pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Damien,

I am not sure if I understood you problem correctly.  Have you tried the
following commands?

set connect_mode, 2 (or other number)
load your_pdb_file_name.pdb, discrete=1

Cheers,
Osvaldo.


On Fri, Nov 28, 2014 at 12:23 PM, Clavel <dc...@ib...> wrote:

>  Hello PyMOL users,
>
> I am currently puzzled by the CONECT card and the display of multi-states.
> After, many trials I cannot end up with a correct representation of my
> work.
>
> I loaded 9 states to PyMOL made of 2 different PDB files. The second files
> of each states contains specific CONECT cards according to the index number
> of each atoms (inter residue connection).
>
> When I run my script, Pymol is working nicely except for the CONECT
> cards...
> Basically, PyMOL only put in memory the CONECT card of the second files of
> the first state and apply it to the rest of the states.
> In addition, I tried pdb_ignore_connect and connect_mode... Despites their
> fancy names those commands were useless.
>
> Does someone knows how to force PyMol to read stricly PDB files when
> loading multi-states?
>
> Many thanks.
>
> --
> *Damien CLAVEL*
>  PhD student at Laboratoire Chimie Physique (UP Sud)
>                 and Institut de Biologie Structurale (EPN Campus)
> --------------------------------------------------------------------------
>     Laboratoire de Chimie Physique
> <" rel="nofollow">http://www.lcp.u-psud.fr/rubrique.php3?id_rubrique=266/>    Institut de
> Biologie Structurale <" rel="nofollow">http://www.ibs.fr/spip.php?lang=en>
>     Bul. 350 Campus Orsay                 EPN Campus
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>
>    [image: Image and video hosting by TinyPic]
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>
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Hello PyMOL users,

I am currently puzzled by the CONECT card and the display of multi-states.
After, many trials I cannot end up with a correct representation of my work.

I loaded 9 states to PyMOL made of 2 different PDB files. The second 
files of each states contains specific CONECT cards according to the 
index number of each atoms (inter residue connection).

When I run my script, Pymol is working nicely except for the CONECT 
cards...
Basically, PyMOL only put in memory the CONECT card of the second files 
of the first state and apply it to the rest of the states.
In addition, I tried pdb_ignore_connect and connect_mode... Despites 
their fancy names those commands were useless.

Does someone knows how to force PyMol to read stricly PDB files when 
loading multi-states?

Many thanks.

-- 
*Damien CLAVEL*
PhD student at Laboratoire Chimie Physique (UP Sud)
                 and Institut de Biologie Structurale (EPN Campus)
--------------------------------------------------------------------------
Laboratoire de Chimie Physique 
<" rel="nofollow">http://www.lcp.u-psud.fr/rubrique.php3?id_rubrique=266/> Institut de 
Biologie Structurale <" rel="nofollow">http://www.ibs.fr/spip.php?lang=en>
     Bul. 350 Campus Orsay                 EPN Campus
     15, Av. Jean Perrin                         6, rue Jules Horowitz
     F-91405 ORSAY Cedex                 F-38000 GRENOBLE

Image and video hosting by TinyPic <" rel="nofollow">http://tinypic.com?ref=28s7yvd>

Thanks Thomas and all the PyMOL Team at Schrödinger for this nice
announcement and for trusting me. I am really excited with this opportunity
to further contribute to PyMOL, to the community and especially to honor
the memory of Warren L. DeLano who gave us this wonderful software that is
PyMOL

As Thomas already said to all of you feel free to contact me for anything
you want or need.

Cheers,
Osvaldo.

On Wed, Nov 26, 2014 at 6:13 PM, Thomas Holder <
tho...@sc...> wrote:

> Greetings PyMOL users worldwide,
>
> Please join me in congratulating Dr. Osvaldo Martin, who has been awarded
> the Warren L. DeLano Memorial PyMOL Open Source Fellowship for 2014-2015.
>
> Osvaldo is an active member of the PyMOL community and author of several
> PyMOL plugins. As a PyMOL fellow, Osvaldo will work on visualization and
> modeling of glycans and glycoconjugated molecules. We are looking forward
> to Osvaldo’s contributions and wish him great success in the following
> year. If you want to send along a personal thank you and congratulations,
> Osvaldo can be reached at aloctavodia at gmail dot com.
>
> The Warren L. DeLano Memorial PyMOL Open-Source Fellowship is awarded by
> Schrӧdinger to supplement the income of an outstanding member of the PyMOL
> open-source community so that s/he can continue to develop free resources
> to help scientific progress and the community as a whole. You can read more
> about the PyMOL Open Source Fellowship Program and the fellows here
> http://pymol.org/fellowship.
>
> Cheers,
>
>   Thomas & the PyMOL Team at Schrödinger
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
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Greetings PyMOL users worldwide,

