pymol-users Mailing List for PyMOL Molecular Graphics System

For some reason, the people doing brew have decided to stop supporting
compiling tcl-tk with X11 support. Not 100% sure, but I'm pretty certain
pymol cannot use tcl-tk with aqua.

If you already had pymol installed, this seems to eliminate the external
gui. If you didn't, new installations of pymol will now crash randomly.

Here's how I got to the old version that worked

$ cd /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/
$ git checkout 46e1ef94247cd2fb9555b724c05aaaa1e8907996 -- tcl-tk.rb
$ cd ../../homebrew-science/
Edit the pymol.rb file so that it depends on "tcl-tk" instead of
"homebrew/dupes/tcl-tk"

$ brew remove tcl-tk python pymol
$ brew install pymol
$ brew pin tcl-tk

Really, I uninstalled all my homebrew packages and then reinstalled
everything because some of their changes over the last 6 months had made
things oddly broken. If you want to do the same, you can try this:

$ brew list > installed
$ <installed xargs brew remove
$ brew cleanup
$ <installed xargs brew install

-David


On Sat, Jul 29, 2017 at 11:26 PM, jacky zhao <jac...@gm...> wrote:

> Hi,
> pymol external gui menus missing, I have compiled pymol in mac os by using
> brew.
>
> Anyone can provide some suggestions?
>
> Jacky
>
> --
> Lei Zhao, Ph.D. & M.D.
> Associate Professor
> National Clinical Research Center for Normal Aging and Geriatric
> National Engineering Research Center for Antibody Medicine
> The Key Lab of Normal Aging and Geriatric
> PLA General Hospital
> Beijing 100853
> P.R.China
> Tel:86-15210661966
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi,
pymol external gui menus missing, I have compiled pymol in mac os by using
brew.

Anyone can provide some suggestions?

Jacky

-- 
Lei Zhao, Ph.D. & M.D.
Associate Professor
National Clinical Research Center for Normal Aging and Geriatric
National Engineering Research Center for Antibody Medicine
The Key Lab of Normal Aging and Geriatric
PLA General Hospital
Beijing 100853
P.R.China
Tel:86-15210661966

Hi Gianluca,

This is a good find, thanks a lot for the bug report. It took me quite a white to understand what's going wrong here. The solution is: use the "load_raw" function instead of "load".

cmd.load_raw(b, "mmtf", "str")

Cheers,
  Thomas

> On Jul 25, 2017, at 8:17 AM, Gianluca Tomasello <gia...@gm...> wrote:
> 
> Hi Thomas, something strange happen when I try to load 4v99.mmtf using this procedure (other PDB files works proprely as far as I know):
> 
> download the file from https://mmtf.rcsb.org/v1.0/full/4V99
> then in script:
> 
> with open(file_path,"rb") as binary:
> 	b = binary.read()	
> cmd.load(b, "str", 0, cmd.loadable.mmtfstr)
> 
> if i try to load the script with pymol, It gives this result:
> 
> ...
> Warning: map key not of type str (type 2).
> Warning: map key not of type str (type 2).
> Warning: map key not of type str (type 2).
> Warning: map key not of type str (type 6).
> Warning: map key not of type str (type 2).
> Warning: map key not of type str (type 7).
> Warning: map key not of type str (type 2).
> Error in MMTF_parser_fetch_typed_array: length mismatch 588367 588120
> Warning: map key not of type str (type 2).
> Warning: map key not of type str (type 2).
> Warning: map key not of type str (type 2).
> Warning: map key not of type str (type 2).
>  MMTF structureId: '4V99', mmtfVersion: '1.0.0'
> Segmentation fault (core dumped)
> 
> The strange thing is that if I try to normally load this file in bash doing  pymol 4v99.mmtf the file is correctly loaded. Is there something I am missing?
> 
> 2017-06-22 17:52 GMT+02:00 Gianluca Tomasello <gia...@gm...>:
> Thank you very much!
> 
> 2017-06-22 13:11 GMT+02:00 Thomas Holder <tho...@sc...>:
> Hi Gianluca,
> 
> Yes this is possible, assuming you're using PyMOL 1.8.6. Use something like this:
> 
> def read_mmtfstr(contents, oname, state=0):
>     return cmd.load(contents, oname, state, cmd.loadable.mmtfstr)
> 
> Cheers,
>   Thomas
> 
> > On Jun 21, 2017, at 12:07 PM, Gianluca Tomasello <gia...@gm...> wrote:
> >
> > Hi, I am using read_pdbstr function to load a strucutres into pymol. Is there a way to do the same for mmtf file formats? (I mean without using temporary files)

