pymol-users Mailing List for PyMOL Molecular Graphics System

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.

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)

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.

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 <" rel="nofollow">https://www.uochb.cz/web/structure/31.html?lang=en>
Prague, Czech Republic
  &
CEITEC - Central European Institute of Technology <" rel="nofollow">https://www.ceitec.eu/>
Brno, Czech Republic

email: te...@gm...

website: https://sites.google.com/site/thomasevangelidishomepage/

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.

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 <" rel="nofollow">https://www.uochb.cz/web/structure/31.html?lang=en>
Prague, Czech Republic
  &
CEITEC - Central European Institute of Technology <" rel="nofollow">https://www.ceitec.eu/>
Brno, Czech Republic

email: te...@gm...

website: https://sites.google.com/site/thomasevangelidishomepage/

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.

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 <" rel="nofollow">https://www.uochb.cz/web/structure/31.html?lang=en>
Prague, Czech Republic
  &
CEITEC - Central European Institute of Technology <" rel="nofollow">https://www.ceitec.eu/>
Brno, Czech Republic

email: te...@gm...

website: https://sites.google.com/site/thomasevangelidishomepage/

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

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.

Hi Heng-Keat,

A "clean" build will probably fix this. It looks like you partially recompiled with --use-msgpackc=no?

To do a clean build: Remove the "build" directory and try again.

Cheers,
  Thomas


> On Feb 14, 2019, at 8:00 PM, Ta...@em... wrote:
> 
> Dear all,
> 
> I installed the pymol on my machine with Ubuntu 18.04.1 LTS. When I launch pymol and error appears:
> 
> Traceback (most recent call last):
>  File "/home/mauricetam/Documents/software/pymol-2.3.0//lib/python2.7/site-packages/pymol/__init__.py", line 64, in <module>
>    import pymol
>  File "/home/mauricetam/Documents/software/pymol-2.3.0/lib/python2.7/site-packages/pymol/__init__.py", line 580, in <module>
>    import pymol._cmd
> ImportError: /home/mauricetam/Documents/software/pymol-2.3.0/lib/python2.7/site-packages/pymol/_cmd.so: undefined symbol: MMTF_unpack_from_string
> 
> Any idea what is going wrong?
> 
> Thank you for your help.
> 
> Best
> Heng-Keat

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear all,

I installed the pymol on my machine with Ubuntu 18.04.1 LTS. When I  
launch pymol and error appears:

Traceback (most recent call last):
   File  
"/home/mauricetam/Documents/software/pymol-2.3.0//lib/python2.7/site-packages/pymol/__init__.py", line 64, in  
<module>
     import pymol
   File  
"/home/mauricetam/Documents/software/pymol-2.3.0/lib/python2.7/site-packages/pymol/__init__.py", line 580, in  
<module>
     import pymol._cmd
ImportError:  
/home/mauricetam/Documents/software/pymol-2.3.0/lib/python2.7/site-packages/pymol/_cmd.so: undefined symbol:  
MMTF_unpack_from_string

Any idea what is going wrong?

Thank you for your help.

Best
Heng-Keat

Hi Heng-Keat,

Getting CCTBX to work with PyMOL is quite a journey. Please read:

https://pymolwiki.org/index.php/CCTBX#Open-Source_PyMOL

Cheers,
  Thomas

> On Feb 14, 2019, at 11:27 AM, Ta...@em... wrote:
> 
> Dear all,
> 
> After I reinstalled the pmw, it ran through and now it said 'no modules named _tkinter' as shown below:
> 
> Warning: GL_DRAW_BUFFER0=0 -> using GL_BACK
> Detected OpenGL version 3.0. Shaders available.
> Geometry shaders not available
> Detected GLSL version 1.30.
> OpenGL graphics engine:
>  GL_VENDOR:   Intel Open Source Technology Center
>  GL_RENDERER: Mesa DRI Intel(R) Haswell Mobile
>  GL_VERSION:  3.0 Mesa 18.2.8
> Traceback (most recent call last):
>  File "/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/__init__.py", line 27, in run
>    from .PMGApp import PMGApp
>  File "/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/PMGApp.py", line 22, in <module>
>    import Pmw
>  File "/home/mauricetam/software/cctbx/cctbx_plus_build/base/lib/python2.7/site-packages/Pmw.py", line 8, in <module>
> Detected 4 CPU cores.  Enabled multithreaded rendering.
>    import Tkinter as tkinter
>  File "/home/mauricetam/software/cctbx/cctbx_plus_build/base/lib/python2.7/lib-tk/Tkinter.py", line 39, in <module>
>    import _tkinter # If this fails your Python may not be configured for Tk
> ImportError: No module named _tkinter
> 
> Thanks for the help.
> 
> Best
> HK
> 
> Quoting Ta...@em...:
> 
>> To whom it may concern,
>> 
>> I installed the pymol on my machine with Ubuntu 18.04.1 LTS
>> 
>> I have a problem with 'Qt not available, using GLUT/Tk interface' when install pymol with:
>> 
>> python setup.py install --prefix=/home/mauricetam/software/pymol-2.3.0/ --use-msgpackc=no
>> 
>> After I installed it with:
>> 
>> python setup.py install --prefix=/home/mauricetam/software/pymol-2.3.0/ --use-msgpackc=no --glut
>> 
>> Now, the problem is I don't see the external GUI and there is an error as shown below:
>> 
>> Warning: GL_DRAW_BUFFER0=0 -> using GL_BACK
>> Detected OpenGL version 3.0. Shaders available.
>> Geometry shaders not available
>> Detected GLSL version 1.30.
>> OpenGL graphics engine:
>>  GL_VENDOR:   Intel Open Source Technology Center
>>  GL_RENDERER: Mesa DRI Intel(R) Haswell Mobile
>>  GL_VERSION:  3.0 Mesa 18.2.2
>> Traceback (most recent call last):
>>  File "/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/__init__.py", line 27, in run
>>    from .PMGApp import PMGApp
>>  File "/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/PMGApp.py", line 22, in <module>
>>    import Pmw
>> ImportError: No module named Pmw
>> Detected 4 CPU cores.  Enabled multithreaded rendering.
>> 
>> Any idea what is going wrong on my machine?
>> 
>> Thank you for the help.
>> 
>> Best
>> Heng-Keat

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear all,

After I reinstalled the pmw, it ran through and now it said 'no  
modules named _tkinter' as shown below:

Warning: GL_DRAW_BUFFER0=0 -> using GL_BACK
  Detected OpenGL version 3.0. Shaders available.
  Geometry shaders not available
  Detected GLSL version 1.30.
  OpenGL graphics engine:
   GL_VENDOR:   Intel Open Source Technology Center
   GL_RENDERER: Mesa DRI Intel(R) Haswell Mobile
   GL_VERSION:  3.0 Mesa 18.2.8
Traceback (most recent call last):
   File  
"/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/__init__.py", line 27, in  
run
     from .PMGApp import PMGApp
   File  
"/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/PMGApp.py", line 22, in  
<module>
     import Pmw
   File  
"/home/mauricetam/software/cctbx/cctbx_plus_build/base/lib/python2.7/site-packages/Pmw.py", line 8, in  
<module>
  Detected 4 CPU cores.  Enabled multithreaded rendering.
     import Tkinter as tkinter
   File  
"/home/mauricetam/software/cctbx/cctbx_plus_build/base/lib/python2.7/lib-tk/Tkinter.py", line 39, in  
<module>
     import _tkinter # If this fails your Python may not be configured for Tk
ImportError: No module named _tkinter

Thanks for the help.

Best
HK

Quoting Ta...@em...:

> To whom it may concern,
>
> I installed the pymol on my machine with Ubuntu 18.04.1 LTS
>
> I have a problem with 'Qt not available, using GLUT/Tk interface'  
> when install pymol with:
>
> python setup.py install  
> --prefix=/home/mauricetam/software/pymol-2.3.0/ --use-msgpackc=no
>
> After I installed it with:
>
> python setup.py install  
> --prefix=/home/mauricetam/software/pymol-2.3.0/ --use-msgpackc=no  
> --glut
>
> Now, the problem is I don't see the external GUI and there is an  
> error as shown below:
>
> Warning: GL_DRAW_BUFFER0=0 -> using GL_BACK
>  Detected OpenGL version 3.0. Shaders available.
>  Geometry shaders not available
>  Detected GLSL version 1.30.
>  OpenGL graphics engine:
>   GL_VENDOR:   Intel Open Source Technology Center
>   GL_RENDERER: Mesa DRI Intel(R) Haswell Mobile
>   GL_VERSION:  3.0 Mesa 18.2.2
> Traceback (most recent call last):
>   File  
> "/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/__init__.py", line 27, in  
> run
>     from .PMGApp import PMGApp
>   File  
> "/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/PMGApp.py", line 22, in  
> <module>
>     import Pmw
> ImportError: No module named Pmw
>  Detected 4 CPU cores.  Enabled multithreaded rendering.
>
> Any idea what is going wrong on my machine?
>
> Thank you for the help.
>
> Best
> Heng-Keat
>
>
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:  
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

