pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] PyMOL-users Digest, How to download and install (Pedro Lacerda)

[ahoneg <ann...@uz...>]

Hi Pedro

For Windows, you can get precompiled open source PyMOL from http://www.lfd.uci.edu/~gohlke/pythonlibs/.
____________________________________________________________

Dr. Annemarie Honegger
Dept. of Biochemistry
Zürich University
Winterthurerstrasse 190
8057 Zürich
Switzerland

e-mail:   hon...@bi...
phone:   +41 44 635 55 62
fax:        +41 44 635 57 12     



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>   1. How to download and install (Pedro Lacerda)
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> Message: 1
> Date: Wed, 14 Aug 2019 08:21:34 -0300
> From: Pedro Lacerda <psl...@gm...>
> To: pym...@li...
> Subject: [PyMOL] How to download and install
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> 
> Hi,
> 
> I'm unable to build or download and install PyMOL for Windows for free in
> our laboratory.
> 
> How can I find a valid license or a free build? Don't need all the features
> of the professional version, but would be very useful.
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[PyMOL] How to download and install

[Pedro L. <psl...@gm...>]

Hi,

I'm unable to build or download and install PyMOL for Windows for free in
our laboratory.

How can I find a valid license or a free build? Don't need all the features
of the professional version, but would be very useful.

[PyMOL] 3rd Call For Papers - 26th Annual Tcl/Tk Conference (Tcl'2019)

[<con...@tc...>]

Hello pymol-users, fyi ...

26th Annual Tcl/Tk Conference (Tcl'2019)
https://www.tcl-lang.org/community/tcl2019/

November 04 - 08, 2019
Crowne Plaza Houston River Oaks
2712 Southwest Freeway, 77098
Houston, Texas, USA

[ NEWS
  * Our keynote speaker is [Will Duquette](https://github.com/wduquette)
    talking about "Tcl, Rust, and the Death of Rube Goldberg"

  * [Submission is open](https://www.tcl-lang.org/community/tcl2019/cfp.html)

    It is 4 weeks to the deadline.

  * Registration is open. Please have a look at

    https://www.tcl-lang.org/community/tcl2019/register.html

  * The tutorials are known. See

    https://www.tcl-lang.org/community/tcl2019/tutorials.html
]

Important Dates:

Abstracts and proposals due   September 09, 2019
Notification to authors       September 16, 2019
WIP and BOF reservations open August 12, 2019     ** may change **
Registration opens            September 09, 2019     ** open already **
Author materials due          October 14, 2019
Tutorials Start               November 04, 2019
Conference starts             November 06, 2019

Email Contact:                tcl...@go...

Submission of Summaries

Tcl/Tk 2019 will be held in Houston, Texas, USA from November 04, 2019 to November 08, 2019.

The program committee is asking for papers and presentation proposals
from anyone using or developing with Tcl/Tk (and extensions). Past
conferences (Proceedings: https://www.tcl-lang.org/community/conferences.html)
have seen submissions covering a wide variety of topics including:

* Scientific and engineering applications
* Industrial controls
* Distributed applications and Network Managment
* Object oriented extensions to Tcl/Tk
* New widgets for Tk
* Simulation and application steering with Tcl/Tk
* Tcl/Tk-centric operating environments
* Tcl/Tk on small and embedded devices
* Medical applications and visualization
* Use of different programming paradigms in Tcl/Tk and proposals for new
  directions.
* New areas of exploration for the Tcl/Tk language

Submissions should consist of an abstract of about 100 words and a
summary of not more than two pages, and should be sent as plain text
to tcl...@go... no later than September 09, 2019. Authors of accepted
abstracts will have until October 14, 2019 to submit their final
paper for the inclusion in the conference proceedings. The proceedings
will be made available on digital media, so extra materials such as
presentation slides, code examples, code for extensions etc. are
encouraged.

Printed proceedings will be produced as an on-demand book at lulu.com
Online proceedings will appear via
	https://www.tcl-lang.org/community/conferences.html

The authors will have 30 minutes to present their paper at
the conference.

The program committee will review and evaluate papers according to the
following criteria:

* Quantity and quality of novel content
* Relevance and interest to the Tcl/Tk community
* Suitability of content for presentation at the conference

Proposals may report on commercial or non-commercial systems, but
those with only blatant marketing content will not be accepted.

Application and experience papers need to strike a balance between
background on the application domain and the relevance of Tcl/Tk to
the application. Application and experience papers should clearly
explain how the application or experience illustrates a novel use of
Tcl/Tk, and what lessons the Tcl/Tk community can derive from the
application or experience to apply to their own development efforts.

Papers accompanied by non-disclosure agreements will be returned to
the author(s) unread. All submissions are held in the highest
confidentiality prior to publication in the Proceedings, both as a
matter of policy and in accord with the U. S. Copyright Act of 1976.

The primary author for each accepted paper will receive registration
to the Technical Sessions portion of the conference at a reduced rate.

Other Forms of Participation

The program committee also welcomes proposals for panel discussions of
up to 90 minutes. Proposals should include a list of confirmed
panelists, a title and format, and a panel description with position
statements from each panelist. Panels should have no more than four
speakers, including the panel moderator, and should allow time for
substantial interaction with attendees. Panels are not presentations
of related research papers.

Slots for Works-in-Progress (WIP) presentations and Birds-of-a-Feather
sessions (BOFs) are available on a first-come, first-served basis
starting in August 12, 2019. Specific instructions for reserving WIP
and BOF time slots will be provided in the registration information
available in August 12, 2019. Some WIP and BOF time slots will be held open
for on-site reservation. All attendees with an interesting work in
progress should consider reserving a WIP slot.

Registration Information

More information on the conference is available the conference Web
site (https://www.tcl-lang.org/community/tcl2019/) and will be
published on various Tcl/Tk-related information channels.

To keep in touch with news regarding the conference, subscribe to the
tcl...@go... list. See:
https://groups.google.com/forum/#!forum/tclconference for list
information, archive, and subscription.

To keep in touch with Tcl events in general, subscribe to the
tcl-announce list. See: https://code.activestate.com/lists/tcl-announce
for list information, archive, and subscription.

Conference Committee

   * Andreas Kupries
   * Arjen Markus    Deltares
   * Brian Griffin   Mentor - A Siemens Business
   * Gerald Lester   KnG Consulting LLC
   * Joe Mistachkin  Mistachkin Systems
   * Ronald Fox      CAEN Technologies
                     NSCL @ Michigan State University

Contact Information     tcl...@go...

Tcl'2019 would like to thank those who are sponsoring the conference:

   * FlightAware
   * Mentor - A Siemens Business
   * Noumena Corp

Re: [PyMOL] Label volume

[Pedro L. <psl...@gm...>]

And how to place a single arbitrary label on the object or segment?