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi all,

 

I have been trying for a while, but cannot seem to figure out how to install
pymol on my unix server so that I can run pymol from within a python script.
(So that I can use it with the command ' import pymol'. I did manage to do
this on my windows with a wheel, but don't know how to solve it on my unix
system) 

 

Any tips would be very welcome!

 

Thanks,

Vivien

Hi Thomas, something strange happen when I try to load 4v99.mmtf using this
procedure (other PDB files works proprely as far as I know):

download the file from https://mmtf.rcsb.org/v1.0/full/4V99
then in script:

with open(file_path,"rb") as binary:
b = binary.read()
cmd.load(b, "str", 0, cmd.loadable.mmtfstr)

if i try to load the script with pymol, It gives this result:

...
Warning: map key not of type str (type 2).
Warning: map key not of type str (type 2).
Warning: map key not of type str (type 2).
Warning: map key not of type str (type 6).
Warning: map key not of type str (type 2).
Warning: map key not of type str (type 7).
Warning: map key not of type str (type 2).
Error in MMTF_parser_fetch_typed_array: length mismatch 588367 588120
Warning: map key not of type str (type 2).
Warning: map key not of type str (type 2).
Warning: map key not of type str (type 2).
Warning: map key not of type str (type 2).
 MMTF structureId: '4V99', mmtfVersion: '1.0.0'
Segmentation fault (core dumped)

The strange thing is that if I try to normally load this file in bash doing
 pymol 4v99.mmtf the file is correctly loaded. Is there something I am
missing?

2017-06-22 17:52 GMT+02:00 Gianluca Tomasello <gia...@gm...>:

> Thank you very much!
>
> 2017-06-22 13:11 GMT+02:00 Thomas Holder <tho...@sc...>:
>
>> Hi Gianluca,
>>
>> Yes this is possible, assuming you're using PyMOL 1.8.6. Use something
>> like this:
>>
>> def read_mmtfstr(contents, oname, state=0):
>>     return cmd.load(contents, oname, state, cmd.loadable.mmtfstr)
>>
>> Cheers,
>>   Thomas
>>
>> > On Jun 21, 2017, at 12:07 PM, Gianluca Tomasello <gia...@gm...>
>> wrote:
>> >
>> > Hi, I am using read_pdbstr function to load a strucutres into pymol. Is
>> there a way to do the same for mmtf file formats? (I mean without using
>> temporary files)
>>
>> --
>> Thomas Holder
>> PyMOL Principal Developer
>> Schrödinger, Inc.
>>
>>
>

Hello,

I need to post a ticket about a question which previous answers cannot solve as far as I can tell, regarding Desmond trajectory import.

Thanks

Hi Jason,

I assume you're using the Educational PyMOL build. That version lacks ray tracing related features (which includes geometry export). You should see a warning message in the log window when attempting to export geometry.

Cheers,
  Thomas

> On Jul 20, 2017, at 4:18 AM, Jason Davis <jas...@ch...> wrote:
> 
> Hi - I have downloaded and installed MacPymol - I used to use this heavily years ago.
> I have opened a PDB file and changing its display in Pymol works fine BUT I am seemingly unable to export as VRML or POV-Ray.  If I select either export option and then the location for export nothing happens (no file is generated).  PNG export works fine.
> Any advice hugely welcome
> Jason

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi, Is there a way to control the size of label outline in pymol?

Hi - I have downloaded and installed MacPymol - I used to use this heavily years ago.
I have opened a PDB file and changing its display in Pymol works fine BUT I am seemingly unable to export as VRML or POV-Ray.  If I select either export option and then the location for export nothing happens (no file is generated).  PNG export works fine.
Any advice hugely welcome
Jason

Thank you Thomas. That worked perfectly!