To whom it may concern,

I installed the pymol on my machine with Ubuntu 18.04.1 LTS

I have a problem with 'Qt not available, using GLUT/Tk interface' when  
install pymol with:

python setup.py install  
--prefix=/home/mauricetam/software/pymol-2.3.0/ --use-msgpackc=no

After I installed it with:

python setup.py install  
--prefix=/home/mauricetam/software/pymol-2.3.0/ --use-msgpackc=no --glut

Now, the problem is I don't see the external GUI and there is an error  
as shown below:

Warning: GL_DRAW_BUFFER0=0 -> using GL_BACK
  Detected OpenGL version 3.0. Shaders available.
  Geometry shaders not available
  Detected GLSL version 1.30.
  OpenGL graphics engine:
   GL_VENDOR:   Intel Open Source Technology Center
   GL_RENDERER: Mesa DRI Intel(R) Haswell Mobile
   GL_VERSION:  3.0 Mesa 18.2.2
Traceback (most recent call last):
   File  
"/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/__init__.py", line 27, in  
run
     from .PMGApp import PMGApp
   File  
"/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/PMGApp.py", line 22, in  
<module>
     import Pmw
ImportError: No module named Pmw
  Detected 4 CPU cores.  Enabled multithreaded rendering.

Any idea what is going wrong on my machine?

Thank you for the help.

Best
Heng-Keat

Thank you

From: Jarrett Johnson <jar...@sc...>
Date: Wednesday, February 13, 2019 at 10:36 AM
To: Jack Vizelter <ja...@ma...>
Cc: Thomas Holder <tho...@sc...>, Pymol User list <pym...@li...>
Subject: Re: [PyMOL] PyMOL 2.3 released

Hi Jack,

We've tested with Mojave since its release and have found no issues.

Jarrett J.

On Tue, Feb 12, 2019 at 12:51 PM Jack Vizelter <ja...@ma...<mailto:ja...@ma...>> wrote:
Hi,

Is this version supported under macOS 10.14.x (Mojave)?   The supported OS listing just says 10.9+ but wanted to confirm.

Thnx,
-jack

-----Original Message-----
From: Thomas Holder <tho...@sc...<mailto:tho...@sc...>>
Date: Monday, February 11, 2019 at 10:54 AM
To: Pymol User list <pym...@li...<mailto:pym...@li...>>
Subject: [PyMOL] PyMOL 2.3 released

    Greetings,

    We are happy to announce the release of PyMOL 2.3. Download ready-to-use bundles from https://urldefense.proofpoint.com/v2/url?u=https-3A__pymol.org_&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=EdVxNaXoTBbrFjOSxSGtf80f5GLwY4UoeoqXOgi2y1Y&s=M9y4i1kkzjJaykmXjFMEB8nDyvQFZ-_3sHaRTTi-rec&e= or update your installation with "conda install -c schrodinger pymol".

    New features include:
    - Atom-level cartoon transparency
    - Fast MMTF export
    - Sequence viewer gaps display

    This is the first time that we provide PyMOL bundles with Python 3. If you use custom or third-party Python 2 scripts, they might stop working until you convert them (e.g. using a converter tool like 2to3).

    Find the complete release notes at:
    https://urldefense.proofpoint.com/v2/url?u=https-3A__pymol.org_d_media-3Anew23&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=EdVxNaXoTBbrFjOSxSGtf80f5GLwY4UoeoqXOgi2y1Y&s=DdMiFFA3kJDoelX1qbJz9t9flE6G53M33MEdaZkRSzA&e=

    We welcome any feedback and bug reports.

    Cheers,
    - The PyMOL Team at Schrödinger

    --
    Thomas Holder
    PyMOL Principal Developer
    Schrödinger, Inc.

    _______________________________________________
    PyMOL-users mailing list
    Archives: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=EdVxNaXoTBbrFjOSxSGtf80f5GLwY4UoeoqXOgi2y1Y&s=9y_R-PjUqUT6wzjEs1ECxF59shYPiWuYB_7fThlDadU&e=
    Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=EdVxNaXoTBbrFjOSxSGtf80f5GLwY4UoeoqXOgi2y1Y&s=WVkM4La4mZsWQ2beQpPA_hXCmu_AFvn6RbGtetuCDqA&e=


_______________________________________________
PyMOL-users mailing list
Archives: " rel="nofollow">http://www.mail-archive.com/pym...@li...<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMFaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=m4zf8mYN6q023jUyyWqELLorohZ0YzUb-w1wtdla7Po&s=OUFEOZun4rrA-HERNreRygqhf0v3Yn365Wx9CcZDYyw&e=>
Unsubscribe: " rel="nofollow">https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMFaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=m4zf8mYN6q023jUyyWqELLorohZ0YzUb-w1wtdla7Po&s=0QjPRJ0PdYYp9Q3AVe45wBkkUSrd9V8-wbsPleBcvZg&e=>


--
Jarrett Johnson
PyMOL Developer
Schrödinger, Inc.