Em seg, 12 de ago de 2019 às 13:55, Pedro Lacerda <psl...@gm...>
escreveu:

> Hi PyMOL list,
>
> Is possible toshow  a label independent of the associated object be
> enabled?
>
> Or is possible to label a volume or map?
> --
> Pedro Sousa Lacerda
>
>
> *Laboratório de Bioinformática e Modelagem Molecular*
> *Faculdade de Farmácia / UFBA*
>
> *@pslacerda*
>
> *+55 71 9 9981-1856*
>


-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*

[PyMOL] Label volume

[Pedro L. <psl...@gm...>]

Hi PyMOL list,

Is possible toshow  a label independent of the associated object be
enabled?

Or is possible to label a volume or map?
-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*

Re: [PyMOL] count_atoms and states

[Christian \Cole\ F. <chr...@sc...>]

Thanks for the info. I also didn't realize that states started at 1. Maybe
the nonexistent state warning is something that should be implemented
elsewhere as well.

As for the implicit *or*, you can find it in
https://pymolwiki.org/index.php/Selection_Algebra#Selection_Operator/Modifier_Table
under the *Logical* section. I agree that it can be easy to miss—good thing
you caught this behavior in your code.

Have a great day,
Cole

On Fri, Aug 9, 2019 at 6:34 PM Pedro Lacerda <psl...@gm...> wrote:

> So missing boolean operators are filled with OR, for me this is should be
> a big and loud WARNING. I almost messed everything up because it almost
> passed in my tests.
>
> Also I mistake states a couple of days on multi-model files because I was
> counting from ZERO but states starts on ONE. That was until I needed
> get_area, it properly stated that my states were nonexistant.
>
> So these were my personal thoughts and issues about.
>
> Have a nice weekend!
>
> Em sex, 9 de ago de 2019 12:41, Pedro Lacerda <psl...@gm...>
> escreveu:
>
>> Question answered.
>>
>> Best regards!
>>
>> Em sex, 9 de ago de 2019 às 12:33, Christian "Cole" French <
>> chr...@sc...> escreveu:
>>
>>> Hi Pedro,
>>>
>>> *count_states* is correct here; there's only 1 state, which is state 1.
>>> The reason for the observed *count_atoms* behavior is that "polymer"
>>> and "state" are different operators in the selection algebra, so putting
>>> them together without a logical operator such as "and" or "or" between them
>>> indicates an implicit "or". So you're actually counting atoms which match
>>> "polymer" *or* "state X", which is why the number only goes up to 8627
>>> when you count state 1.
>>>
>>> This might clear up your scope question as well, but please indicate if
>>> otherwise.
>>>
>>> Best,
>>> Cole
>>>
>>> On Fri, Aug 9, 2019 at 10:55 AM Pedro Lacerda <psl...@gm...>
>>> wrote:
>>>
>>>> I'm also puzzled by the scope of state:
>>>>
>>>> *PyMOL>count_atoms polymer state 1 within 5 of resn NAP*
>>>>>  count_atoms: 8205 atoms
>>>>>
>>>>> *PyMOL>count_atoms polymer state 1 within 0 of resn NAP*
>>>>>  count_atoms: 8109 atoms
>>>>>
>>>>> *PyMOL>count_atoms polymer (state 1) within 0 of resn NAP*
>>>>>  count_atoms: 8109 atoms
>>>>>
>>>>> *PyMOL>count_atoms (polymer (state 1)) within 0 of resn NAP*
>>>>>  count_atoms: 192 atoms
>>>>>
>>>>> *PyMOL>count_atoms (polymer (state 0)) within 0 of resn NAP*
>>>>>  count_atoms: 0 atoms
>>>>>
>>>>
>>>> Em sex, 9 de ago de 2019 às 11:31, Pedro Lacerda <psl...@gm...>
>>>> escreveu:
>>>>
>>>>> Hi,
>>>>>
>>>>> There is only one state but the atom counting changes between states
>>>>> 0, 1 and 2.
>>>>>
>>>>>
>>>>> What this means?
>>>>>
>>>>> *PyMOL>fetch 1e92*
>>>>>>
>>>>>> TITLE     Pteridine reductase 1 from Leishmania major complexed with NADP+ and dihydrobiopterin
>>>>>>  ExecutiveLoad-Detail: Detected mmCIF
>>>>>>  CmdLoad: loaded as "1e92".
>>>>>>
>>>>>> *PyMOL>count_atoms polymer state 0*
>>>>>>  count_atoms: 7917 atoms
>>>>>>
>>>>>> *PyMOL>count_atoms polymer state 1*
>>>>>>  count_atoms: 8627 atoms
>>>>>>
>>>>> *PyMOL>count_atoms polymer state 2*
>>>>>>  count_atoms: 7917 atoms
>>>>>>
>>>>> *PyMOL>count_states *
>>>>>>  cmd.count_states: 1 states.
>>>>>>
>>>>>
>>>>> --
>>>>> Pedro Sousa Lacerda
>>>>>
>>>>>
>>>>> *Laboratório de Bioinformática e Modelagem Molecular*
>>>>> *Faculdade de Farmácia / UFBA*
>>>>>
>>>>> *@pslacerda*
>>>>>
>>>>> *+55 71 9 9981-1856*
>>>>>
>>>>
>>>>
>>>> --
>>>> Pedro Sousa Lacerda
>>>>
>>>>
>>>> *Laboratório de Bioinformática e Modelagem Molecular*
>>>> *Faculdade de Farmácia / UFBA*
>>>>
>>>> *@pslacerda*
>>>>
>>>> *+55 71 9 9981-1856*
>>>> _______________________________________________
>>>> PyMOL-users mailing list
>>>> Archives: http://www.mail-archive.com/pym...@li...
>>>> Unsubscribe:
>>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>>
>>>
>>
>> --
>> Pedro Sousa Lacerda
>>
>>
>> *Laboratório de Bioinformática e Modelagem Molecular*
>> *Faculdade de Farmácia / UFBA*
>>
>> *@pslacerda*
>>
>> *+55 71 9 9981-1856*
>>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] count_atoms and states

[Pedro L. <psl...@gm...>]

So missing boolean operators are filled with OR, for me this is should be a
big and loud WARNING. I almost messed everything up because it almost
passed in my tests.

Also I mistake states a couple of days on multi-model files because I was
counting from ZERO but states starts on ONE. That was until I needed
get_area, it properly stated that my states were nonexistant.

So these were my personal thoughts and issues about.

Have a nice weekend!