Best,

Kelly

On Tue, Jul 18, 2017 at 4:04 PM, Thomas Holder <
tho...@sc...> wrote:

> Hi Kelly,
>
> With retain_order=1, PyMOL will sort by rank, which is the order of time
> of loading the structure. By setting all rank values to the same value,
> you'll get segi/chain/resi sorting. So to preserve rank based sorting only
> for non-solvent, you can do this:
>
> set retain_order
> alter solvent, rank=-1
> sort
>
> This will sort solvent to the beginning. To put it to the end, pick a
> number which is beyond the atom count.
>
> set retain_order
> alter solvent, rank=9999
> sort
>
> The atom ID is never used for sorting. But you could incorporate it in the
> ranks:
>
> set retain_order
> alter solvent, rank=9999 + ID
> sort
>
> Cheers,
>   Thomas
>
> > On Jul 18, 2017, at 2:09 PM, Kelly Tran <kn...@ge...> wrote:
> >
> > Hi,
> >
> > I'm using PSICO to write a DCD. Is it possible to retain the original
> order for one segment (protein) while sorting by atom ID for another
> segment (water).
> >
> > Thank you,
> >
> > Kelly
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Hi all,


I am trying to add modified Cysteine molecules which have a Nitroxide group attached on the Sulphur atom of the Cysteine by using the mutagenesis menu. I have saved my modified molecule as a .pdb file however cannot work out how to add it to the list of residues in the mutagenesis menu.


I have also tried saving the nitroxide group as a fragment as a .pkl file and adding it into C:\Program Files\PyMOL\PyMOL\data\chempy\fragments then using the command editor.attach_fragment('pk1','nit',11,0) where my Nitroxide group is saved as "nit.pkl". This however is no use as instead of connecting the two Sulphur atoms, the Sulphur on the cysteine gets connected to a methyl group on the Nitroxide.


I am adding the Nitroxide so that I can use spin-labelling data for electron paramagnetic resonance in a docking software package.


A resolution to this problem would be greatly appreciated ,

Thanks,

Josh




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Hi Kelly,

With retain_order=1, PyMOL will sort by rank, which is the order of time of loading the structure. By setting all rank values to the same value, you'll get segi/chain/resi sorting. So to preserve rank based sorting only for non-solvent, you can do this:

set retain_order
alter solvent, rank=-1
sort

This will sort solvent to the beginning. To put it to the end, pick a number which is beyond the atom count. 

set retain_order
alter solvent, rank=9999
sort

The atom ID is never used for sorting. But you could incorporate it in the ranks:

set retain_order
alter solvent, rank=9999 + ID
sort

Cheers,
  Thomas

> On Jul 18, 2017, at 2:09 PM, Kelly Tran <kn...@ge...> wrote:
> 
> Hi,
> 
> I'm using PSICO to write a DCD. Is it possible to retain the original order for one segment (protein) while sorting by atom ID for another segment (water).
> 
> Thank you,
> 
> Kelly

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

The link wasn't a direct link to the fixed setup.py file. The direct link is:
https://raw.githubusercontent.com/speleo3/pymol-psico/master/setup.py

MacPyMOL 1.7.4 is recent enough for this exercise. However, your MacPyMOL installation and your Anaconda3 Python are unrelated, so installing PSICO with Anaconda won't make it work with MacPyMOL.

The simplest approach to install PSICO with MacPyMOL is to copy the "psico" directory here:
/Applications/MacPyMOL.app/Contents/pymol/modules/