Please join me in congratulating Dr. Osvaldo Martin, who has been awarded the Warren L. DeLano Memorial PyMOL Open Source Fellowship for 2014-2015.

Osvaldo is an active member of the PyMOL community and author of several PyMOL plugins. As a PyMOL fellow, Osvaldo will work on visualization and modeling of glycans and glycoconjugated molecules. We are looking forward to Osvaldo’s contributions and wish him great success in the following year. If you want to send along a personal thank you and congratulations, Osvaldo can be reached at aloctavodia at gmail dot com.

The Warren L. DeLano Memorial PyMOL Open-Source Fellowship is awarded by Schrӧdinger to supplement the income of an outstanding member of the PyMOL open-source community so that s/he can continue to develop free resources to help scientific progress and the community as a whole. You can read more about the PyMOL Open Source Fellowship Program and the fellows here http://pymol.org/fellowship.

Cheers,

  Thomas & the PyMOL Team at Schrödinger

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Spencer,

If you are interested I have implemented a (preliminary version) of a
superposition algorithm (similar to super) using Python/PyMOL.

Cheers,
Osvaldo.



On Wed, Nov 26, 2014 at 2:40 PM, Sampson, Jared <Jar...@ny...>
wrote:

>  Hi Spencer -
>
>  If you need a superposition algorithm with a published reference, try
> CEAlign <." rel="nofollow">http://www.pymolwiki.org/index.php/Cealign>.  Some references
> are listed on the page for the former CEAlign Plugin
> <" rel="nofollow">http://www.pymolwiki.org/index.php/Cealign_plugin#References>  from
> before it was incorporated into PyMOL (in version 1.3).
>
>  Just be careful to note that the order of the first two arguments
> (target, mobile) is switched compared to the `super` and `align` commands
> (mobile, target).
>
>  Cheers,
> Jared
>
>   --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> http://kong.med.nyu.edu/
>
>
>
>
>
>
>  On Nov 26, 2014, at 7:13 AM, Spencer Bliven <sb...@uc...> wrote:
>
>  I would also be interested if there is any documentation about the super
> algorithm and the differences to align.
>
>  -Spencer
>
> On Fri, Nov 14, 2014 at 10:25 PM, Osvaldo Martin <alo...@gm...>
> wrote:
>
>>  Hi,
>>
>>  Exactly which algorithm is behind the super command? How the outliers
>> pairs are defined?  The is some scientific paper related to super or it is
>> really an experimental idea?
>>
>>  Thanks.
>>
>>
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>
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>
>

Hi Spencer -

If you need a superposition algorithm with a published reference, try CEAlign<." rel="nofollow">http://www.pymolwiki.org/index.php/Cealign>.  Some references are listed on the page for the former CEAlign Plugin<" rel="nofollow">http://www.pymolwiki.org/index.php/Cealign_plugin#References>  from before it was incorporated into PyMOL (in version 1.3).

Just be careful to note that the order of the first two arguments (target, mobile) is switched compared to the `super` and `align` commands (mobile, target).

Cheers,
Jared

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






On Nov 26, 2014, at 7:13 AM, Spencer Bliven <sb...@uc...<mailto:sb...@uc...>> wrote:

I would also be interested if there is any documentation about the super algorithm and the differences to align.

-Spencer

On Fri, Nov 14, 2014 at 10:25 PM, Osvaldo Martin <alo...@gm...<mailto:alo...@gm...>> wrote:
Hi,

Exactly which algorithm is behind the super command? How the outliers pairs are defined?  The is some scientific paper related to super or it is really an experimental idea?

Thanks.