On Wed, Feb 13, 2019 at 05:53:33PM +0100, Thomas Holder wrote:
> Don't split "build" and "install" (or pass --glut to both calls):
> 
>     python setup.py --glut build install --prefix=...
that just works :D

Thanks

Tru

-- 
Dr Tru Huynh | mailto:tr...@pa... | tel +33 1 45 68 87 37
https://research.pasteur.fr/en/team/structural-bioinformatics/
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France  

Don't split "build" and "install" (or pass --glut to both calls):

    python setup.py --glut build install --prefix=...

Cheers,
  Thomas

> On Feb 13, 2019, at 5:44 PM, Tru Huynh <tr...@pa...> wrote:
> 
> On Wed, Feb 13, 2019 at 05:21:09PM +0100, Tru Huynh wrote:
> ...
>> 
>> Trying to install PyQt4_gpl_x11-4.12. on CentOS-7 is another issue :)
>> ...
>> 
> 
> I went the easy route and pip3 install PyQt5-sip PyQt5,
> and rebuild ...
> 
> the Python-3.5.2 version now works fine, but not the Python-3.6.6
> which still fails!
> 
> [tru@sillage ~]$ module add pymol/release/2.3.0-Python-3.5.2 
> [tru@sillage ~]$ pymol
> PyMOL(TM) Molecular Graphics System, Version 2.3.0.
> Copyright (c) Schrodinger, LLC.
> All Rights Reserved.
> 
>    Created by Warren L. DeLano, Ph.D. 
> 
>    PyMOL is user-supported open-source software.  Although some versions
>    are freely available, PyMOL is not in the public domain.
> 
>    If PyMOL is helpful in your work or study, then please volunteer 
>    support for our ongoing efforts to create open and affordable scientific
>    software by purchasing a PyMOL Maintenance and/or Support subscription.
> 
>    More information can be found at "http://www.pymol.org".
> 
>    Enter "help" for a list of commands.
>    Enter "help <command-name>" for information on a specific command.
> 
> Hit ESC anytime to toggle between text and graphics.
> 
> Detected OpenGL version 4.6. Shaders available.
> Detected GLSL version 4.60.
> OpenGL graphics engine:
>  GL_VENDOR:   NVIDIA Corporation
>  GL_RENDERER: GeForce GT 1030/PCIe/SSE2
>  GL_VERSION:  4.6.0 NVIDIA 410.93
> Detected 6 CPU cores.  Enabled multithreaded rendering.
> 
> 
> [tru@sillage ~]$ module add pymol/release/2.3.0-Python-3.6.6
> [tru@sillage ~]$ pymol
> Traceback (most recent call last):
>  File "/c7/shared/pymol/release/2.3.0-Python-3.6.6/lib/python3.6/site-packages/pymol/__init__.py", line 64, in <module>
>    import pymol
>  File "/c7/shared/pymol/release/2.3.0-Python-3.6.6/lib/python3.6/site-packages/pymol/__init__.py", line 580, in <module>
>    import pymol._cmd
> ImportError: /c7/shared/pymol/release/2.3.0-Python-3.6.6/lib/python3.6/site-packages/pymol/_cmd.cpython-36m-x86_64-linux-gnu.so: undefined symbol: glutSwapBuffers
> 
> Cheers
> 
> Tru
> -- 
> Dr Tru Huynh | mailto:tr...@pa... | tel +33 1 45 68 87 37
> https://research.pasteur.fr/en/team/structural-bioinformatics/
> Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France  

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

On Wed, Feb 13, 2019 at 05:21:09PM +0100, Tru Huynh wrote:
...
> 
> Trying to install PyQt4_gpl_x11-4.12. on CentOS-7 is another issue :)
> ...
> 

I went the easy route and pip3 install PyQt5-sip PyQt5,
and rebuild ...

the Python-3.5.2 version now works fine, but not the Python-3.6.6
which still fails!

[tru@sillage ~]$ module add pymol/release/2.3.0-Python-3.5.2 
[tru@sillage ~]$ pymol
 PyMOL(TM) Molecular Graphics System, Version 2.3.0.
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.
 
    Created by Warren L. DeLano, Ph.D. 
 
    PyMOL is user-supported open-source software.  Although some versions
    are freely available, PyMOL is not in the public domain.
 
    If PyMOL is helpful in your work or study, then please volunteer 
    support for our ongoing efforts to create open and affordable scientific
    software by purchasing a PyMOL Maintenance and/or Support subscription.

    More information can be found at "http://www.pymol.org".
 