Cheers,
  Thomas

> On Jul 18, 2017, at 2:53 PM, James Starlight <jms...@gm...> wrote:
> 
> There were some errors in the executing pymol script with your commands using
> @ script.pml
> or
> run script.pml
> 
> probably because of my MAC Pymol which is v 1.74 mb outdated, no?
> 
> BTW on the same MAC I just have tried to install updated setup.py and
> it was the following error:
> 
> Glebs-MacBook-Pro:pymol-psico-master Own$ python setup.py
>  File "setup.py", line 7
>    <!DOCTYPE html>
>    ^
> SyntaxError: invalid syntax
> 
> 2017-07-18 19:52 GMT+02:00 Thomas Holder <tho...@sc...>:
>> With super instead of tmalign:
>> 
>> loadall *.pdb
>> extra_fit *, reference, method=super, object=aln
>> remove not (byres aln)
>> 
>> The PSICO setup.py installation script wasn't Python 3 ready. It's fixed now:
>> https://github.com/speleo3/pymol-psico/commit/e92f09374cc5ef7b562e5332292cee4f57f168af
>> 
>> Cheers,
>>  Thomas
>> 
>>> On Jul 18, 2017, at 1:39 PM, James Starlight <jms...@gm...> wrote:
>>> 
>>> Hi Thomas,
>>> 
>>> could you also send the same script but just with the Super command
>>> for the superimposition without PSICO?
>>> 
>>> it's strange I have a problems of PSICO installation on MAC with python 3
>>> 
>>> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:52:12)
>>> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
>>> Type "help", "copyright", "credits" or "license" for more information.
>>>>>> 
>>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t
>>> README        psico        setup.py
>>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py
>>> File "setup.py", line 10
>>>   print 'Warning: could not import version'
>>>                                           ^
>>> 
>>> 2017-07-18 19:37 GMT+02:00 James Starlight <jms...@gm...>:
>>>> Hi Thomas,
>>>> 
>>>> could you also send the same script but just with the Super command
>>>> for the superimposition without PSICO?
>>>> 
>>>> it's strange I have a problems of PSICO installation on MAC with python 3
>>>> 
>>>> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:52:12)
>>>> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
>>>> Type "help", "copyright", "credits" or "license" for more information.
>>>>>>> 
>>>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t
>>>> README        psico        setup.py
>>>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py
>>>> File "setup.py", line 10
>>>>   print 'Warning: could not import version'
>>>>                                           ^
>>>> SyntaxError: Missing parentheses in call to 'print'
>>>> 
>>>> 2017-07-18 19:05 GMT+02:00 Thomas Holder <tho...@sc...>:
>>>>> Hi Gleb,
>>>>> 
>>>>> If you have PSICO installed (which provides a TMalign wrapper), then this script should be sufficient:
>>>>> 
>>>>> loadall *.pdb
>>>>> import psico.fitting
>>>>> extra_fit *, reference, method=tmalign, object=aln
>>>>> remove not (byres aln)
>>>>> 
>>>>> https://pymolwiki.org/index.php/Psico
>>>>> 
>>>>> Cheers,
>>>>> Thomas
>>>>> 
>>>>>> On Jul 18, 2017, at 11:35 AM, James Starlight <jms...@gm...> wrote:
>>>>>> 
>>>>>> Dear Pymol Users!
>>>>>> 
>>>>>> In my work dir I have 200 pdb files of GPCRs and one receptor
>>>>>> reference.pdb (it consist of only one GPCR monomer - seven
>>>>>> transmbembrane scaffold).
>>>>>> 
>>>>>> I need to write a simple script which will do the following things:
>>>>>> 
>>>>>> 1 - allign (in loop) each structure against reference.pdb using
>>>>>> "super" or "TMalign" (is better!)
>>>>>> 
>>>>>> 2 - from each of the aligned pdbs, remove not superimposed regions
>>>>>> (assuming that each pdb has several chains, some insertions like
>>>>>> lyzocyme which were not aligned against reference), thus keeping only
>>>>>> seven-transmembrane scaffold present in reference.pdb.
>>>>>> 
>>>>>> I thanks so much for the help!
>>>>>> 
>>>>>> Gleb

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

if just add strings in pymol's cmd the "Super version" of the script
works fine so the problem is indeed in MAC :)