Em sex, 9 de ago de 2019 12:41, Pedro Lacerda <psl...@gm...>
escreveu:

> Question answered.
>
> Best regards!
>
> Em sex, 9 de ago de 2019 às 12:33, Christian "Cole" French <
> chr...@sc...> escreveu:
>
>> Hi Pedro,
>>
>> *count_states* is correct here; there's only 1 state, which is state 1.
>> The reason for the observed *count_atoms* behavior is that "polymer" and
>> "state" are different operators in the selection algebra, so putting them
>> together without a logical operator such as "and" or "or" between them
>> indicates an implicit "or". So you're actually counting atoms which match
>> "polymer" *or* "state X", which is why the number only goes up to 8627
>> when you count state 1.
>>
>> This might clear up your scope question as well, but please indicate if
>> otherwise.
>>
>> Best,
>> Cole
>>
>> On Fri, Aug 9, 2019 at 10:55 AM Pedro Lacerda <psl...@gm...>
>> wrote:
>>
>>> I'm also puzzled by the scope of state:
>>>
>>> *PyMOL>count_atoms polymer state 1 within 5 of resn NAP*
>>>>  count_atoms: 8205 atoms
>>>>
>>>> *PyMOL>count_atoms polymer state 1 within 0 of resn NAP*
>>>>  count_atoms: 8109 atoms
>>>>
>>>> *PyMOL>count_atoms polymer (state 1) within 0 of resn NAP*
>>>>  count_atoms: 8109 atoms
>>>>
>>>> *PyMOL>count_atoms (polymer (state 1)) within 0 of resn NAP*
>>>>  count_atoms: 192 atoms
>>>>
>>>> *PyMOL>count_atoms (polymer (state 0)) within 0 of resn NAP*
>>>>  count_atoms: 0 atoms
>>>>
>>>
>>> Em sex, 9 de ago de 2019 às 11:31, Pedro Lacerda <psl...@gm...>
>>> escreveu:
>>>
>>>> Hi,
>>>>
>>>> There is only one state but the atom counting changes between states 0,
>>>> 1 and 2.
>>>>
>>>>
>>>> What this means?
>>>>
>>>> *PyMOL>fetch 1e92*
>>>>>
>>>>> TITLE     Pteridine reductase 1 from Leishmania major complexed with NADP+ and dihydrobiopterin
>>>>>  ExecutiveLoad-Detail: Detected mmCIF
>>>>>  CmdLoad: loaded as "1e92".
>>>>>
>>>>> *PyMOL>count_atoms polymer state 0*
>>>>>  count_atoms: 7917 atoms
>>>>>
>>>>> *PyMOL>count_atoms polymer state 1*
>>>>>  count_atoms: 8627 atoms
>>>>>
>>>> *PyMOL>count_atoms polymer state 2*
>>>>>  count_atoms: 7917 atoms
>>>>>
>>>> *PyMOL>count_states *
>>>>>  cmd.count_states: 1 states.
>>>>>
>>>>
>>>> --
>>>> Pedro Sousa Lacerda
>>>>
>>>>
>>>> *Laboratório de Bioinformática e Modelagem Molecular*
>>>> *Faculdade de Farmácia / UFBA*
>>>>
>>>> *@pslacerda*
>>>>
>>>> *+55 71 9 9981-1856*
>>>>
>>>
>>>
>>> --
>>> Pedro Sousa Lacerda
>>>
>>>
>>> *Laboratório de Bioinformática e Modelagem Molecular*
>>> *Faculdade de Farmácia / UFBA*
>>>
>>> *@pslacerda*
>>>
>>> *+55 71 9 9981-1856*
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> Archives: http://www.mail-archive.com/pym...@li...
>>> Unsubscribe:
>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
>>
>
> --
> Pedro Sousa Lacerda
>
>
> *Laboratório de Bioinformática e Modelagem Molecular*
> *Faculdade de Farmácia / UFBA*
>
> *@pslacerda*
>
> *+55 71 9 9981-1856*
>

Re: [PyMOL] count_atoms and states

[Christian \Cole\ F. <chr...@sc...>]

Hi Pedro,

*count_states* is correct here; there's only 1 state, which is state 1. The
reason for the observed *count_atoms* behavior is that "polymer" and
"state" are different operators in the selection algebra, so putting them
together without a logical operator such as "and" or "or" between them
indicates an implicit "or". So you're actually counting atoms which match
"polymer" *or* "state X", which is why the number only goes up to 8627 when
you count state 1.

This might clear up your scope question as well, but please indicate if
otherwise.

Best,
Cole

On Fri, Aug 9, 2019 at 10:55 AM Pedro Lacerda <psl...@gm...> wrote:

> I'm also puzzled by the scope of state:
>
> *PyMOL>count_atoms polymer state 1 within 5 of resn NAP*
>>  count_atoms: 8205 atoms
>>
>> *PyMOL>count_atoms polymer state 1 within 0 of resn NAP*
>>  count_atoms: 8109 atoms
>>
>> *PyMOL>count_atoms polymer (state 1) within 0 of resn NAP*
>>  count_atoms: 8109 atoms
>>
>> *PyMOL>count_atoms (polymer (state 1)) within 0 of resn NAP*
>>  count_atoms: 192 atoms
>>
>> *PyMOL>count_atoms (polymer (state 0)) within 0 of resn NAP*
>>  count_atoms: 0 atoms
>>
>
> Em sex, 9 de ago de 2019 às 11:31, Pedro Lacerda <psl...@gm...>
> escreveu:
>
>> Hi,
>>
>> There is only one state but the atom counting changes between states 0, 1
>> and 2.
>>
>>
>> What this means?
>>
>> *PyMOL>fetch 1e92*
>>>
>>> TITLE     Pteridine reductase 1 from Leishmania major complexed with NADP+ and dihydrobiopterin
>>>  ExecutiveLoad-Detail: Detected mmCIF
>>>  CmdLoad: loaded as "1e92".
>>>
>>> *PyMOL>count_atoms polymer state 0*
>>>  count_atoms: 7917 atoms
>>>
>>> *PyMOL>count_atoms polymer state 1*
>>>  count_atoms: 8627 atoms
>>>
>> *PyMOL>count_atoms polymer state 2*
>>>  count_atoms: 7917 atoms
>>>
>> *PyMOL>count_states *
>>>  cmd.count_states: 1 states.
>>>
>>
>> --
>> Pedro Sousa Lacerda
>>
>>
>> *Laboratório de Bioinformática e Modelagem Molecular*
>> *Faculdade de Farmácia / UFBA*
>>
>> *@pslacerda*
>>
>> *+55 71 9 9981-1856*
>>
>
>
> --
> Pedro Sousa Lacerda
>
>
> *Laboratório de Bioinformática e Modelagem Molecular*
> *Faculdade de Farmácia / UFBA*
>
> *@pslacerda*
>
> *+55 71 9 9981-1856*
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] count_atoms and states

[Pedro L. <psl...@gm...>]

Question answered.

Best regards!