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Hi Spencer,

thanks for bringing this to our attention. Since OS X 10.9 ships with scipy preinstalled, you can try this workaround which imports scipy from the system python:

import sys
sys.path.insert(1, '/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python')
import scipy.linalg

Hope that helps.

Cheers,
  Thomas

On 25 Nov 2014, at 04:46, Spencer Bliven <sb...@uc...> wrote:

> Importing scipy.linalg in MacPyMOL crashes the program for me. Probably the linalg module shipped with MacPyMOL is corrupt or incorrectly linked. I've reproduced it with MacPyMOL 1.6 and 1.7, with both X11 and aqua, and on Mac OS 10.9 and 10.10.
> 
> I discovered this problem because importing the full pymol script repo crashes, due to the pyanm plugin. Maybe this will save someone a headache in the future.
> 
> -Spencer

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Spencer,

unfortunately, to our knowledge, no formal documentation for the "super" align method exists. It's a "sequence-independant" (means: residue name independent) sequence alignment method based on 3D coordinates of CA atoms.

The RMSD minimizing superposition with outlier rejection is identical to the "align" command.

Cheers,
  Thomas

On 26 Nov 2014, at 07:13, Spencer Bliven <sb...@uc...> wrote:

> I would also be interested if there is any documentation about the super algorithm and the differences to align.
> 
> -Spencer
> 
> On Fri, Nov 14, 2014 at 10:25 PM, Osvaldo Martin <alo...@gm...> wrote:
> Hi,
> 
> Exactly which algorithm is behind the super command? How the outliers pairs are defined?  The is some scientific paper related to super or it is really an experimental idea?
> 
> Thanks.

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Spencer,

We have no plans to move the community wiki to the pymol.org domain. Schrödinger keeps wiki.pymol.org as a read-only backup mirror of pymolwiki.org, and it's up-to-date with sometimes a few days delay. Thanks for your suggestion about the sitenotice - we've put it into place.

Cheers,
  Thomas

On 26 Nov 2014, at 05:48, Spencer Bliven <sb...@uc...> wrote:

> What's the deal with wiki.pymol.org? It looks like a mirror of pymolwiki.org from June 9th. Are there plans to move the community wiki into the pymol namespace?
> 
> Since google indexes them both now, it would be nice to have a indication on wiki.pymol.org that the information is not fully up-to-date (e.g. through a sitenotice).
> 
> -Spencer

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

I would also be interested if there is any documentation about the super
algorithm and the differences to align.

-Spencer

On Fri, Nov 14, 2014 at 10:25 PM, Osvaldo Martin <alo...@gm...>
wrote:

> Hi,
>
> Exactly which algorithm is behind the super command? How the outliers
> pairs are defined?  The is some scientific paper related to super or it is
> really an experimental idea?
>
> Thanks.
>
>
> ------------------------------------------------------------------------------
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

What's the deal with wiki.pymol.org? It looks like a mirror of pymolwiki.org
from June 9th. Are there plans to move the community wiki into the pymol
namespace?

Since google indexes them both now, it would be nice to have a indication
on wiki.pymol.org that the information is not fully up-to-date (e.g.
through a sitenotice
<)." rel="nofollow">http://www.mediawiki.org/wiki/Manual:Interface/Sitenotice>).

-Spencer

Importing scipy.linalg in MacPyMOL crashes the program for me. Probably the
linalg module shipped with MacPyMOL is corrupt or incorrectly linked. I've
reproduced it with MacPyMOL 1.6 and 1.7, with both X11 and aqua, and on Mac
OS 10.9 and 10.10.

I discovered this problem because importing the full pymol script repo
crashes, due to the pyanm plugin. Maybe this will save someone a headache
in the future.

-Spencer

Hi Surya,

Using the interactive builder is usually the way to go. To get you started
you may need a starting atom, which you could create using the pseudoatom
command:
http://www.pymolwiki.org/index.php/Pseudoatom

Note that the builder has some templates, e.g. the cyclopendadiene that you
can use and then replace carbons by nitogens.
Another alternative is to make use of pre-existing structres, e.g.

frag HIS

will give you a histidine that you can edit using the "remove" command to
work on the ring. You may want to rename some of the atoms though.

This page has some general hints for structure editing:
http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures

Note that when you save non amino acid structures, PyMOL may not interpret
them as intended if you save your imidazole in .pdb format.
I recommend using .pkl format, as this will preserve information concerning
double bonds etc.