2017-07-18 20:53 GMT+02:00 James Starlight <jms...@gm...>:
> There were some errors in the executing pymol script with your commands using
> @ script.pml
> or
> run script.pml
>
> probably because of my MAC Pymol which is v 1.74 mb outdated, no?
>
> BTW on the same MAC I just have tried to install updated setup.py and
> it was the following error:
>
> Glebs-MacBook-Pro:pymol-psico-master Own$ python setup.py
>   File "setup.py", line 7
>     <!DOCTYPE html>
>     ^
> SyntaxError: invalid syntax
>
> 2017-07-18 19:52 GMT+02:00 Thomas Holder <tho...@sc...>:
>> With super instead of tmalign:
>>
>> loadall *.pdb
>> extra_fit *, reference, method=super, object=aln
>> remove not (byres aln)
>>
>> The PSICO setup.py installation script wasn't Python 3 ready. It's fixed now:
>> https://github.com/speleo3/pymol-psico/commit/e92f09374cc5ef7b562e5332292cee4f57f168af
>>
>> Cheers,
>>   Thomas
>>
>>> On Jul 18, 2017, at 1:39 PM, James Starlight <jms...@gm...> wrote:
>>>
>>> Hi Thomas,
>>>
>>> could you also send the same script but just with the Super command
>>> for the superimposition without PSICO?
>>>
>>> it's strange I have a problems of PSICO installation on MAC with python 3
>>>
>>> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:52:12)
>>> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
>>> Type "help", "copyright", "credits" or "license" for more information.
>>>>>>
>>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t
>>> README        psico        setup.py
>>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py
>>>  File "setup.py", line 10
>>>    print 'Warning: could not import version'
>>>                                            ^
>>>
>>> 2017-07-18 19:37 GMT+02:00 James Starlight <jms...@gm...>:
>>>> Hi Thomas,
>>>>
>>>> could you also send the same script but just with the Super command
>>>> for the superimposition without PSICO?
>>>>
>>>> it's strange I have a problems of PSICO installation on MAC with python 3
>>>>
>>>> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:52:12)
>>>> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
>>>> Type "help", "copyright", "credits" or "license" for more information.
>>>>>>>
>>>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t
>>>> README        psico        setup.py
>>>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py
>>>>  File "setup.py", line 10
>>>>    print 'Warning: could not import version'
>>>>                                            ^
>>>> SyntaxError: Missing parentheses in call to 'print'
>>>>
>>>> 2017-07-18 19:05 GMT+02:00 Thomas Holder <tho...@sc...>:
>>>>> Hi Gleb,
>>>>>
>>>>> If you have PSICO installed (which provides a TMalign wrapper), then this script should be sufficient:
>>>>>
>>>>> loadall *.pdb
>>>>> import psico.fitting
>>>>> extra_fit *, reference, method=tmalign, object=aln
>>>>> remove not (byres aln)
>>>>>
>>>>> https://pymolwiki.org/index.php/Psico
>>>>>
>>>>> Cheers,
>>>>>  Thomas
>>>>>
>>>>>> On Jul 18, 2017, at 11:35 AM, James Starlight <jms...@gm...> wrote:
>>>>>>
>>>>>> Dear Pymol Users!
>>>>>>
>>>>>> In my work dir I have 200 pdb files of GPCRs and one receptor
>>>>>> reference.pdb (it consist of only one GPCR monomer - seven
>>>>>> transmbembrane scaffold).
>>>>>>
>>>>>> I need to write a simple script which will do the following things:
>>>>>>
>>>>>> 1 - allign (in loop) each structure against reference.pdb using
>>>>>> "super" or "TMalign" (is better!)
>>>>>>
>>>>>> 2 - from each of the aligned pdbs, remove not superimposed regions
>>>>>> (assuming that each pdb has several chains, some insertions like
>>>>>> lyzocyme which were not aligned against reference), thus keeping only
>>>>>> seven-transmembrane scaffold present in reference.pdb.
>>>>>>
>>>>>> I thanks so much for the help!
>>>>>>
>>>>>> Gleb
>>
>> --
>> Thomas Holder
>> PyMOL Principal Developer
>> Schrödinger, Inc.
>>

There were some errors in the executing pymol script with your commands using
@ script.pml
or
run script.pml

probably because of my MAC Pymol which is v 1.74 mb outdated, no?