Em sex, 9 de ago de 2019 às 12:33, Christian "Cole" French <
chr...@sc...> escreveu:

> Hi Pedro,
>
> *count_states* is correct here; there's only 1 state, which is state 1.
> The reason for the observed *count_atoms* behavior is that "polymer" and
> "state" are different operators in the selection algebra, so putting them
> together without a logical operator such as "and" or "or" between them
> indicates an implicit "or". So you're actually counting atoms which match
> "polymer" *or* "state X", which is why the number only goes up to 8627
> when you count state 1.
>
> This might clear up your scope question as well, but please indicate if
> otherwise.
>
> Best,
> Cole
>
> On Fri, Aug 9, 2019 at 10:55 AM Pedro Lacerda <psl...@gm...> wrote:
>
>> I'm also puzzled by the scope of state:
>>
>> *PyMOL>count_atoms polymer state 1 within 5 of resn NAP*
>>>  count_atoms: 8205 atoms
>>>
>>> *PyMOL>count_atoms polymer state 1 within 0 of resn NAP*
>>>  count_atoms: 8109 atoms
>>>
>>> *PyMOL>count_atoms polymer (state 1) within 0 of resn NAP*
>>>  count_atoms: 8109 atoms
>>>
>>> *PyMOL>count_atoms (polymer (state 1)) within 0 of resn NAP*
>>>  count_atoms: 192 atoms
>>>
>>> *PyMOL>count_atoms (polymer (state 0)) within 0 of resn NAP*
>>>  count_atoms: 0 atoms
>>>
>>
>> Em sex, 9 de ago de 2019 às 11:31, Pedro Lacerda <psl...@gm...>
>> escreveu:
>>
>>> Hi,
>>>
>>> There is only one state but the atom counting changes between states 0,
>>> 1 and 2.
>>>
>>>
>>> What this means?
>>>
>>> *PyMOL>fetch 1e92*
>>>>
>>>> TITLE     Pteridine reductase 1 from Leishmania major complexed with NADP+ and dihydrobiopterin
>>>>  ExecutiveLoad-Detail: Detected mmCIF
>>>>  CmdLoad: loaded as "1e92".
>>>>
>>>> *PyMOL>count_atoms polymer state 0*
>>>>  count_atoms: 7917 atoms
>>>>
>>>> *PyMOL>count_atoms polymer state 1*
>>>>  count_atoms: 8627 atoms
>>>>
>>> *PyMOL>count_atoms polymer state 2*
>>>>  count_atoms: 7917 atoms
>>>>
>>> *PyMOL>count_states *
>>>>  cmd.count_states: 1 states.
>>>>
>>>
>>> --
>>> Pedro Sousa Lacerda
>>>
>>>
>>> *Laboratório de Bioinformática e Modelagem Molecular*
>>> *Faculdade de Farmácia / UFBA*
>>>
>>> *@pslacerda*
>>>
>>> *+55 71 9 9981-1856*
>>>
>>
>>
>> --
>> Pedro Sousa Lacerda
>>
>>
>> *Laboratório de Bioinformática e Modelagem Molecular*
>> *Faculdade de Farmácia / UFBA*
>>
>> *@pslacerda*
>>
>> *+55 71 9 9981-1856*
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>

-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*

Re: [PyMOL] count_atoms and states

[Pedro L. <psl...@gm...>]

I'm also puzzled by the scope of state:

*PyMOL>count_atoms polymer state 1 within 5 of resn NAP*
>  count_atoms: 8205 atoms
>
> *PyMOL>count_atoms polymer state 1 within 0 of resn NAP*
>  count_atoms: 8109 atoms
>
> *PyMOL>count_atoms polymer (state 1) within 0 of resn NAP*
>  count_atoms: 8109 atoms
>
> *PyMOL>count_atoms (polymer (state 1)) within 0 of resn NAP*
>  count_atoms: 192 atoms
>
> *PyMOL>count_atoms (polymer (state 0)) within 0 of resn NAP*
>  count_atoms: 0 atoms
>

Em sex, 9 de ago de 2019 às 11:31, Pedro Lacerda <psl...@gm...>
escreveu:

> Hi,
>
> There is only one state but the atom counting changes between states 0, 1
> and 2.
>
>
> What this means?
>
> *PyMOL>fetch 1e92*
>>
>> TITLE     Pteridine reductase 1 from Leishmania major complexed with NADP+ and dihydrobiopterin
>>  ExecutiveLoad-Detail: Detected mmCIF
>>  CmdLoad: loaded as "1e92".
>>
>> *PyMOL>count_atoms polymer state 0*
>>  count_atoms: 7917 atoms
>>
>> *PyMOL>count_atoms polymer state 1*
>>  count_atoms: 8627 atoms
>>
> *PyMOL>count_atoms polymer state 2*
>>  count_atoms: 7917 atoms
>>
> *PyMOL>count_states *
>>  cmd.count_states: 1 states.
>>
>
> --
> Pedro Sousa Lacerda
>
>
> *Laboratório de Bioinformática e Modelagem Molecular*
> *Faculdade de Farmácia / UFBA*
>
> *@pslacerda*
>
> *+55 71 9 9981-1856*
>


-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*

[PyMOL] count_atoms and states

[Pedro L. <psl...@gm...>]

Hi,

There is only one state but the atom counting changes between states 0, 1
and 2.


What this means?

*PyMOL>fetch 1e92*
>
> TITLE     Pteridine reductase 1 from Leishmania major complexed with NADP+ and dihydrobiopterin
>  ExecutiveLoad-Detail: Detected mmCIF
>  CmdLoad: loaded as "1e92".
>
> *PyMOL>count_atoms polymer state 0*
>  count_atoms: 7917 atoms
>
> *PyMOL>count_atoms polymer state 1*
>  count_atoms: 8627 atoms
>
*PyMOL>count_atoms polymer state 2*
>  count_atoms: 7917 atoms
>
*PyMOL>count_states *
>  cmd.count_states: 1 states.
>

-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*

[PyMOL] Cavity detection radius and cavity detection cutoff

[Hyun <bio...@gm...>]

Hi,

I have some questions about how to detect the cavity in Pymol

1. Could you explain what cavity detection radius and cavity detection
cutoff mean?
2. How can I determine the optimal values for cavity detection radius and
cavity detection cutoff?

Thanks


Hyun

[PyMOL] APBS "%x format: an integer is required, not float" error in pymol installed with python 3.7 and "Qt not available, using GLUT/Tk interface" error

[sunyeping <sun...@al...>]

Dear everyone,

I am trying to use the APBS plugin in pymol to calculate protein electrostatic potentials. My system is centos 7. The pymol was installed with python 3.7 (~/software/build/anaconda3/bin/python). When I try to lauch the APBS Tool 2.1 from the plugin menu of pymol, a window jumps out which reads: "%x format: an integer is required, not float". I've googled it and learned that this error may related to python version. So I try to swith to pymol installed with python2.7 (/usr/bin/python)
 I install pymol following the guide at https://pymolwiki.org/index.php/Linux_Install, with the command:

 /usr/bin/python setup.py  install --prefix=~/software/pymol/pymol-python2.7-install

After the installation finished, I tried to lauch pymol, but meet the error:

Qt not available, using GLUT/Tk interface
Traceback (most recent call last):
  File "/home/sunyp/software/pymol/pymol-python2.7-install/lib64/python2.7/site-packages/pymol/__init__.py", line 65, in <module>
    pymol.launch(args)
  File "/home/sunyp/software/pymol/pymol-python2.7-install/lib64/python2.7/site-packages/pymol/__init__.py", line 436, in launch
    _cmd.runpymol(_cmd._get_global_C_object(), block_input_hook)
NotImplementedError: compile with --glut

Acturally the PyQt4 have been install in my system, I don't understand why it is not available by pymol. And why pymol installed with python3.7 doesn't have such a problem.  Even if I reinstall pymol with --glut option:

 /usr/bin/python setup.py  --glut build install --prefix=~/software/pymol/pymol-python2.7-install

the same error still comes out. Could you help me with this problem? Thank you in advance.
Best regards

Re: [PyMOL] Selection algebra

[Pedro L. <psl...@gm...>]

Thank you, it was really what I asked!