    Enter "help" for a list of commands.
    Enter "help <command-name>" for information on a specific command.

 Hit ESC anytime to toggle between text and graphics.

 Detected OpenGL version 4.6. Shaders available.
 Detected GLSL version 4.60.
 OpenGL graphics engine:
  GL_VENDOR:   NVIDIA Corporation
  GL_RENDERER: GeForce GT 1030/PCIe/SSE2
  GL_VERSION:  4.6.0 NVIDIA 410.93
 Detected 6 CPU cores.  Enabled multithreaded rendering.


[tru@sillage ~]$ module add pymol/release/2.3.0-Python-3.6.6
[tru@sillage ~]$ pymol
Traceback (most recent call last):
  File "/c7/shared/pymol/release/2.3.0-Python-3.6.6/lib/python3.6/site-packages/pymol/__init__.py", line 64, in <module>
    import pymol
  File "/c7/shared/pymol/release/2.3.0-Python-3.6.6/lib/python3.6/site-packages/pymol/__init__.py", line 580, in <module>
    import pymol._cmd
ImportError: /c7/shared/pymol/release/2.3.0-Python-3.6.6/lib/python3.6/site-packages/pymol/_cmd.cpython-36m-x86_64-linux-gnu.so: undefined symbol: glutSwapBuffers

Cheers

Tru
-- 
Dr Tru Huynh | mailto:tr...@pa... | tel +33 1 45 68 87 37
https://research.pasteur.fr/en/team/structural-bioinformatics/
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France  

Hi Thomas,

On Wed, Feb 13, 2019 at 04:28:10PM +0100, Thomas Holder wrote:
> Hi Tru,
> 
> There is one thing we changed: The legacy GLUT support is not enabled by default anymore. If that's the issue here, you have two options:
> 
> 1) install PyQt (recommended)
> 2) or compile PyMOL with --glut

I am trying the --glut way and that fixed the Python/2.7.15 build
and run fine, thanks!

	python setup.py --glut  build 
	python setup.py install --prefix=...

[tru@sillage ~]$ module add pymol/release/2.3.0-Python-2.7.15 
[tru@sillage ~]$ pymol
Qt not available, using GLUT/Tk interface
 PyMOL(TM) Molecular Graphics System, Version 2.3.0.
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.
 
    Created by Warren L. DeLano, Ph.D. 
 
    PyMOL is user-supported open-source software.  Although some versions
    are freely available, PyMOL is not in the public domain.
 
    If PyMOL is helpful in your work or study, then please volunteer 
    support for our ongoing efforts to create open and affordable scientific
    software by purchasing a PyMOL Maintenance and/or Support subscription.

    More information can be found at "http://www.pymol.org".
 
    Enter "help" for a list of commands.
    Enter "help <command-name>" for information on a specific command.

 Hit ESC anytime to toggle between text and graphics.

Warning: GL_DRAW_BUFFER0=0 -> using GL_BACK
 Detected OpenGL version 4.6. Shaders available.
 Detected GLSL version 4.60.
 OpenGL graphics engine:
  GL_VENDOR:   NVIDIA Corporation
  GL_RENDERER: GeForce GT 1030/PCIe/SSE2
  GL_VERSION:  4.6.0 NVIDIA 410.93
 Detected 6 CPU cores.  Enabled multithreaded rendering.

PyMOL>viewport 640,480
Plugin 'lightingsettings_gui' only available with PyQt GUI.
...

But the same build option fails for both Python/3.5.2 and 3.6.6 with:
[tru@sillage ~]$ pymol
Traceback (most recent call last):
  File "/c7/shared/pymol/release/2.3.0-Python-3.5.2/lib/python3.5/site-packages/pymol/__init__.py", line 64, in <module>
    import pymol
  File "/c7/shared/pymol/release/2.3.0-Python-3.5.2/lib/python3.5/site-packages/pymol/__init__.py", line 580, in <module>
    import pymol._cmd
ImportError: /c7/shared/pymol/release/2.3.0-Python-3.5.2/lib/python3.5/site-packages/pymol/_cmd.cpython-35m-x86_64-linux-gnu.so: undefined symbol: glutSwapBuffers

Traceback (most recent call last):
  File "/c7/shared/pymol/release/2.3.0-Python-3.6.6/lib/python3.6/site-packages/pymol/__init__.py", line 64, in <module>
    import pymol
  File "/c7/shared/pymol/release/2.3.0-Python-3.6.6/lib/python3.6/site-packages/pymol/__init__.py", line 580, in <module>
    import pymol._cmd
ImportError: /c7/shared/pymol/release/2.3.0-Python-3.6.6/lib/python3.6/site-packages/pymol/_cmd.cpython-36m-x86_64-linux-gnu.so: undefined symbol: glutSwapBuffers

