pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Marcelo -

Is Object 2 actually a pseudoatom?  Or, if not, can it be placed separately from Object 1?  If either of those are the case, it would be much easier to place the pseudoatom at a point equidistant from the two ends of Object 1 than mess with rotation matrices, etc.  Here’s what I worked out.


# get a long protein, e.g. collagen
fetch 1bkv, async=0
as cartoon

# place a couple helper pseudoatoms at the "ends" of the collagen (approximately)
pseudoatom nterm, resi 2+31+61, vdw=2
pseudoatom cterm, resi 30+60+90, vdw=2
select ends, nterm or cterm
show spheres, ends

# orient the helper pseudoatoms along one of the display axes (usually ends up being x)
orient ends

# place another helper pseudoatom at the "midpoint" of the object
pseudoatom obj_b, ends, vdw=4
show spheres, obj_b

# move it (e.g.) 50Å away
translate [0,0,-50], obj_b

# make sure it looks right
orient ends or obj_b


You could then load your “real” Object 2 (if necessary) and move it to the obj_2 pseudoatom using a combination of `origin` and the COM script (http://www.pymolwiki.org/index.php/Com), for example.  Haven’t tested that, but it should be possible.

Hope that helps!

Cheers,
Jared

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

On Apr 28, 2015, at 1:57 PM, Marcelo Marcet <MM...@na...<mailto:MM...@na...>> wrote:

Hi Pymol Users,

I have 2 objects (objects 1 and 2) and I would like to re-orient object 1 so that the distance from either end of object 1 becomes the same to object 2 (see image). Is there a way to achieve this in PyMol?

I have tried using the mouse in edit mode and I have tried using the rotate/translate commands. Neither method can move object 1 without altering the position of the lower end of object 1.

Regards,
Marcelo

<image.jpeg>
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Dear Thomas

Thanks very much. Great, It works well.  I think it will attract more
people to switch from VMD to Pymol. Possibly, since the new version of
VASP have change the format of XDATCAR, a update of VMD plugin may be
needed.

A stupid question: When the pymol read the CHGCAR file, it will
produce a set of data like spin up+down and spin up-down. How can i
access different data in pymol?

Thanks again

Best

Wei-Bing

On 29/04/2015, Thomas Holder <tho...@sc...> wrote:
> Hi Wei-Bing,
>
> thank you for the example files. I added support for CHGCAR, POSCAR and
> OUTCAR. In theory there is also XDATCAR support, but that didn't work for
> me. The changes are available as of SVN rev 4118.
>
> Cheers,
>   Thomas
>
> On 24 Apr 2015, at 10:05, Wei-Bing Zhang <wei...@gm...> wrote:
>
>> Dear Thomas
>>
>> Thanks very much for your prompt reply and kindness. I am using VASP
>> to do some DFT calculation and want to use pymol to visualize the
>> geometry structure (i.e. POSCAR/CONTCAR file) and charge density
>> (CHGCAR). The corresponding VASP plugins for VMD has been developed
>> and integrated in official VMD. The VASP geometry is always periodic.
>> The related files of a simple example (a relax CO molecule,the main
>> output file : POSCAR/CONTCAR, CHGCAR/CHG) are enclosed. The
>> corresponding help file can be also found at
>> http://cms.mpi.univie.ac.at/vasp/vasp/POSCAR_file.html;http://cms.mpi.univie.ac.at/vasp/vasp/CHGCAR_file.html
>>
>> Thanks very much for your help again.
>>
>> Best wishes
>>
>> On 24/04/2015, Thomas Holder <tho...@sc...> wrote:
>>> Hi Wei-Bing,
>>>
>>> support to load topology files with the vmd plugins was added in PyMOL
>>> 1.7.4
>>> (previous versions only supported trajectories and maps).
>>>
>>> Unfortunately, every supported filetype has to be registered in PyMOL,
>>> right
>>> now only CMS files (Desmond topology) are registered to be passed to the
>>> vmd
>>> plugin loader. You could of course modify open-source PyMOL yourself to
>>> add
>>> a filetype, but you have to edit about 5 files!
>>>
>>> If you send me example input files (topology and trajectory) I can
>>> register
>>> their extensions and check it in to the SVN repo.
>>>
>>> Cheers,
>>>  Thomas
>>>
>>> On 24 Apr 2015, at 06:13, Wei-Bing Zhang <wei...@gm...>
>>> wrote:
>>>
>>>> Dear all
>>>>
>>>> Recently, i plan to use the pymol as my main visualize tools.  I have
>>>> complied the latest version successfully and the vmd plugin seems to
>>>> be complied as well at least the stage of build (i did not find these
>>>> during the install ). However, when i open the pymol and i find i
>>>> still can not load some format geometry such as vasp POSCAR which is
>>>> included in vmd pludins. Could you tell me how to enable and use the
>>>> vmd plugin in pymol.
>>>>
>>>> Best
>>>>
>>>> Wei-Bing
>>
>> --
>> ----------------------------------------------------------------------
>> Dr. Wei-Bing Zhang
>>
>> School of Physics and Electronic Sciences
>> Changsha University of Science and Technology, Changsha 410004,
>> People's Republic of China
>> Phone : +86 186 73108538
>> E-mail: zh...@cs..., wei...@gm...
>> ----------------------------------------------------------------------
>> <CHGCAR><POSCAR><XDATCAR><OUTCAR>
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>