Cheers,

Andreas

On Sat, Nov 15, 2014 at 2:32 PM, Osvaldo Martin <alo...@gm...>
wrote:

> Hi Surya,
>
> I don't know exactly what problem are you experiencing (I tried to do
> something similar without any problem). I guess that maybe the problem is
> that when you are rebuilding the ring, you are positioning the atoms in a
> not very good position and maybe PyMOL is having trouble to figure-out the
> connectivity.
>
> I think one possible solution is to optimize the geometry of the molecule
> (before saving the pdb file) using the optimize plugin
> http://www.pymolwiki.org/index.php/Optimize. This will give you the
> correct bond angles and bond lenght and also will (hopefully) write the
> correct connectivity to the pdb file.
>
> Best regards,
> Osvaldo.
>
>
>
> On Sat, Nov 15, 2014 at 10:08 AM, Seera Suryanarayana <pal...@gm...
> > wrote:
>
>> Dear pymol users
>>
>> I have been trying to build imidazol ring to one incomplete His of my pdb
>> file by using builder in pymol. After finishing this ring I saved and
>> opened once again by pymol. I have seen some thing like mess formation with
>> in the residues. I request you to tell me what could be the reason and how
>> do I overcome it.
>>
>> Thanks in advance
>>
>> Surya
>> Graduate student
>> India.
>>
>>
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>
>
>
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Hi Erica,

I prefer to leave the vdw value untouched, as this may affect operations
that rely on this value.
Instead you can alter the sphere scale:
set sphere_scale, <value>, <selection>

e.g.:
set sphere_scale, 1.5, hetatm
show_as spheres

will increase the sphere scale of heteroatoms (i.e. non-bonded) to 1.5

Cheers,

Andreas

On Thu, Nov 20, 2014 at 3:41 PM, Matthew Baumgartner <mp...@pi...> wrote:

>  Hi,
> Just to chime in, you might need to call 'sort' and/or 'rebuild' after
> using the alter command to see the changes.
> Matt Baumgartner
>
>
> On 11/20/2014 08:20 AM, Osvaldo Martin wrote:
>
>  Hi Erica,
>
>  I think something like:
>
> alter name ca, vdw=10
>
> should help. Change "10" for the value you want.
>
>
>  Best Regards,
>  Osvaldo.
>
> On Wed, Nov 19, 2014 at 11:16 AM, Erica Valentini <er...@em...>
> wrote:
>
>> Dear all,
>>
>> I would like to change the size of nonbonded spheres.
>> They are nonbonded c-alpha atoms not heteroatoms therefore I don't
>> know how to specifically select them in order to change them.
>>
>> Thanks a lot in advance,
>>
>> Erica
>>
>> --
>> Erica Valentini
>>
>> EMBL-Hamburg
>> Notkestrasse 85,
>> +49 040 899 02 182
>>
>>
>>
>>
>>
>>
>>
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>
>
>
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That's alright, I only discovered the "Volume" feature yesterday and  
that's been around since v1.4 ...



Quoting joh...@cs... on Thu, 20 Nov 2014 11:06:39 -0700:

> It does! Thank you very much; I don't know how I missed that command.
>
>> Hi John,
>>
>> Does the 'torsion' command work?
>>
>> Cheers,
>> Doug
>>
>>
>> Quoting joh...@cs... on Thu, 20 Nov 2014 01:06:04 -0700:
>>
>>> Hello, PyMOL users!
>>>
>>> I am trying to figure out within the Python interface how to rotate the
>>> parts of a molecule on one side of a bond about that bond's axis, given
>>> only the two atoms defining the bond and a angle to rotate by (that is,
>>> without requiring me to specify four atoms and a final dihedral angle
>>> value as required by set_dihedral). While I understand the "rotate"
>>> function, I can't figure out how, in the Python interface, to select the
>>> atoms on one side of a bond given the bond's two defining atoms.
>>>
>>> I've looked through the PyMOL C++ code, and it appears that this
>>> functionality is provided by the layer3/Selector.cpp function
>>> "SelectorSubdivide" when its "bondMode" flag set to true and given two
>>> atoms; set_dihedral's C++ implementation seems to use this functionality
>>> to select the atoms it will rotate. I tried to look through the rest of
>>> the source to see if this selection behavior was somehow exposed to the
>>> Python interface, but as best as I could tell it doesn't seem to be.
>>>
>>> If anyone can work out a good way from the Python interface to select
>>> the
>>> atoms of a molecule on one side of a bond, or if there is a
>>> Python-accessible function that acts similar to set_dihedral but rotates
>>> about any bond by a given angular change without requiring a bonded
>>> sequence of four atoms to define an arbitrary dihedral plane (and an
>>> otherwise unnecessary call to get_dihedral to to calculate the change
>>> needed to know what angle I would need to give set_dihedral), I would be
>>> very appreciative.
>>>
>>> Thank you very much for your time!
>>>
>>> -John
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
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>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>>
>>
>>
>>
>>
>> _____________________________________________________
>> Dr. Douglas R. Houston
>> Lecturer
>> Institute of Structural and Molecular Biology
>> Room 3.23, Michael Swann Building
>> King's Buildings
>> University of Edinburgh
>> Edinburgh, EH9 3JR, UK
>> Tel. 0131 650 7358
>> http://tinyurl.com/douglasrhouston
>>
>> --
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
>>
>>
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>
>
>
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>




_____________________________________________________
Dr. Douglas R. Houston
Lecturer
Institute of Structural and Molecular Biology
Room 3.23, Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358
http://tinyurl.com/douglasrhouston

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

It does! Thank you very much; I don't know how I missed that command.

> Hi John,
>
> Does the 'torsion' command work?
>
> Cheers,
> Doug
>
>
> Quoting joh...@cs... on Thu, 20 Nov 2014 01:06:04 -0700:
>
>> Hello, PyMOL users!
>>
>> I am trying to figure out within the Python interface how to rotate the
>> parts of a molecule on one side of a bond about that bond's axis, given
>> only the two atoms defining the bond and a angle to rotate by (that is,
>> without requiring me to specify four atoms and a final dihedral angle
>> value as required by set_dihedral). While I understand the "rotate"
>> function, I can't figure out how, in the Python interface, to select the
>> atoms on one side of a bond given the bond's two defining atoms.
>>
>> I've looked through the PyMOL C++ code, and it appears that this
>> functionality is provided by the layer3/Selector.cpp function
>> "SelectorSubdivide" when its "bondMode" flag set to true and given two
>> atoms; set_dihedral's C++ implementation seems to use this functionality
>> to select the atoms it will rotate. I tried to look through the rest of
>> the source to see if this selection behavior was somehow exposed to the
>> Python interface, but as best as I could tell it doesn't seem to be.
>>
>> If anyone can work out a good way from the Python interface to select
>> the
>> atoms of a molecule on one side of a bond, or if there is a
>> Python-accessible function that acts similar to set_dihedral but rotates
>> about any bond by a given angular change without requiring a bonded
>> sequence of four atoms to define an arbitrary dihedral plane (and an
>> otherwise unnecessary call to get_dihedral to to calculate the change
>> needed to know what angle I would need to give set_dihedral), I would be
>> very appreciative.
>>
>> Thank you very much for your time!
>>
>> -John
>>
>>
>> ------------------------------------------------------------------------------
>> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
>> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
>> with Interactivity, Sharing, Native Excel Exports, App Integration &
>> more
>> Get technology previously reserved for billion-dollar corporations, FREE
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>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>>
>
>
>
>
> _____________________________________________________
> Dr. Douglas R. Houston
> Lecturer
> Institute of Structural and Molecular Biology
> Room 3.23, Michael Swann Building
> King's Buildings
> University of Edinburgh
> Edinburgh, EH9 3JR, UK
> Tel. 0131 650 7358
> http://tinyurl.com/douglasrhouston
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
>
> ------------------------------------------------------------------------------
> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> with Interactivity, Sharing, Native Excel Exports, App Integration & more
> Get technology previously reserved for billion-dollar corporations, FREE
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> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hello,
PHENIX has calculated a *_refine_001_mFo-DFc.ccp4 map for me, which I
“meshed” with isomesh mesh, map, 3. I understand map_auto_expand_sym is
enabled by default. Yet when I translate using the middle mouse button, I
can easily go beyond the extent of the mesh. How can I make the mesh fellow
the canvas center? Do I need a different map?
Thank you,
Wolfram Tempel
​