Trying to install PyQt4_gpl_x11-4.12. on CentOS-7 is another issue :)
[tru@borma PyQt4_gpl_x11-4.12.3]$ python3 configure-ng.py  --confirm-license --destdir /dev/shm/PyQt4_gpl_x11-4.12.3 --qmake=/usr/lib64/qt4/bin/qmake
Querying qmake about your Qt installation...
Determining the details of your Qt installation...
This is the GPL version of PyQt 4.12.3 (licensed under the GNU General Public
License) for Python 3.6.6 on linux.
Found the license file pyqt-gpl.sip.
Error: This version of PyQt4 requires sip 4.19.12 or later.
[tru@borma PyQt4_gpl_x11-4.12.3]$ rpm -qa sip\*
sip-macros-4.14.6-4.el7.x86_64
sip-devel-4.14.6-4.el7.x86_64
sip-4.14.6-4.el7.x86_64
...

Cheers

Tru
-- 
Dr Tru Huynh | mailto:tr...@pa... | tel +33 1 45 68 87 37
https://research.pasteur.fr/en/team/structural-bioinformatics/
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France  

Hi Jack,

We've tested with Mojave since its release and have found no issues.

Jarrett J.

On Tue, Feb 12, 2019 at 12:51 PM Jack Vizelter <ja...@ma...>
wrote:

> Hi,
>
> Is this version supported under macOS 10.14.x (Mojave)?   The supported OS
> listing just says 10.9+ but wanted to confirm.
>
> Thnx,
> -jack
>
> -----Original Message-----
> From: Thomas Holder <tho...@sc...>
> Date: Monday, February 11, 2019 at 10:54 AM
> To: Pymol User list <pym...@li...>
> Subject: [PyMOL] PyMOL 2.3 released
>
>     Greetings,
>
>     We are happy to announce the release of PyMOL 2.3. Download
> ready-to-use bundles from
> https://urldefense.proofpoint.com/v2/url?u=https-3A__pymol.org_&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=EdVxNaXoTBbrFjOSxSGtf80f5GLwY4UoeoqXOgi2y1Y&s=M9y4i1kkzjJaykmXjFMEB8nDyvQFZ-_3sHaRTTi-rec&e=
> or update your installation with "conda install -c schrodinger pymol".
>
>     New features include:
>     - Atom-level cartoon transparency
>     - Fast MMTF export
>     - Sequence viewer gaps display
>
>     This is the first time that we provide PyMOL bundles with Python 3. If
> you use custom or third-party Python 2 scripts, they might stop working
> until you convert them (e.g. using a converter tool like 2to3).
>
>     Find the complete release notes at:
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__pymol.org_d_media-3Anew23&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=EdVxNaXoTBbrFjOSxSGtf80f5GLwY4UoeoqXOgi2y1Y&s=DdMiFFA3kJDoelX1qbJz9t9flE6G53M33MEdaZkRSzA&e=
>
>     We welcome any feedback and bug reports.
>
>     Cheers,
>     - The PyMOL Team at Schrödinger
>
>     --
>     Thomas Holder
>     PyMOL Principal Developer
>     Schrödinger, Inc.
>
>     _______________________________________________
>     PyMOL-users mailing list
>     Archives:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=EdVxNaXoTBbrFjOSxSGtf80f5GLwY4UoeoqXOgi2y1Y&s=9y_R-PjUqUT6wzjEs1ECxF59shYPiWuYB_7fThlDadU&e=
>     Unsubscribe:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=EdVxNaXoTBbrFjOSxSGtf80f5GLwY4UoeoqXOgi2y1Y&s=WVkM4La4mZsWQ2beQpPA_hXCmu_AFvn6RbGtetuCDqA&e=
>
>
> _______________________________________________
> 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.

Hi Tru,

There is one thing we changed: The legacy GLUT support is not enabled by default anymore. If that's the issue here, you have two options:

1) install PyQt (recommended)
2) or compile PyMOL with --glut

Cheers,
  Thomas


> On Feb 13, 2019, at 3:44 PM, Tru Huynh <tr...@pa...> wrote:
> 
> Hi,
> 
> I have some issue with the latest released version (2.3.0) and
> manually build Python 2.7.15, 3.5.2 and 3.6.6 on our CentOS-7 machines.
> 
> [tru@sillage ~]$ module add pymol/release/2.3.0-Python-3.6.6
> [tru@sillage ~]$ module li
> Currently Loaded Modulefiles:
>  1) Python/3.6.6                       3) pymol/release/2.3.0-Python-3.6.6
>  2) msgpack/2.1.5
> [tru@sillage ~]$ pymol
> Qt not available, using GLUT/Tk interface
> [tru@sillage ~]$ echo $?
> 0
> 
> The different Python versions are isolated through the environment
> modules and the issue has only appeared with 2.3.0 and all the python
> versions except the version using the system provided python version.
> 
> these fails:
> pymol/release/2.3.0-Python-2.7.15  pymol/release/2.3.0-Python-3.6.6
> pymol/release/2.3.0-Python-3.5.2 
> 
> this works:
> pymol/release/2.3.0-Python-centos7
> 
> [tru@sillage ~]$ module add pymol/release/2.3.0-Python-centos7
> [tru@sillage ~]$ pymol
> PyMOL(TM) Molecular Graphics System, Version 2.3.0.
> Copyright (c) Schrodinger, LLC.
> All Rights Reserved.
> 
>    Created by Warren L. DeLano, Ph.D. 
> 
>    PyMOL is user-supported open-source software.  Although some versions
>    are freely available, PyMOL is not in the public domain.
> 
>    If PyMOL is helpful in your work or study, then please volunteer 
>    support for our ongoing efforts to create open and affordable scientific
>    software by purchasing a PyMOL Maintenance and/or Support subscription.
> 
>    More information can be found at "http://www.pymol.org".
> 
>    Enter "help" for a list of commands.
>    Enter "help <command-name>" for information on a specific command.
> 
> Hit ESC anytime to toggle between text and graphics.
> 
> Detected OpenGL version 4.6. Shaders available.
> Detected GLSL version 4.60.
> OpenGL graphics engine:
>  GL_VENDOR:   NVIDIA Corporation
>  GL_RENDERER: GeForce GT 1030/PCIe/SSE2
>  GL_VERSION:  4.6.0 NVIDIA 410.93
> Detected 6 CPU cores.  Enabled multithreaded rendering.
> 
> and all the previous versions of pymol are perfectly fine...
> 
> pymol/release/1.8.7-Python-2.7.12  pymol/release/2.1.0-Python-3.6.6
> pymol/release/1.8.7-Python-2.7.15  pymol/release/2.1.0-Python-centos7
> pymol/release/1.8.7-Python-3.5.2   pymol/release/2.2.0-Python-2.7.15
> pymol/release/1.8.7-Python-3.6.3   pymol/release/2.2.0-Python-3.5.2
> pymol/release/1.8.7-Python-3.6.6   pymol/release/2.2.0-Python-3.6.6
> pymol/release/1.8.7-Python-centos7 pymol/release/2.2.0-Python-centos7
> pymol/release/2.1.0-Python-2.7.12  
> pymol/release/2.1.0-Python-2.7.15  
> pymol/release/2.1.0-Python-3.5.2   
> pymol/release/2.1.0-Python-3.6.3   
> 
> Any idea where I can start looking at?
> 
> python3 build process details:
> module purge && module add Python/${PYTHON_V}
> python3 setup.py build
> python3 setup.py install --prefix=/....
> 
> for python2, I just resplaced python3 by python in the lines above.
> 
> Any idea what could be causing this behaviour?
> 
> Cheers
> 
> Tru
> 
> -- 
> Dr Tru Huynh | mailto:tr...@pa... | tel +33 1 45 68 87 37
> https://research.pasteur.fr/en/team/structural-bioinformatics/
> Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France  

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi,

I have some issue with the latest released version (2.3.0) and
manually build Python 2.7.15, 3.5.2 and 3.6.6 on our CentOS-7 machines.

[tru@sillage ~]$ module add pymol/release/2.3.0-Python-3.6.6
[tru@sillage ~]$ module li
Currently Loaded Modulefiles:
  1) Python/3.6.6                       3) pymol/release/2.3.0-Python-3.6.6
  2) msgpack/2.1.5
[tru@sillage ~]$ pymol
Qt not available, using GLUT/Tk interface
[tru@sillage ~]$ echo $?
0

The different Python versions are isolated through the environment
modules and the issue has only appeared with 2.3.0 and all the python
versions except the version using the system provided python version.

these fails:
pymol/release/2.3.0-Python-2.7.15  pymol/release/2.3.0-Python-3.6.6
pymol/release/2.3.0-Python-3.5.2 

this works:
pymol/release/2.3.0-Python-centos7

[tru@sillage ~]$ module add pymol/release/2.3.0-Python-centos7
[tru@sillage ~]$ pymol
 PyMOL(TM) Molecular Graphics System, Version 2.3.0.
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.
 
    Created by Warren L. DeLano, Ph.D. 
 
    PyMOL is user-supported open-source software.  Although some versions
    are freely available, PyMOL is not in the public domain.
 