Em seg, 5 de ago de 2019 15:50, Christian "Cole" French <
chr...@sc...> escreveu:

> select_with_filter allows you to make a selection as you would with the
> select command, so it supports all selection algebra including byres,
> chain, organic, etc. Here's a modified example from the wiki:
>
> # Select all residues within 5 Ang. of any organic small molecules whose
> x-coordinate is at least 50
> select_with_filter sele, br. all within 5 of (organic and flag 8), lambda
> s: cmd.get_extent(s)[0][0] >= 50
>
> Best,
> Cole
>
> On Mon, Aug 5, 2019 at 1:06 PM Pedro Lacerda <psl...@gm...> wrote:
>
>> Yes, one more question.
>>
>> How to use all other "functions", like byres, "chain A" or "organic"?
>>
>> Em seg, 5 de ago de 2019 12:36, Christian "Cole" French <
>> chr...@sc...> escreveu:
>>
>>> I see now. I updated the code at the link in my previous email to
>>> provide behavior which should allow you to do what you want. Here are your
>>> examples written using the command:
>>>
>>> select_with_filter sele, flag 8, lambda s: len(cmd.get_chains(s)) < 2
>>> select_with_filter sele, flag 8, lambda s: cmd.get_fastastr(s) < 2
>>> select_with_filter sele, flag 8 and chain A, lambda s: peplength(s) < 15
>>>
>>> If you want to write and use your own multi-line function, you can write
>>> a script and cmd.extend('your_function', your_function), then use
>>> your_function in select_with_filter.
>>>
>>> Please let me know if you have any further questions.
>>>
>>> Best,
>>> Cole
>>>
>>> On Mon, Aug 5, 2019 at 8:30 AM Pedro Lacerda <psl...@gm...>
>>> wrote:
>>>
>>>> I expressed myself wrong, I'm looking something like:
>>>>
>>>>    select peplength < 15 and chain A
>>>>
>>>> Where peplength is an user defined function like:
>>>>
>>>> def peplength(atom):
>>>>     return compute_peplength(atom)
>>>>
>>>> I'm looking for the availability of user defined functions on selection
>>>> expressions. How to?
>>>>
>>>> Em sex, 2 de ago de 2019 às 15:44, Christian "Cole" French <
>>>> chr...@sc...> escreveu:
>>>>
>>>>> Edit: remove the cmd. part when running select_with_filter. (Since
>>>>> it's a custom command, it doesn't belong to the cmd module.)
>>>>>
>>>>> On Fri, Aug 2, 2019 at 2:41 PM Christian "Cole" French <
>>>>> chr...@sc...> wrote:
>>>>>
>>>>>> Hi Pedro Lacerda,
>>>>>>
>>>>>> Here is a link to a script I wrote which adds a command which does
>>>>>> what you ask:
>>>>>> https://gist.github.com/ColeFrench/6f68fa5f04a67bb6234f10c25debb865.
>>>>>> To use it, download the file to the directory where you run PyMOL from,
>>>>>> then open PyMOL and run run select_with_filter.py.
>>>>>>
>>>>>> For your examples, the commands would be cmd.select_with_filter(predicate=lambda
>>>>>> s: len(cmd.get_chains(s)) < 2) and cmd.select_with_filter(predicate=lambda
>>>>>> s: cmd.get_fastastr(s) < 2).
>>>>>>
>>>>>> Commands which can be simply run are a convenience which allows you
>>>>>> to type less (e.g., select chain A instead of cmd.select('chain A')).
>>>>>> Some commands require different arguments and can only be run the longer
>>>>>> way, such as the one I wrote which takes a function as an argument.
>>>>>>
>>>>>> Hope this helps,
>>>>>> Cole
>>>>>>
>>>>>> On Fri, Aug 2, 2019 at 11:45 AM Pedro Lacerda <psl...@gm...>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi PyMOL users,
>>>>>>>
>>>>>>> It there any way to enhance the selecion algebra with functions? For
>>>>>>> instance:
>>>>>>>
>>>>>>> select len(get_chains(*)) < 2
>>>>>>>>
>>>>>>>
>>>>>>> Or even:
>>>>>>>
>>>>>>> select cmd.get_fastastr(*) < 2
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> By the way, why some commands we can simply run (like get_chains)
>>>>>>> and others are different (like cmd.get_fastastr())?
>>>>>>>
>>>>>>> --
>>>>>>> Pedro Sousa Lacerda
>>>>>>>
>>>>>>>
>>>>>>> *Laboratório de Bioinformática e Modelagem Molecular*
>>>>>>> *Faculdade de Farmácia / UFBA*
>>>>>>>
>>>>>>> *@pslacerda*
>>>>>>>
>>>>>>> *+55 71 9 9981-1856*
>>>>>>> _______________________________________________
>>>>>>> PyMOL-users mailing list
>>>>>>> Archives:
>>>>>>> http://www.mail-archive.com/pym...@li...
>>>>>>> Unsubscribe:
>>>>>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>>>>>
>>>>>>
>>>>
>>>> --
>>>> Pedro Sousa Lacerda
>>>>
>>>>
>>>> *Laboratório de Bioinformática e Modelagem Molecular*
>>>> *Faculdade de Farmácia / UFBA*
>>>>
>>>> *@pslacerda*
>>>>
>>>> *+55 71 9 9981-1856*
>>>>
>>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>

Re: [PyMOL] Selection algebra

[Christian \Cole\ F. <chr...@sc...>]

select_with_filter allows you to make a selection as you would with the
select command, so it supports all selection algebra including byres,
chain, organic, etc. Here's a modified example from the wiki:

# Select all residues within 5 Ang. of any organic small molecules whose
x-coordinate is at least 50
select_with_filter sele, br. all within 5 of (organic and flag 8), lambda
s: cmd.get_extent(s)[0][0] >= 50

Best,
Cole

On Mon, Aug 5, 2019 at 1:06 PM Pedro Lacerda <psl...@gm...> wrote:

> Yes, one more question.
>
> How to use all other "functions", like byres, "chain A" or "organic"?
>
> Em seg, 5 de ago de 2019 12:36, Christian "Cole" French <
> chr...@sc...> escreveu:
>
>> I see now. I updated the code at the link in my previous email to provide
>> behavior which should allow you to do what you want. Here are your examples
>> written using the command:
>>
>> select_with_filter sele, flag 8, lambda s: len(cmd.get_chains(s)) < 2
>> select_with_filter sele, flag 8, lambda s: cmd.get_fastastr(s) < 2
>> select_with_filter sele, flag 8 and chain A, lambda s: peplength(s) < 15
>>
>> If you want to write and use your own multi-line function, you can write
>> a script and cmd.extend('your_function', your_function), then use
>> your_function in select_with_filter.
>>
>> Please let me know if you have any further questions.
>>
>> Best,
>> Cole
>>
>> On Mon, Aug 5, 2019 at 8:30 AM Pedro Lacerda <psl...@gm...> wrote:
>>
>>> I expressed myself wrong, I'm looking something like:
>>>
>>>    select peplength < 15 and chain A
>>>
>>> Where peplength is an user defined function like:
>>>
>>> def peplength(atom):
>>>     return compute_peplength(atom)
>>>
>>> I'm looking for the availability of user defined functions on selection
>>> expressions. How to?
>>>
>>> Em sex, 2 de ago de 2019 às 15:44, Christian "Cole" French <
>>> chr...@sc...> escreveu:
>>>
>>>> Edit: remove the cmd. part when running select_with_filter. (Since
>>>> it's a custom command, it doesn't belong to the cmd module.)
>>>>
>>>> On Fri, Aug 2, 2019 at 2:41 PM Christian "Cole" French <
>>>> chr...@sc...> wrote:
>>>>
>>>>> Hi Pedro Lacerda,
>>>>>
>>>>> Here is a link to a script I wrote which adds a command which does
>>>>> what you ask:
>>>>> https://gist.github.com/ColeFrench/6f68fa5f04a67bb6234f10c25debb865.
>>>>> To use it, download the file to the directory where you run PyMOL from,
>>>>> then open PyMOL and run run select_with_filter.py.
>>>>>
>>>>> For your examples, the commands would be cmd.select_with_filter(predicate=lambda
>>>>> s: len(cmd.get_chains(s)) < 2) and cmd.select_with_filter(predicate=lambda
>>>>> s: cmd.get_fastastr(s) < 2).
>>>>>
>>>>> Commands which can be simply run are a convenience which allows you to
>>>>> type less (e.g., select chain A instead of cmd.select('chain A')).
>>>>> Some commands require different arguments and can only be run the longer
>>>>> way, such as the one I wrote which takes a function as an argument.
>>>>>
>>>>> Hope this helps,
>>>>> Cole
>>>>>
>>>>> On Fri, Aug 2, 2019 at 11:45 AM Pedro Lacerda <psl...@gm...>
>>>>> wrote:
>>>>>
>>>>>> Hi PyMOL users,
>>>>>>
>>>>>> It there any way to enhance the selecion algebra with functions? For
>>>>>> instance:
>>>>>>
>>>>>> select len(get_chains(*)) < 2
>>>>>>>
>>>>>>
>>>>>> Or even:
>>>>>>
>>>>>> select cmd.get_fastastr(*) < 2
>>>>>>>
>>>>>>
>>>>>>
>>>>>> By the way, why some commands we can simply run (like get_chains) and
>>>>>> others are different (like cmd.get_fastastr())?
>>>>>>
>>>>>> --
>>>>>> Pedro Sousa Lacerda
>>>>>>
>>>>>>
>>>>>> *Laboratório de Bioinformática e Modelagem Molecular*
>>>>>> *Faculdade de Farmácia / UFBA*
>>>>>>
>>>>>> *@pslacerda*
>>>>>>
>>>>>> *+55 71 9 9981-1856*
>>>>>> _______________________________________________
>>>>>> PyMOL-users mailing list
>>>>>> Archives:
>>>>>> http://www.mail-archive.com/pym...@li...
>>>>>> Unsubscribe:
>>>>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>>>>
>>>>>
>>>
>>> --
>>> Pedro Sousa Lacerda
>>>
>>>
>>> *Laboratório de Bioinformática e Modelagem Molecular*
>>> *Faculdade de Farmácia / UFBA*
>>>
>>> *@pslacerda*
>>>
>>> *+55 71 9 9981-1856*
>>>
>> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Selection algebra

[Pedro L. <psl...@gm...>]

Yes, one more question.

How to use all other "functions", like byres, "chain A" or "organic"?

Em seg, 5 de ago de 2019 12:36, Christian "Cole" French <
chr...@sc...> escreveu:

> I see now. I updated the code at the link in my previous email to provide
> behavior which should allow you to do what you want. Here are your examples
> written using the command:
>
> select_with_filter sele, flag 8, lambda s: len(cmd.get_chains(s)) < 2
> select_with_filter sele, flag 8, lambda s: cmd.get_fastastr(s) < 2
> select_with_filter sele, flag 8 and chain A, lambda s: peplength(s) < 15
>
> If you want to write and use your own multi-line function, you can write a
> script and cmd.extend('your_function', your_function), then use
> your_function in select_with_filter.
>
> Please let me know if you have any further questions.
>
> Best,
> Cole
>
> On Mon, Aug 5, 2019 at 8:30 AM Pedro Lacerda <psl...@gm...> wrote:
>
>> I expressed myself wrong, I'm looking something like:
>>
>>    select peplength < 15 and chain A
>>
>> Where peplength is an user defined function like:
>>
>> def peplength(atom):
>>     return compute_peplength(atom)
>>
>> I'm looking for the availability of user defined functions on selection
>> expressions. How to?
>>
>> Em sex, 2 de ago de 2019 às 15:44, Christian "Cole" French <
>> chr...@sc...> escreveu:
>>
>>> Edit: remove the cmd. part when running select_with_filter. (Since it's
>>> a custom command, it doesn't belong to the cmd module.)
>>>
>>> On Fri, Aug 2, 2019 at 2:41 PM Christian "Cole" French <
>>> chr...@sc...> wrote:
>>>
>>>> Hi Pedro Lacerda,
>>>>
>>>> Here is a link to a script I wrote which adds a command which does what
>>>> you ask:
>>>> https://gist.github.com/ColeFrench/6f68fa5f04a67bb6234f10c25debb865.
>>>> To use it, download the file to the directory where you run PyMOL from,
>>>> then open PyMOL and run run select_with_filter.py.
>>>>
>>>> For your examples, the commands would be cmd.select_with_filter(predicate=lambda
>>>> s: len(cmd.get_chains(s)) < 2) and cmd.select_with_filter(predicate=lambda
>>>> s: cmd.get_fastastr(s) < 2).
>>>>
>>>> Commands which can be simply run are a convenience which allows you to
>>>> type less (e.g., select chain A instead of cmd.select('chain A')).
>>>> Some commands require different arguments and can only be run the longer
>>>> way, such as the one I wrote which takes a function as an argument.
>>>>
>>>> Hope this helps,
>>>> Cole
>>>>
>>>> On Fri, Aug 2, 2019 at 11:45 AM Pedro Lacerda <psl...@gm...>
>>>> wrote:
>>>>
>>>>> Hi PyMOL users,
>>>>>
>>>>> It there any way to enhance the selecion algebra with functions? For
>>>>> instance:
>>>>>
>>>>> select len(get_chains(*)) < 2
>>>>>>
>>>>>
>>>>> Or even:
>>>>>
>>>>> select cmd.get_fastastr(*) < 2
>>>>>>
>>>>>
>>>>>
>>>>> By the way, why some commands we can simply run (like get_chains) and
>>>>> others are different (like cmd.get_fastastr())?
>>>>>
>>>>> --
>>>>> Pedro Sousa Lacerda
>>>>>
>>>>>
>>>>> *Laboratório de Bioinformática e Modelagem Molecular*
>>>>> *Faculdade de Farmácia / UFBA*
>>>>>
>>>>> *@pslacerda*
>>>>>
>>>>> *+55 71 9 9981-1856*
>>>>> _______________________________________________
>>>>> PyMOL-users mailing list
>>>>> Archives:
>>>>> http://www.mail-archive.com/pym...@li...
>>>>> Unsubscribe:
>>>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>>>
>>>>
>>
>> --
>> Pedro Sousa Lacerda
>>
>>
>> *Laboratório de Bioinformática e Modelagem Molecular*
>> *Faculdade de Farmácia / UFBA*
>>
>> *@pslacerda*
>>
>> *+55 71 9 9981-1856*
>>
>