Hi,
Just to chime in, you might need to call 'sort' and/or 'rebuild' after 
using the alter command to see the changes.
Matt Baumgartner

On 11/20/2014 08:20 AM, Osvaldo Martin wrote:
> Hi Erica,
>
> I think something like:
>
> alter name ca, vdw=10
>
> should help. Change "10" for the value you want.
>
>
> Best Regards,
> Osvaldo.
>
> On Wed, Nov 19, 2014 at 11:16 AM, Erica Valentini 
> <er...@em... <mailto:er...@em...>> wrote:
>
>     Dear all,
>
>     I would like to change the size of nonbonded spheres.
>     They are nonbonded c-alpha atoms not heteroatoms therefore I don't
>     know how to specifically select them in order to change them.
>
>     Thanks a lot in advance,
>
>     Erica
>
>     --
>     Erica Valentini
>
>     EMBL-Hamburg
>     Notkestrasse 85,
>     +49 040 899 02 182
>
>
>
>
>
>
>     ------------------------------------------------------------------------------
>     Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
>     from Actuate! Instantly Supercharge Your Business Reports and
>     Dashboards
>     with Interactivity, Sharing, Native Excel Exports, App Integration
>     & more
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>     corporations, FREE
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>     _______________________________________________
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>     Archives:
>     http://www.mail-archive.com/pym...@li...
>
>
>
>
> ------------------------------------------------------------------------------
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Hi Tumpa,

What about using the builder <." rel="nofollow">http://www.pymolwiki.org/index.php/Builder>.
Is this what you need?

Osvaldo.

On Thu, Nov 20, 2014 at 4:02 AM, <t.s...@ch...> wrote:

Hi,
>   I am a new user of pymol. My question is how to add an oxygen atom in
> carbonyl group?
>
> Thanks,
> Tumpa Sadhukhan.
> Ph.D Scholar,
> IIT Bombay,
> India.
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> with Interactivity, Sharing, Native Excel Exports, App Integration & more
> Get technology previously reserved for billion-dollar corporations, FREE
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
​

Hi Erica,

I think something like:

alter name ca, vdw=10

should help. Change "10" for the value you want.


Best Regards,
Osvaldo.

On Wed, Nov 19, 2014 at 11:16 AM, Erica Valentini <er...@em...>
wrote:

> Dear all,
>
> I would like to change the size of nonbonded spheres.
> They are nonbonded c-alpha atoms not heteroatoms therefore I don't
> know how to specifically select them in order to change them.
>
> Thanks a lot in advance,
>
> Erica
>
> --
> Erica Valentini
>
> EMBL-Hamburg
> Notkestrasse 85,
> +49 040 899 02 182
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> with Interactivity, Sharing, Native Excel Exports, App Integration & more
> Get technology previously reserved for billion-dollar corporations, FREE
>
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> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
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> Archives: http://www.mail-archive.com/pym...@li...
>

Hi John,

Does the 'torsion' command work?

Cheers,
Doug


Quoting joh...@cs... on Thu, 20 Nov 2014 01:06:04 -0700:

> Hello, PyMOL users!
>
> I am trying to figure out within the Python interface how to rotate the
> parts of a molecule on one side of a bond about that bond's axis, given
> only the two atoms defining the bond and a angle to rotate by (that is,
> without requiring me to specify four atoms and a final dihedral angle
> value as required by set_dihedral). While I understand the "rotate"
> function, I can't figure out how, in the Python interface, to select the
> atoms on one side of a bond given the bond's two defining atoms.
>
> I've looked through the PyMOL C++ code, and it appears that this
> functionality is provided by the layer3/Selector.cpp function
> "SelectorSubdivide" when its "bondMode" flag set to true and given two
> atoms; set_dihedral's C++ implementation seems to use this functionality
> to select the atoms it will rotate. I tried to look through the rest of
> the source to see if this selection behavior was somehow exposed to the
> Python interface, but as best as I could tell it doesn't seem to be.
>
> If anyone can work out a good way from the Python interface to select the
> atoms of a molecule on one side of a bond, or if there is a
> Python-accessible function that acts similar to set_dihedral but rotates
> about any bond by a given angular change without requiring a bonded
> sequence of four atoms to define an arbitrary dihedral plane (and an
> otherwise unnecessary call to get_dihedral to to calculate the change
> needed to know what angle I would need to give set_dihedral), I would be
> very appreciative.
>
> Thank you very much for your time!
>
> -John
>
>
> ------------------------------------------------------------------------------
> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> with Interactivity, Sharing, Native Excel Exports, App Integration & more
> Get technology previously reserved for billion-dollar corporations, FREE
> http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
>




