gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python2.6 -c layer5/PyMOL.cpp -o build/temp.linux-x86_64-2.6/layer5/PyMOL.o -Werror=implicit-function-declaration -Werror=declaration-after-statement -Wno-write-strings -Wno-unused-function -Wno-empty-body -Wno-char-subscripts -ffast-math -funroll-loops -O3 -fcommon
layer2/ObjectMap.cpp: In function ‘int ObjectMapCCP4StrToMap(ObjectMap*, char*, int, int, int)’:
layer2/ObjectMap.cpp:2487: warning: comparison between signed and unsigned integer expressions
layer3/Executive.cpp: In function ‘void ExecutiveFullScreen(PyMOLGlobals*, int)’:
layer3/Executive.cpp:13998: error: ‘glutLeaveFullScreen’ was not declared in this scope
layer3/Executive.cpp:13981: warning: unused variable ‘I’
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python2.6 -c layer1/Symmetry.cpp -o build/temp.linux-x86_64-2.6/layer1/Symmetry.o -Werror=implicit-function-declaration -Werror=declaration-after-statement -Wno-write-strings -Wno-unused-function -Wno-empty-body -Wno-char-subscripts -ffast-math -funroll-loops -O3 -fcommon
error: command 'gcc' failed with exit status 1gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python2.6 -c contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c -o build/temp.linux-x86_64-2.6/contrib/uiuc/plugins/molfi
le_plugin/src/vaspoutcarplugin.o -Werror=implicit-function-declaration -Werror=declaration-after-statement -Wno-write-strings -Wno-unused-function -Wno-empty-body -Wno-char-subscripts -ffast-math -funroll-loops -O3 -fcommon
[root@tb3-2e32-linux pymol]# contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function ‘open_vaspoutcar_read’:
contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:88: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function ‘read_vaspoutcar_structure’:
contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:205: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function ‘read_vaspoutcar_timestep’:
contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:240: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:243: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
layer2/RepCartoon.cpp: In function ‘void do_ring(PyMOLGlobals*, short int, int, int*, ObjectMolecule*, CoordSet*, float, CGO*, int, int, float, int, int, int, int, int*, int, float, float, int*, float*, float)’:
layer2/RepCartoon.cpp:263: warning: ‘ai’ may be used uninitialized in this function
layer2/ObjectMap.cpp: In function ‘int ObjectMapNumPyArrayToMapState(PyMOLGlobals*, ObjectMapState*, PyObject*, int)’:
layer2/ObjectMap.cpp:5533: warning: ‘dens’ may be used uninitialized in this function
layer5/PyMOL.cpp: In function ‘PyMOLreturn_status Loader(CPyMOL*, char*, char*, int, char*, char*, int, int, int, int, int, int)’:
layer5/PyMOL.cpp:3106: warning: comparison between signed and unsigned integer expressions
layer2/ObjectMap.cpp: In function ‘int ObjectMapStateTrim(PyMOLGlobals*, ObjectMapState*, float*, float*, int)’:
layer2/ObjectMap.cpp:491: warning: ‘frac_mn’ may be used uninitialized in this function
layer2/ObjectMap.cpp:492: warning: ‘frac_mx’ may be used uninitialized in this function

Thanks to both of you, guys.

I settled on something far more trivial, sparked by the hide everything command in Tsjerk’s suggestion ☺  Involves a tiny bit of manual labor but works for me.

Cheers and Thanks!
Markus

From: Tsjerk Wassenaar [mailto:ts...@gm...]
Sent: Wednesday, January 21, 2015 1:49 PM
To: H. Adam Steinberg
Cc: Markus Heller; pym...@li...
Subject: Re: [PyMOL] Clip surface only


Hey :)

If you want to do it using only Pymol in just a few minutes, try this:

set auto_zoom, 0
scale=1.0
import numpy
M=numpy.array(cmd.get_view()).reshape(6,3)
cmd.pseudoatom("dummy",pos=list(M[4,:]-scale*numpy.dot(M[:3,:3],M[3,:])))
hide everything, (not ligand) within 150 of dummy
Adjust the scale to get a more curved or more planar clip.

Hope it helps,

Tsjerk

On Wed, Jan 21, 2015 at 10:21 PM, H. Adam Steinberg <h.a...@gm...<mailto:h.a...@gm...>> wrote:
if you have access to Gimp or photoshop and want to do this in just a few minutes… clip and render the surface how you want it, then without moving anything, unclip and render just the ligand. In any bitmap editing program layer the ligand image over the clipped surface image and merge the two into one image.