BTW on the same MAC I just have tried to install updated setup.py and
it was the following error:

Glebs-MacBook-Pro:pymol-psico-master Own$ python setup.py
  File "setup.py", line 7
    <!DOCTYPE html>
    ^
SyntaxError: invalid syntax

2017-07-18 19:52 GMT+02:00 Thomas Holder <tho...@sc...>:
> With super instead of tmalign:
>
> loadall *.pdb
> extra_fit *, reference, method=super, object=aln
> remove not (byres aln)
>
> The PSICO setup.py installation script wasn't Python 3 ready. It's fixed now:
> https://github.com/speleo3/pymol-psico/commit/e92f09374cc5ef7b562e5332292cee4f57f168af
>
> Cheers,
>   Thomas
>
>> On Jul 18, 2017, at 1:39 PM, James Starlight <jms...@gm...> wrote:
>>
>> Hi Thomas,
>>
>> could you also send the same script but just with the Super command
>> for the superimposition without PSICO?
>>
>> it's strange I have a problems of PSICO installation on MAC with python 3
>>
>> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:52:12)
>> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
>> Type "help", "copyright", "credits" or "license" for more information.
>>>>>
>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t
>> README        psico        setup.py
>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py
>>  File "setup.py", line 10
>>    print 'Warning: could not import version'
>>                                            ^
>>
>> 2017-07-18 19:37 GMT+02:00 James Starlight <jms...@gm...>:
>>> Hi Thomas,
>>>
>>> could you also send the same script but just with the Super command
>>> for the superimposition without PSICO?
>>>
>>> it's strange I have a problems of PSICO installation on MAC with python 3
>>>
>>> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:52:12)
>>> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
>>> Type "help", "copyright", "credits" or "license" for more information.
>>>>>>
>>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t
>>> README        psico        setup.py
>>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py
>>>  File "setup.py", line 10
>>>    print 'Warning: could not import version'
>>>                                            ^
>>> SyntaxError: Missing parentheses in call to 'print'
>>>
>>> 2017-07-18 19:05 GMT+02:00 Thomas Holder <tho...@sc...>:
>>>> Hi Gleb,
>>>>
>>>> If you have PSICO installed (which provides a TMalign wrapper), then this script should be sufficient:
>>>>
>>>> loadall *.pdb
>>>> import psico.fitting
>>>> extra_fit *, reference, method=tmalign, object=aln
>>>> remove not (byres aln)
>>>>
>>>> https://pymolwiki.org/index.php/Psico
>>>>
>>>> Cheers,
>>>>  Thomas
>>>>
>>>>> On Jul 18, 2017, at 11:35 AM, James Starlight <jms...@gm...> wrote:
>>>>>
>>>>> Dear Pymol Users!
>>>>>
>>>>> In my work dir I have 200 pdb files of GPCRs and one receptor
>>>>> reference.pdb (it consist of only one GPCR monomer - seven
>>>>> transmbembrane scaffold).
>>>>>
>>>>> I need to write a simple script which will do the following things:
>>>>>
>>>>> 1 - allign (in loop) each structure against reference.pdb using
>>>>> "super" or "TMalign" (is better!)
>>>>>
>>>>> 2 - from each of the aligned pdbs, remove not superimposed regions
>>>>> (assuming that each pdb has several chains, some insertions like
>>>>> lyzocyme which were not aligned against reference), thus keeping only
>>>>> seven-transmembrane scaffold present in reference.pdb.
>>>>>
>>>>> I thanks so much for the help!
>>>>>
>>>>> Gleb
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>

Hi,

I'm using PSICO to write a DCD. Is it possible to retain the original order
for one segment (protein) while sorting by atom ID for another segment
(water).

Thank you,

Kelly

With super instead of tmalign:

loadall *.pdb
extra_fit *, reference, method=super, object=aln
remove not (byres aln)

The PSICO setup.py installation script wasn't Python 3 ready. It's fixed now:
https://github.com/speleo3/pymol-psico/commit/e92f09374cc5ef7b562e5332292cee4f57f168af