Re: [PyMOL] Selection algebra

[Christian \Cole\ F. <chr...@sc...>]

I see now. I updated the code at the link in my previous email to provide
behavior which should allow you to do what you want. Here are your examples
written using the command:

select_with_filter sele, flag 8, lambda s: len(cmd.get_chains(s)) < 2
select_with_filter sele, flag 8, lambda s: cmd.get_fastastr(s) < 2
select_with_filter sele, flag 8 and chain A, lambda s: peplength(s) < 15

If you want to write and use your own multi-line function, you can write a
script and cmd.extend('your_function', your_function), then use
your_function in select_with_filter.

Please let me know if you have any further questions.

Best,
Cole

On Mon, Aug 5, 2019 at 8:30 AM Pedro Lacerda <psl...@gm...> wrote:

> I expressed myself wrong, I'm looking something like:
>
>    select peplength < 15 and chain A
>
> Where peplength is an user defined function like:
>
> def peplength(atom):
>     return compute_peplength(atom)
>
> I'm looking for the availability of user defined functions on selection
> expressions. How to?
>
> Em sex, 2 de ago de 2019 às 15:44, Christian "Cole" French <
> chr...@sc...> escreveu:
>
>> Edit: remove the cmd. part when running select_with_filter. (Since it's
>> a custom command, it doesn't belong to the cmd module.)
>>
>> On Fri, Aug 2, 2019 at 2:41 PM Christian "Cole" French <
>> chr...@sc...> wrote:
>>
>>> Hi Pedro Lacerda,
>>>
>>> Here is a link to a script I wrote which adds a command which does what
>>> you ask:
>>> https://gist.github.com/ColeFrench/6f68fa5f04a67bb6234f10c25debb865. To
>>> use it, download the file to the directory where you run PyMOL from, then
>>> open PyMOL and run run select_with_filter.py.
>>>
>>> For your examples, the commands would be cmd.select_with_filter(predicate=lambda
>>> s: len(cmd.get_chains(s)) < 2) and cmd.select_with_filter(predicate=lambda
>>> s: cmd.get_fastastr(s) < 2).
>>>
>>> Commands which can be simply run are a convenience which allows you to
>>> type less (e.g., select chain A instead of cmd.select('chain A')). Some
>>> commands require different arguments and can only be run the longer way,
>>> such as the one I wrote which takes a function as an argument.
>>>
>>> Hope this helps,
>>> Cole
>>>
>>> On Fri, Aug 2, 2019 at 11:45 AM Pedro Lacerda <psl...@gm...>
>>> wrote:
>>>
>>>> Hi PyMOL users,
>>>>
>>>> It there any way to enhance the selecion algebra with functions? For
>>>> instance:
>>>>
>>>> select len(get_chains(*)) < 2
>>>>>
>>>>
>>>> Or even:
>>>>
>>>> select cmd.get_fastastr(*) < 2
>>>>>
>>>>
>>>>
>>>> By the way, why some commands we can simply run (like get_chains) and
>>>> others are different (like cmd.get_fastastr())?
>>>>
>>>> --
>>>> Pedro Sousa Lacerda
>>>>
>>>>
>>>> *Laboratório de Bioinformática e Modelagem Molecular*
>>>> *Faculdade de Farmácia / UFBA*
>>>>
>>>> *@pslacerda*
>>>>
>>>> *+55 71 9 9981-1856*
>>>> _______________________________________________
>>>> PyMOL-users mailing list
>>>> Archives: http://www.mail-archive.com/pym...@li...
>>>> Unsubscribe:
>>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>>
>>>
>
> --
> Pedro Sousa Lacerda
>
>
> *Laboratório de Bioinformática e Modelagem Molecular*
> *Faculdade de Farmácia / UFBA*
>
> *@pslacerda*
>
> *+55 71 9 9981-1856*
>

Re: [PyMOL] Selection algebra

[Pedro L. <psl...@gm...>]

I expressed myself wrong, I'm looking something like:

   select peplength < 15 and chain A

Where peplength is an user defined function like:

def peplength(atom):
    return compute_peplength(atom)

I'm looking for the availability of user defined functions on selection
expressions. How to?

Em sex, 2 de ago de 2019 às 15:44, Christian "Cole" French <
chr...@sc...> escreveu:

> Edit: remove the cmd. part when running select_with_filter. (Since it's a
> custom command, it doesn't belong to the cmd module.)
>
> On Fri, Aug 2, 2019 at 2:41 PM Christian "Cole" French <
> chr...@sc...> wrote:
>
>> Hi Pedro Lacerda,
>>
>> Here is a link to a script I wrote which adds a command which does what
>> you ask:
>> https://gist.github.com/ColeFrench/6f68fa5f04a67bb6234f10c25debb865. To
>> use it, download the file to the directory where you run PyMOL from, then
>> open PyMOL and run run select_with_filter.py.
>>
>> For your examples, the commands would be cmd.select_with_filter(predicate=lambda
>> s: len(cmd.get_chains(s)) < 2) and cmd.select_with_filter(predicate=lambda
>> s: cmd.get_fastastr(s) < 2).
>>
>> Commands which can be simply run are a convenience which allows you to
>> type less (e.g., select chain A instead of cmd.select('chain A')). Some
>> commands require different arguments and can only be run the longer way,
>> such as the one I wrote which takes a function as an argument.
>>
>> Hope this helps,
>> Cole
>>
>> On Fri, Aug 2, 2019 at 11:45 AM Pedro Lacerda <psl...@gm...>
>> wrote:
>>
>>> Hi PyMOL users,
>>>
>>> It there any way to enhance the selecion algebra with functions? For
>>> instance:
>>>
>>> select len(get_chains(*)) < 2
>>>>
>>>
>>> Or even:
>>>
>>> select cmd.get_fastastr(*) < 2
>>>>
>>>
>>>
>>> By the way, why some commands we can simply run (like get_chains) and
>>> others are different (like cmd.get_fastastr())?
>>>
>>> --
>>> Pedro Sousa Lacerda
>>>
>>>
>>> *Laboratório de Bioinformática e Modelagem Molecular*
>>> *Faculdade de Farmácia / UFBA*
>>>
>>> *@pslacerda*
>>>
>>> *+55 71 9 9981-1856*
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> Archives: http://www.mail-archive.com/pym...@li...
>>> Unsubscribe:
>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
>>

-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*

Re: [PyMOL] Selection algebra

[Christian \Cole\ F. <chr...@sc...>]

Edit: remove the cmd. part when running select_with_filter. (Since it's a
custom command, it doesn't belong to the cmd module.)

