[PyMOL] Increase label outline size

[Gianluca Tomasello <giagitom@gm...>]

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

[PyMOL] Export problems

[Jason Davis <jason.davis@ch...>]

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

Re: [PyMOL] Retain order for select segment and write trajectory

[Kelly Tran <knt8@ge...>]

Thank you Thomas. That worked perfectly!

Best,

Kelly

On Tue, Jul 18, 2017 at 4:04 PM, Thomas Holder <
thomas.holder@...> 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 <knt8@...> 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.
>
>

[PyMOL] Creating my own molecule to use with mutagenesis

[Joshua Hay <ppyjh6@no...>]

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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Re: [PyMOL] Retain order for select segment and write trajectory

[Thomas Holder <thomas.holder@sc...>]

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 <knt8@...> 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.

Re: [PyMOL] A structural superimposition and further post-processing

[Thomas Holder <thomas.holder@sc...>]

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 <jmsstarlight@...> 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 <thomas.holder@...>:
>> 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 <jmsstarlight@...> 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 <jmsstarlight@...>:
>>>> 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 <thomas.holder@...>:
>>>>> 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 <jmsstarlight@...> 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.

Re: [PyMOL] A structural superimposition and further post-processing

[James Starlight <jmsstarlight@gm...>]

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 <jmsstarlight@...>:
> 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 <thomas.holder@...>:
>> 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 <jmsstarlight@...> 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 <jmsstarlight@...>:
>>>> 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 <thomas.holder@...>:
>>>>> 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 <jmsstarlight@...> 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.
>>

Re: [PyMOL] A structural superimposition and further post-processing

[James Starlight <jmsstarlight@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 <thomas.holder@...>:
> 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 <jmsstarlight@...> 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 <jmsstarlight@...>:
>>> 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 <thomas.holder@...>:
>>>> 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 <jmsstarlight@...> 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.
>

[PyMOL] Retain order for select segment and write trajectory

[Kelly Tran <knt8@ge...>]

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

Re: [PyMOL] A structural superimposition and further post-processing

[Thomas Holder <thomas.holder@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 <jmsstarlight@...> 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 <jmsstarlight@...>:
>> 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 <thomas.holder@...>:
>>> 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 <jmsstarlight@...> 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.

Re: [PyMOL] A structural superimposition and further post-processing

[James Starlight <jmsstarlight@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'
                                            ^

2017-07-18 19:37 GMT+02:00 James Starlight <jmsstarlight@...>:
> 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 <thomas.holder@...>:
>> 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 <jmsstarlight@...> 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.
>>

Re: [PyMOL] A structural superimposition and further post-processing

[Thomas Holder <thomas.holder@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 <jmsstarlight@...> 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.

[PyMOL] A structural superimposition and further post-processing

[James Starlight <jmsstarlight@gm...>]

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

Re: [PyMOL] How to identify the pocket of a protein?

[Mohammad Goodarzi <mohammad.godarzi@gm...>]

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 <
thomas.holder@...> 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 <
> mohammad.godarzi@...> 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.
>
>

Re: [PyMOL] How to identify the pocket of a protein?

[Thomas Holder <thomas.holder@sc...>]

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 <mohammad.godarzi@...> 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.

[PyMOL] How to identify the pocket of a protein?

[Mohammad Goodarzi <mohammad.godarzi@gm...>]

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

Re: [PyMOL] show nonbonded atoms with stick representation

[Thomas Holder <thomas.holder@sc...>]

Hi Gianluca,

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

Cheers,
  Thomas

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


--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] show nonbonded atoms with stick representation

[Gianluca Tomasello <giagitom@gm...>]

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

[PyMOL] Pymolhybrid Caver plugin error

[Shivangi Nangia <shivangi_nangia@ya...>]

Hello,
This might be a naive question as I am new to PyMol.
I recently installed MacPyMol and followed the instructions on Plugins - PyMOLWiki  to install the plugin Caver.
After successfully installing Caver, I loaded  the trajectory I want to analyze to compute tunnels, I get the following messages:
*** Caver will be called using command ***java -Xmx500m -cp "/Users/shivangi/Downloads/caver_3.0_plugin/linux_mac/Caver3/lib" -jar "/Users/shivangi/Downloads/caver_3.0_plugin/linux_mac/Caver3/caver.jar" -home "/Users/shivangi/Downloads/caver_3.0_plugin/linux_mac/Caver3" -pdb "/Users/shivangi/caver_output/3/inputs" -conf "/Users/shivangi/caver_output/3/inputs/config_2017-07-08-13-53.txt" -out "/Users/shivangi/caver_output/3"******************************************Update of your Python or PyMOL is recommended, some error messages may not be visible with current version./Users/shivangirun /Users/shivangi/caver_output/3/pymol/view_plugin.pyPyMOL>run /Users/shivangi/caver_output/3/pymol/view_plugin.pyTraceback (most recent call last):  File "/Applications/PyMOLX11Hybrid.app/Contents/pymol/modules/pymol/parsing.py", line 533, in run_file    execfile(file,global_ns,local_ns)  File "/Applications/PyMOLX11Hybrid.app/Contents/pymol/modules/pymol/parsing.py", line 527, in execfile    co = compile(pi.file_read(filename), filename, 'exec')  File "/Applications/PyMOLX11Hybrid.app/Contents/pymol/modules/pymol/internal.py", line 327, in file_read    raise pymol.CmdException('failed to open file "%s"' % finfo)CmdException:  Error: failed to open file "/Users/shivangi/caver_output/3/pymol/view_plugin.py" 
Along with these messages a window pops up which says update Java JDK, which I did, restarted my computer.On checking with Safari browser, it tells me I have the correct version of Java on my computer.
I do have python3 installed on my mac.
I am very confused as to how to make caver work on Mac.
Kindly guide.
  