    If PyMOL is helpful in your work or study, then please volunteer 
    support for our ongoing efforts to create open and affordable scientific
    software by purchasing a PyMOL Maintenance and/or Support subscription.

    More information can be found at "http://www.pymol.org".
 
    Enter "help" for a list of commands.
    Enter "help <command-name>" for information on a specific command.

 Hit ESC anytime to toggle between text and graphics.

 Detected OpenGL version 4.6. Shaders available.
 Detected GLSL version 4.60.
 OpenGL graphics engine:
  GL_VENDOR:   NVIDIA Corporation
  GL_RENDERER: GeForce GT 1030/PCIe/SSE2
  GL_VERSION:  4.6.0 NVIDIA 410.93
 Detected 6 CPU cores.  Enabled multithreaded rendering.

and all the previous versions of pymol are perfectly fine...

pymol/release/1.8.7-Python-2.7.12  pymol/release/2.1.0-Python-3.6.6
pymol/release/1.8.7-Python-2.7.15  pymol/release/2.1.0-Python-centos7
pymol/release/1.8.7-Python-3.5.2   pymol/release/2.2.0-Python-2.7.15
pymol/release/1.8.7-Python-3.6.3   pymol/release/2.2.0-Python-3.5.2
pymol/release/1.8.7-Python-3.6.6   pymol/release/2.2.0-Python-3.6.6
pymol/release/1.8.7-Python-centos7 pymol/release/2.2.0-Python-centos7
pymol/release/2.1.0-Python-2.7.12  
pymol/release/2.1.0-Python-2.7.15  
pymol/release/2.1.0-Python-3.5.2   
pymol/release/2.1.0-Python-3.6.3   

Any idea where I can start looking at?

python3 build process details:
module purge && module add Python/${PYTHON_V}
python3 setup.py build
python3 setup.py install --prefix=/....

for python2, I just resplaced python3 by python in the lines above.

Any idea what could be causing this behaviour?

Cheers

Tru

-- 
Dr Tru Huynh | mailto:tr...@pa... | tel +33 1 45 68 87 37
https://research.pasteur.fr/en/team/structural-bioinformatics/
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France  

Dear all,

I used to use PyMol with a fast refreshing CRT and page flipping, but the
monitor has died.....

What would you buy if you had $2,000 to replace it?

Just a new monitor?

Or any VR supported, maybe with an interface other than mice?

Thanks!

Bruce

Hi,

Is this version supported under macOS 10.14.x (Mojave)?   The supported OS listing just says 10.9+ but wanted to confirm.

Thnx,
-jack

-----Original Message-----
From: Thomas Holder <tho...@sc...>
Date: Monday, February 11, 2019 at 10:54 AM
To: Pymol User list <pym...@li...>
Subject: [PyMOL] PyMOL 2.3 released

    Greetings,
    
    We are happy to announce the release of PyMOL 2.3. Download ready-to-use bundles from https://urldefense.proofpoint.com/v2/url?u=https-3A__pymol.org_&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=EdVxNaXoTBbrFjOSxSGtf80f5GLwY4UoeoqXOgi2y1Y&s=M9y4i1kkzjJaykmXjFMEB8nDyvQFZ-_3sHaRTTi-rec&e= or update your installation with "conda install -c schrodinger pymol".
    
    New features include:
    - Atom-level cartoon transparency
    - Fast MMTF export
    - Sequence viewer gaps display
    
    This is the first time that we provide PyMOL bundles with Python 3. If you use custom or third-party Python 2 scripts, they might stop working until you convert them (e.g. using a converter tool like 2to3).
    
    Find the complete release notes at:
    https://urldefense.proofpoint.com/v2/url?u=https-3A__pymol.org_d_media-3Anew23&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=EdVxNaXoTBbrFjOSxSGtf80f5GLwY4UoeoqXOgi2y1Y&s=DdMiFFA3kJDoelX1qbJz9t9flE6G53M33MEdaZkRSzA&e= 
    
    We welcome any feedback and bug reports.
    
    Cheers,
    - The PyMOL Team at Schrödinger
    
    --
    Thomas Holder
    PyMOL Principal Developer
    Schrödinger, Inc.
    
    _______________________________________________
    PyMOL-users mailing list
    Archives: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=EdVxNaXoTBbrFjOSxSGtf80f5GLwY4UoeoqXOgi2y1Y&s=9y_R-PjUqUT6wzjEs1ECxF59shYPiWuYB_7fThlDadU&e=
    Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=EdVxNaXoTBbrFjOSxSGtf80f5GLwY4UoeoqXOgi2y1Y&s=WVkM4La4mZsWQ2beQpPA_hXCmu_AFvn6RbGtetuCDqA&e=