Cheers,
  Thomas

> On Jul 18, 2017, at 1:39 PM, James Starlight <jms...@gm...> wrote:
> 
> Hi Thomas,
> 
> could you also send the same script but just with the Super command
> for the superimposition without PSICO?
> 
> it's strange I have a problems of PSICO installation on MAC with python 3
> 
> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:52:12)
> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>>>> 
> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t
> README        psico        setup.py
> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py
>  File "setup.py", line 10
>    print 'Warning: could not import version'
>                                            ^
> 
> 2017-07-18 19:37 GMT+02:00 James Starlight <jms...@gm...>:
>> Hi Thomas,
>> 
>> could you also send the same script but just with the Super command
>> for the superimposition without PSICO?
>> 
>> it's strange I have a problems of PSICO installation on MAC with python 3
>> 
>> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:52:12)
>> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
>> Type "help", "copyright", "credits" or "license" for more information.
>>>>> 
>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t
>> README        psico        setup.py
>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py
>>  File "setup.py", line 10
>>    print 'Warning: could not import version'
>>                                            ^
>> SyntaxError: Missing parentheses in call to 'print'
>> 
>> 2017-07-18 19:05 GMT+02:00 Thomas Holder <tho...@sc...>:
>>> Hi Gleb,
>>> 
>>> If you have PSICO installed (which provides a TMalign wrapper), then this script should be sufficient:
>>> 
>>> loadall *.pdb
>>> import psico.fitting
>>> extra_fit *, reference, method=tmalign, object=aln
>>> remove not (byres aln)
>>> 
>>> https://pymolwiki.org/index.php/Psico
>>> 
>>> Cheers,
>>>  Thomas
>>> 
>>>> On Jul 18, 2017, at 11:35 AM, James Starlight <jms...@gm...> wrote:
>>>> 
>>>> Dear Pymol Users!
>>>> 
>>>> In my work dir I have 200 pdb files of GPCRs and one receptor
>>>> reference.pdb (it consist of only one GPCR monomer - seven
>>>> transmbembrane scaffold).
>>>> 
>>>> I need to write a simple script which will do the following things:
>>>> 
>>>> 1 - allign (in loop) each structure against reference.pdb using
>>>> "super" or "TMalign" (is better!)
>>>> 
>>>> 2 - from each of the aligned pdbs, remove not superimposed regions
>>>> (assuming that each pdb has several chains, some insertions like
>>>> lyzocyme which were not aligned against reference), thus keeping only
>>>> seven-transmembrane scaffold present in reference.pdb.
>>>> 
>>>> I thanks so much for the help!
>>>> 
>>>> Gleb

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Thomas,

could you also send the same script but just with the Super command
for the superimposition without PSICO?

it's strange I have a problems of PSICO installation on MAC with python 3

Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:52:12)
[GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>
Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t
README        psico        setup.py
Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py
  File "setup.py", line 10
    print 'Warning: could not import version'
                                            ^

2017-07-18 19:37 GMT+02:00 James Starlight <jms...@gm...>:
> Hi Thomas,
>
> could you also send the same script but just with the Super command
> for the superimposition without PSICO?
>
> it's strange I have a problems of PSICO installation on MAC with python 3
>
> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:52:12)
> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>>>>
> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t
> README        psico        setup.py
> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py
>   File "setup.py", line 10
>     print 'Warning: could not import version'
>                                             ^
> SyntaxError: Missing parentheses in call to 'print'
>
> 2017-07-18 19:05 GMT+02:00 Thomas Holder <tho...@sc...>:
>> Hi Gleb,
>>
>> If you have PSICO installed (which provides a TMalign wrapper), then this script should be sufficient:
>>
>> loadall *.pdb
>> import psico.fitting
>> extra_fit *, reference, method=tmalign, object=aln
>> remove not (byres aln)
>>
>> https://pymolwiki.org/index.php/Psico
>>
>> Cheers,
>>   Thomas
>>
>>> On Jul 18, 2017, at 11:35 AM, James Starlight <jms...@gm...> wrote:
>>>
>>> Dear Pymol Users!
>>>
>>> In my work dir I have 200 pdb files of GPCRs and one receptor
>>> reference.pdb (it consist of only one GPCR monomer - seven
>>> transmbembrane scaffold).
>>>
>>> I need to write a simple script which will do the following things:
>>>
>>> 1 - allign (in loop) each structure against reference.pdb using
>>> "super" or "TMalign" (is better!)
>>>
>>> 2 - from each of the aligned pdbs, remove not superimposed regions
>>> (assuming that each pdb has several chains, some insertions like
>>> lyzocyme which were not aligned against reference), thus keeping only
>>> seven-transmembrane scaffold present in reference.pdb.
>>>
>>> I thanks so much for the help!
>>>
>>> Gleb
>>
>> --
>> Thomas Holder
>> PyMOL Principal Developer
>> Schrödinger, Inc.
>>