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|   
|   
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Plugins - PyMOLWiki
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Regards,Shivangi

[PyMOL] Antwort: interface surface Area and distances in two dimeres (Ashwani Kumar)

[<honegger@bi...>]

Dear Ashwani Kumar

To get the interface area between two molecular entities, you calculate the accessible surface of the complex and that of the separated entities, the difference between the two is twice the interface area. Any tool that allows you to calculate a solvent accessible surface area can be used for this, including the get_area command in Pymol. I personally like to use the program NACCESS, as it also gives me the per-atom and per-residue contributions, divided into hydrophobic and hydrophilic, main-chain and side chain contributions, or the rosetta interface analysis tool if I am interested in the energetics of the interface.
The PISA analysis is most relevant for assessing the probability of an interface observed in the crystal being biologically relevant. As to the distance, there is no general definition: VdW and hydrogen bonding contacts determine how close the two entities can approach each other. In assessing e.g. docked complexes, the center-of-gravity - center-of-gravity distance may help to sort different solutions as to how close the two entities get to each other (in PyMOL, you calculate the center of gravity using the appropriate center of mass script - it returns the coordinates of the cog as well as a pseudo atom indicating the position.

Annemarie Honegger


Message: 1
Date: Sat, 8 Jul 2017 02:12:05 +0530
From: Ashwani Kumar <ashwanikr.iitb@...>
To: pymol-users@...
Subject: [PyMOL] interface surface Area and distances in two dimeres
Message-ID:
<CAG=kqZRdKTnRakBu5V2Qp5p3kcfkyQ=r61D2_6kzJ7hTU4zJOQ@...>
Content-Type: text/plain; charset="utf-8"

Dear All
I would like know interface surface area between two dimers and distances
like if protein has 4 monomer (A, B,C,D chains ) in ASU.
chainA an D are forming biological unit as dimer   similarly chain B&C also
.
I would like know interface  area  between dimer ( chainAD) and Chain BC.
I have trired PISA of CCP4 and PDBe PISA.
it calculate the interface surface area between dimer of chain AD or chain
BC etc.
i have also find the  interface Residues  two chains  in pymol.

 Kindly help please

Regards
Ashwani Kumar
SRF - ICMR
Structural Biology lab
NCCS PUNE

[PyMOL] interface surface Area and distances in two dimeres

[Ashwani Kumar <ashwanikr.iitb@gm...>]

Dear All
I would like know interface surface area between two dimers and distances
like if protein has 4 monomer (A, B,C,D chains ) in ASU.
chainA an D are forming biological unit as dimer   similarly chain B&C also
.
I would like know interface  area  between dimer ( chainAD) and Chain BC.
I have trired PISA of CCP4 and PDBe PISA.
it calculate the interface surface area between dimer of chain AD or chain
BC etc.
i have also find the  interface Residues  two chains  in pymol.

 Kindly help please

Regards
Ashwani Kumar
SRF - ICMR
Structural Biology lab
NCCS PUNE

[PyMOL] Getting full screen PyMol after Installing pymol on Windows 10

[Ndonwi, Maze <ndonwimaze@wu...>]

Hi,

Anyone had this experience? I need some help with my new PyMOL installation.

I have just installed PyMOL on Windows 10 and by default, the full screen mode installed on my menu list. When I navigate to my start menu to open PyMOL, opens in Full screen mode and covers my whole screen. How do I get out of the full screen mode?

I have tried running the full screen command with no success. So, I typed “full_screen off”but this close the screen mode.

Thanks so much for your help,
Maze


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Re: [PyMOL] Valence bonding ray trace in batch mode

[Gianluca Tomasello <giagitom@gm...>]

Great! Thanks for the help Thomas. It works fine!