_____________________________________________________
Dr. Douglas R. Houston
Lecturer
Institute of Structural and Molecular Biology
Room 3.23, Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358
http://tinyurl.com/douglasrhouston

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

Hello, PyMOL users!

I am trying to figure out within the Python interface how to rotate the
parts of a molecule on one side of a bond about that bond's axis, given
only the two atoms defining the bond and a angle to rotate by (that is,
without requiring me to specify four atoms and a final dihedral angle
value as required by set_dihedral). While I understand the "rotate"
function, I can't figure out how, in the Python interface, to select the
atoms on one side of a bond given the bond's two defining atoms.

I've looked through the PyMOL C++ code, and it appears that this
functionality is provided by the layer3/Selector.cpp function
"SelectorSubdivide" when its "bondMode" flag set to true and given two
atoms; set_dihedral's C++ implementation seems to use this functionality
to select the atoms it will rotate. I tried to look through the rest of
the source to see if this selection behavior was somehow exposed to the
Python interface, but as best as I could tell it doesn't seem to be.

If anyone can work out a good way from the Python interface to select the
atoms of a molecule on one side of a bond, or if there is a
Python-accessible function that acts similar to set_dihedral but rotates
about any bond by a given angular change without requiring a bonded
sequence of four atoms to define an arbitrary dihedral plane (and an
otherwise unnecessary call to get_dihedral to to calculate the change
needed to know what angle I would need to give set_dihedral), I would be
very appreciative.

Thank you very much for your time!

-John

Hi,
  I am a new user of pymol. My question is how to add an oxygen atom in
carbonyl group?

Thanks,
Tumpa Sadhukhan.
Ph.D Scholar,
IIT Bombay,
India.

Hi Louris -

If your view is centered on the atom from which you would like to draw the line, and oriented the way you want it, you can achieve something similar to what it sounds like you want with the following commands.

center myAtom
move x, -4           # `move` works in camera space
pseudoatom myMarker  # creates a pseudoatom called “marker” at the center of the screen
move x, 4            # move it back
distance myLine, myAtom, myMarker

To customize the line, have a look at the dash_* settings.  You can show the pseudoatom as a sphere as well.  If you want to draw something else (triangle, square, etc.) rather than a sphere, you’ll have to do it as a CGO, and the “axes.py" script Takanori suggested will be helpful.  You can get the coordinates of the pseudoatom using iterate_state<." rel="nofollow">http://www.pymolwiki.org/index.php/Iterate_state>.

Hope that helps.

Cheers,
Jared

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






On Nov 19, 2014, at 7:14 AM, Feitsma, L.J. <L.J...@uu...<mailto:L.J...@uu...>> wrote:

Hi all,

I have a small question about transformations with the view matrix in pymol, since I’m not very familiar with the architecture of the matrix.

E.g. I take some coordinates [x1,y1,z1], and using cgo objects, I want to draw a line/triangle/square to a point distance 4 to the right on the screen (so not 4 in object x-coördinates!).
How can I use the information in [0:8] of the view matrix to calculate object coordinates [x2, y2, z2] needed to draw the line between [x1, y1, z1] and [x2, y2, z2]?

Does anyone has an example script, or link about which matrix operation I need for this?

Kind regards,

Louris Feitsma

Crystal and Structural Chemistry

Utrecht University

Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539182

------------------------------------------------------------------------------
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Dear all,

I would like to change the size of nonbonded spheres.
They are nonbonded c-alpha atoms not heteroatoms therefore I don't  
know how to specifically select them in order to change them.

Thanks a lot in advance,

Erica

-- 
Erica Valentini

EMBL-Hamburg
Notkestrasse 85,
+49 040 899 02 182