> On Jan 21, 2015, at 2:57 PM, Markus Heller <mh...@cd...<mailto:mh...@cd...>> wrote:
>
> Hello all,
>
> I'm trying to show a ligand in a binding site, and I'd like to selectively clip the surface only.  I haven't found anything on the web, only that it was not possible a few years ago.
>
> Surely this has changed?
>
> Thanks and Cheers
> Markus
>
>
> --
> Markus Heller, Ph.D.
> NMR Scientist
> CDRD - The Centre for Drug Research and Development
> 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC  V6T 1Z3 | Main: (604) 827-1147<tel:%28604%29%20827-1147>
> Direct: (604) 827-1122<tel:%28604%29%20827-1122> | F: (604) 827-1299<tel:%28604%29%20827-1299> | E: mh...@cd...<mailto:mh...@cd...> | www.cdrd.ca<http://www.cdrd.ca>
>
>
>
>
>
>
> Follow us:
>
> This email and any files transmitted with it are confidential and intended solely for the addressee.  If you are not the named addressee you should not disseminate, distribute, copy, or alter this email.
>
>
>
> ------------------------------------------------------------------------------
> New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
> GigeNET is offering a free month of service with a new server in Ashburn.
> Choose from 2 high performing configs, both with 100TB of bandwidth.
> Higher redundancy.Lower latency.Increased capacity.Completely compliant.
> http://p.sf.net/sfu/gigenet
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...<mailto:PyM...@li...>)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...


------------------------------------------------------------------------------
New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
GigeNET is offering a free month of service with a new server in Ashburn.
Choose from 2 high performing configs, both with 100TB of bandwidth.
Higher redundancy.Lower latency.Increased capacity.Completely compliant.
http://p.sf.net/sfu/gigenet
_______________________________________________
PyMOL-users mailing list (PyM...@li...<mailto:PyM...@li...>)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pym...@li...



--
Tsjerk A. Wassenaar, Ph.D.

Hey :)

If you want to do it using only Pymol in just a few minutes, try this:

set auto_zoom, 0
scale=1.0
import numpy
M=numpy.array(cmd.get_view()).reshape(6,3)
cmd.pseudoatom("dummy",pos=list(M[4,:]-scale*numpy.dot(M[:3,:3],M[3,:])))
hide everything, (not ligand) within 150 of dummy

Adjust the scale to get a more curved or more planar clip.

Hope it helps,

Tsjerk

On Wed, Jan 21, 2015 at 10:21 PM, H. Adam Steinberg <
h.a...@gm...> wrote:

> if you have access to Gimp or photoshop and want to do this in just a few
> minutes… clip and render the surface how you want it, then without moving
> anything, unclip and render just the ligand. In any bitmap editing program
> layer the ligand image over the clipped surface image and merge the two
> into one image.
>
>
> > On Jan 21, 2015, at 2:57 PM, Markus Heller <mh...@cd...> wrote:
> >
> > Hello all,
> >
> > I'm trying to show a ligand in a binding site, and I'd like to
> selectively clip the surface only.  I haven't found anything on the web,
> only that it was not possible a few years ago.
> >
> > Surely this has changed?
> >
> > Thanks and Cheers
> > Markus
> >
> >
> > --
> > Markus Heller, Ph.D.
> > NMR Scientist
> > CDRD - The Centre for Drug Research and Development
> > 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC  V6T 1Z3 | Main: (604)
> 827-1147
> > Direct: (604) 827-1122 | F: (604) 827-1299 | E: mh...@cd... |
> www.cdrd.ca
> >
> >
> >
> >
> >
> >
> > Follow us:
> >
> > This email and any files transmitted with it are confidential and
> intended solely for the addressee.  If you are not the named addressee you
> should not disseminate, distribute, copy, or alter this email.
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
> > GigeNET is offering a free month of service with a new server in Ashburn.
> > Choose from 2 high performing configs, both with 100TB of bandwidth.
> > Higher redundancy.Lower latency.Increased capacity.Completely compliant.
> > http://p.sf.net/sfu/gigenet
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pym...@li...
>
>
>
> ------------------------------------------------------------------------------
> New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
> GigeNET is offering a free month of service with a new server in Ashburn.
> Choose from 2 high performing configs, both with 100TB of bandwidth.
> Higher redundancy.Lower latency.Increased capacity.Completely compliant.
> http://p.sf.net/sfu/gigenet
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Tsjerk A. Wassenaar, Ph.D.