2017-07-05 12:34 GMT+02:00 Thomas Holder <thomas.holder@...>:

> Hi Gianluca,
>
> I can reproduce the problem and found the bug. This is already fixed in
> Incentive PyMOL. For Open-Source PyMOL, you can apply the attached patch.
>
> Cheers,
>   Thomas
>
>
>
>
> > On Jul 4, 2017, at 3:39 PM, Gianluca Tomasello <giagitom@...>
> wrote:
> >
> > Hi Thomas,
> >
> > the script below reproduce the behavior for me. I don't use pymolrc file
> or k flag.
> >
> > I loaded the script like this and two different behaviors were detected
> on the renderised image.
> >
> > 1)   pymol script.py
> >
> > 2)   pymol -c scritp.py
> >
> >
> >
> > from pymol import cmd
> > cmd.fetch("1c0k","a",async=0)
> > cmd.show_as("sticks")
> > cmd.set("stick_radius",0.3)
> > cmd.set("stick_ball",1)
> > cmd.set("stick_ball_ratio",2)
> > cmd.set("valence",1)
> > cmd.set("valence_mode",0)
> > cmd.set_view (
> >      [0.922998726,   -0.368575215,    0.110539697,
> >     -0.093491152,   -0.493465245,   -0.864722848,
> >      0.373262018,    0.787807524,   -0.489932150,
> >     -0.000001901,   -0.000001147,  -21.332012177,
> >     34.310882568,  117.484252930,   39.097888947,
> >     17.685882568,   24.978404999,  -20.000000000] )
> > cmd.png("test.png",width=1185, ray=1)
> >
> > 2017-07-04 14:09 GMT+02:00 Thomas Holder <thomas.holder@...
> >:
> > Hi Gianluca,
> >
> > You get the sphere with stick_ball=on. It's unexpected that batch mode
> and GUI mode give different results. Could it be that you have the
> stick_ball setting in a (directory specific) pymolrc file, and/or do you
> pass -k flag (ignores pymolrc files) in batch mode?
> >
> > Cheers,
> >   Thomas
> >
> > > On Jul 2, 2017, at 5:32 PM, Gianluca Tomasello <giagitom@...>
> wrote:
> > >
> > > Hi, I am trying to execute a script that sets valence bonding on
> sticks and then it gives me back a rendered image. There seems there is a
> difference when i try to run the script normally or in batch mode (pymol
> -cq script.py).  If i run it in batch mode, each atom with a double bond is
> rendered without the sphere in the atom center (only double bond is shown).
> > >
> > > Instead, if i try to execute the script in default mode the central
> atom sphere is correctly rendered.
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
>

Re: [PyMOL] Valence bonding ray trace in batch mode

[Thomas Holder <thomas.holder@sc...>]

Hi Gianluca,

I can reproduce the problem and found the bug. This is already fixed in Incentive PyMOL. For Open-Source PyMOL, you can apply the attached patch.

Cheers,
  Thomas

Re: [PyMOL] Valence bonding ray trace in batch mode

[Gianluca Tomasello <giagitom@gm...>]

Hi Thomas,

the script below reproduce the behavior for me. I don't use pymolrc file or
k flag.

I loaded the script like this and two different behaviors were detected on
the renderised image.

1)   pymol script.py

2)   pymol -c scritp.py



from pymol import cmd
cmd.fetch("1c0k","a",async=0)
cmd.show_as("sticks")
cmd.set("stick_radius",0.3)
cmd.set("stick_ball",1)
cmd.set("stick_ball_ratio",2)
cmd.set("valence",1)
cmd.set("valence_mode",0)
cmd.set_view (
     [0.922998726,   -0.368575215,    0.110539697,
    -0.093491152,   -0.493465245,   -0.864722848,
     0.373262018,    0.787807524,   -0.489932150,
    -0.000001901,   -0.000001147,  -21.332012177,
    34.310882568,  117.484252930,   39.097888947,
    17.685882568,   24.978404999,  -20.000000000] )
cmd.png("test.png",width=1185, ray=1)

2017-07-04 14:09 GMT+02:00 Thomas Holder <thomas.holder@...>:

> Hi Gianluca,
>
> You get the sphere with stick_ball=on. It's unexpected that batch mode and
> GUI mode give different results. Could it be that you have the stick_ball
> setting in a (directory specific) pymolrc file, and/or do you pass -k flag
> (ignores pymolrc files) in batch mode?
>
> Cheers,
>   Thomas
>
> > On Jul 2, 2017, at 5:32 PM, Gianluca Tomasello <giagitom@...>
> wrote:
> >
> > Hi, I am trying to execute a script that sets valence bonding on sticks
> and then it gives me back a rendered image. There seems there is a
> difference when i try to run the script normally or in batch mode (pymol
> -cq script.py).  If i run it in batch mode, each atom with a double bond is
> rendered without the sphere in the atom center (only double bond is shown).
> >
> > Instead, if i try to execute the script in default mode the central atom
> sphere is correctly rendered.
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>