On Fri, Aug 2, 2019 at 2:41 PM Christian "Cole" French <
chr...@sc...> wrote:

> Hi Pedro Lacerda,
>
> Here is a link to a script I wrote which adds a command which does what
> you ask:
> https://gist.github.com/ColeFrench/6f68fa5f04a67bb6234f10c25debb865. To
> use it, download the file to the directory where you run PyMOL from, then
> open PyMOL and run run select_with_filter.py.
>
> For your examples, the commands would be cmd.select_with_filter(predicate=lambda
> s: len(cmd.get_chains(s)) < 2) and cmd.select_with_filter(predicate=lambda
> s: cmd.get_fastastr(s) < 2).
>
> Commands which can be simply run are a convenience which allows you to
> type less (e.g., select chain A instead of cmd.select('chain A')). Some
> commands require different arguments and can only be run the longer way,
> such as the one I wrote which takes a function as an argument.
>
> Hope this helps,
> Cole
>
> On Fri, Aug 2, 2019 at 11:45 AM Pedro Lacerda <psl...@gm...> wrote:
>
>> Hi PyMOL users,
>>
>> It there any way to enhance the selecion algebra with functions? For
>> instance:
>>
>> select len(get_chains(*)) < 2
>>>
>>
>> Or even:
>>
>> select cmd.get_fastastr(*) < 2
>>>
>>
>>
>> By the way, why some commands we can simply run (like get_chains) and
>> others are different (like cmd.get_fastastr())?
>>
>> --
>> Pedro Sousa Lacerda
>>
>>
>> *Laboratório de Bioinformática e Modelagem Molecular*
>> *Faculdade de Farmácia / UFBA*
>>
>> *@pslacerda*
>>
>> *+55 71 9 9981-1856*
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>

Re: [PyMOL] Selection algebra

[Christian \Cole\ F. <chr...@sc...>]

Hi Pedro Lacerda,

Here is a link to a script I wrote which adds a command which does what you
ask: https://gist.github.com/ColeFrench/6f68fa5f04a67bb6234f10c25debb865.
To use it, download the file to the directory where you run PyMOL from,
then open PyMOL and run run select_with_filter.py.

For your examples, the commands would be
cmd.select_with_filter(predicate=lambda
s: len(cmd.get_chains(s)) < 2) and cmd.select_with_filter(predicate=lambda
s: cmd.get_fastastr(s) < 2).

Commands which can be simply run are a convenience which allows you to type
less (e.g., select chain A instead of cmd.select('chain A')). Some commands
require different arguments and can only be run the longer way, such as the
one I wrote which takes a function as an argument.

Hope this helps,
Cole

On Fri, Aug 2, 2019 at 11:45 AM Pedro Lacerda <psl...@gm...> wrote:

> Hi PyMOL users,
>
> It there any way to enhance the selecion algebra with functions? For
> instance:
>
> select len(get_chains(*)) < 2
>>
>
> Or even:
>
> select cmd.get_fastastr(*) < 2
>>
>
>
> By the way, why some commands we can simply run (like get_chains) and
> others are different (like cmd.get_fastastr())?
>
> --
> Pedro Sousa Lacerda
>
>
> *Laboratório de Bioinformática e Modelagem Molecular*
> *Faculdade de Farmácia / UFBA*
>
> *@pslacerda*
>
> *+55 71 9 9981-1856*
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Selection algebra

[Pedro L. <psl...@gm...>]

Hi PyMOL users,

It there any way to enhance the selecion algebra with functions? For
instance:

select len(get_chains(*)) < 2
>

Or even:

select cmd.get_fastastr(*) < 2
>


By the way, why some commands we can simply run (like get_chains) and
others are different (like cmd.get_fastastr())?

-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*

[PyMOL] pymol2 and multiprocessing issues

[Pedro L. <psl...@gm...>]

Hi,

I'm using pymol2.PyMOL() to instantiate a PyMOL session per process but it
is struggling at threading locks wasting all the time locked (ie doing
nothing).

My job function only the following commands from PyMOL: fetch, align,
get_model and delete. It clean all the objects within the function itself.

I didn't even tried start()/stop() because the pool has only eight
processes.

-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*

Re: [PyMOL] how to delete frames from a trajectory loaded by the "load_traj" command?

[Mateusz B. <bie...@gm...>]

Hi Yeping Sun,

A non-pymol solution to this would be to extract your first frame (in the
form of .gro) from the .xtc file, and then load your .xtc trajectory
starting from the 2nd frame.

To get the first frame as a new .gro, a similar command to this can be used:
gmx trjconv -f .xtc -s .tpr -e 1 -o myNewFirstFrame.gro


Hope this helps,
Mat

On Wed, 31 Jul 2019 at 04:58, sunyeping via PyMOL-users <
pym...@li...> wrote:

> Dear all,
>
> I loaded a gromacs trajetory containing about 1000 frames by the following
> command in pymol:
>
> load protein.gro
> load_traj protein.xtc
>
> I want to use these frames to make a movie. However, I find that the
> position of the protein in first frame is very different from the other
> frames some I want to delete the first frame so the protein stays in the
> same position in all frame. Could you tell me the command of removing the
> first frame?
>
> Thank you.
>
> Best regards.
> Yeping Sun
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] how to delete frames from a trajectory loaded by the "load_traj" command?

[sunyeping <sun...@al...>]

Dear all,

I loaded a gromacs trajetory containing about 1000 frames by the following command in pymol:

load protein.gro
load_traj protein.xtc

I want to use these frames to make a movie. However, I find that the position of the protein in first frame is very different from the other frames some I want to delete the first frame so the protein stays in the same position in all frame. Could you tell me the command of removing the first frame?

Thank you.

Best regards.
Yeping Sun

[PyMOL] Customizing label using cmd.label()

[유재원 <dbw...@gm...>]

Hello,

I'm new to PyMOL and am trying to find ways to label specific
sequences/domains with custom text blocks AND displaying text blocks on the
screen that are non sequence-specific.

It seems like cmd.label() only retrieves certain features from PDB files
using in-built algorithms. Would there be other ways to customize labels in
PyMOL (e.g. extract text from txt files) ?

Any form of help would be greatly appreciated.

Thank you