Hi Gleb,

If you have PSICO installed (which provides a TMalign wrapper), then this script should be sufficient:

loadall *.pdb
import psico.fitting
extra_fit *, reference, method=tmalign, object=aln
remove not (byres aln)

https://pymolwiki.org/index.php/Psico

Cheers,
  Thomas

> On Jul 18, 2017, at 11:35 AM, James Starlight <jms...@gm...> wrote:
> 
> Dear Pymol Users!
> 
> In my work dir I have 200 pdb files of GPCRs and one receptor
> reference.pdb (it consist of only one GPCR monomer - seven
> transmbembrane scaffold).
> 
> I need to write a simple script which will do the following things:
> 
> 1 - allign (in loop) each structure against reference.pdb using
> "super" or "TMalign" (is better!)
> 
> 2 - from each of the aligned pdbs, remove not superimposed regions
> (assuming that each pdb has several chains, some insertions like
> lyzocyme which were not aligned against reference), thus keeping only
> seven-transmembrane scaffold present in reference.pdb.
> 
> I thanks so much for the help!
> 
> Gleb

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear Pymol Users!

In my work dir I have 200 pdb files of GPCRs and one receptor
reference.pdb (it consist of only one GPCR monomer - seven
transmbembrane scaffold).

I need to write a simple script which will do the following things:

1 - allign (in loop) each structure against reference.pdb using
"super" or "TMalign" (is better!)

2 - from each of the aligned pdbs, remove not superimposed regions
(assuming that each pdb has several chains, some insertions like
lyzocyme which were not aligned against reference), thus keeping only
seven-transmembrane scaffold present in reference.pdb.

I thanks so much for the help!

Gleb

HI Thomas,

I have a protein with two chain A and B. both have only one ligand in them.
As I explained before, I want to identify the size of the pocket , and also
I replace the ligand with another ligand that I have ,

do you know how I do it?

Many thanks
Mohammad

On Sun, Jul 16, 2017 at 3:58 PM, Thomas Holder <
tho...@sc...> wrote:

> Hi Mohammad,
>
> If there is already a ligand in the pocket and you just want to know its
> center x,y,z, you can simply type:
>
> centerofmass organic
>
> Or if there are multiple organic molecules and you are interested in one
> with the unique residue name "LIG":
>
> centerofmass resn LIG
>
> I wound't call that "finding" a pocket though.
>
> Cheers,
>   Thomas
>
> > On Jul 11, 2017, at 7:42 PM, Mohammad Goodarzi <
> moh...@gm...> wrote:
> >
> > Hello,
> >
> > I am wondering whether it is possible to find the pocket of a protein in
> Pymol?
> > lets say I have a protein and a ligand inside the pocket. I want to
> estimate the x, y and z
> >
> > Best Regards,
> > Mohammad
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Hi Mohammad,

If there is already a ligand in the pocket and you just want to know its center x,y,z, you can simply type:

centerofmass organic

Or if there are multiple organic molecules and you are interested in one with the unique residue name "LIG":

centerofmass resn LIG

I wound't call that "finding" a pocket though.

Cheers,
  Thomas

> On Jul 11, 2017, at 7:42 PM, Mohammad Goodarzi <moh...@gm...> wrote:
> 
> Hello, 
> 
> I am wondering whether it is possible to find the pocket of a protein in Pymol?
> lets say I have a protein and a ligand inside the pocket. I want to estimate the x, y and z
> 
> Best Regards,
> Mohammad

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hello,

I am wondering whether it is possible to find the pocket of a protein in
Pymol?
lets say I have a protein and a ligand inside the pocket. I want to
estimate the x, y and z

Best Regards,
Mohammad

Hi Gianluca,

https://pymolwiki.org/index.php/nb_spheres

Cheers,
  Thomas

> On Jul 10, 2017, at 1:31 PM, Gianluca Tomasello <gia...@gm...> wrote:
> 
> Hi, is it possible to render nonbonded atoms as small spheres using only stick representation?


--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi, is it possible to render nonbonded atoms as small spheres using only
stick representation?