-- 
----------------------------------------------------------------------
Dr. Wei-Bing Zhang

School of Physics and Electronic Sciences
Changsha University of Science and Technology, Changsha 410004,
People's Republic of China
Phone : +86 186 73108538
E-mail: zh...@cs..., wei...@gm...
----------------------------------------------------------------------

Hi Bharat,

your residue numbers don't match. Read about the "matchmaker" argument here:
http://pymolwiki.org/index.php/Fit

Cheers,
  Thomas

On 27 Apr 2015, at 05:46, bharat gupta <bha...@gm...> wrote:

> Hi,
> 
> I am using rms_cur for calculating rmsd for two sets of structures. It works for the first set but for the second one its gives error:
> PyMOL>rms_cur sel1,sel2
> ExecutiveRMS-Error: No atoms selected.
> 
> Here's the result for set1:
> 
> PyMOL>select sel1, native and resid 1:53+56:72 and name P and chain M
>  Selector: selection "sel1" defined with 0 atoms.
> PyMOL>select sel1, native and resid 142:237 and name P and chain M
>  Selector: selection "sel1" defined with 95 atoms.
> PyMOL>select sel2, best and resid 142:237 and name P and chain B
>  Selector: selection "sel2" defined with 95 atoms.
> PyMOL>alter all,segi=""
>  Alter: modified 10424 atoms.
> PyMOL>alter all,chain=""
>  Alter: modified 10424 atoms.
> PyMOL>rms_cur sel1,sel2
>  Executive: RMS =    7.985 (95 to 95 atoms)
> 
> 
> ============
> 
> Here's the result for set2:
> PyMOL>select sel1, 1sj3-1_16715 and chain R and name P and resid 764:835
>  Selector: selection "sel1" defined with 72 atoms.
> PyMOL>select sel2, 1sj3 and chain R and name P and resid 101:172
>  Selector: selection "sel2" defined with 72 atoms.
> PyMOL>alter all,segi=""
>  Alter: modified 6110 atoms.
> PyMOL>alter all,chain=""
>  Alter: modified 6110 atoms.
> PyMOL>rms_cur sel1,sel2
> ExecutiveRMS-Error: No atoms selected.
> PyMOL>rms_cur sel1,sel2
> ExecutiveRMS-Error: No atoms selected.
> 
> What is the reason behind this ??
> 
> -- 
> Best Regards
> Bharat

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Filip,

there is no function to query map values with 3D coordinates. There is, however, a cmd.get_volume_field() function that returns the raw map data on the grid (works with maps and volumes, PyMOL 1.7.4). With cmd.get_extend() you could put together a mapping from 3D coordinate to grid cell.

See also:
https://sourceforge.net/p/pymol/mailman/message/33229404/

Hope that helps.

Cheers,
  Thomas

On 24 Apr 2015, at 10:03, Filip Leonarski <fle...@gm...> wrote:

> Dear All,
> 
>      I'm trying to develop a plugin to Pymol. Do you know about an option to get value of a map (e.g. electron density) at a particular coordinates? I would like to know sigma value for a particular atom. Is there any way, using python, to achieve that?
> 
> Best regards,
> Filip

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Wei-Bing,

thank you for the example files. I added support for CHGCAR, POSCAR and OUTCAR. In theory there is also XDATCAR support, but that didn't work for me. The changes are available as of SVN rev 4118.

Cheers,
  Thomas

On 24 Apr 2015, at 10:05, Wei-Bing Zhang <wei...@gm...> wrote:

> Dear Thomas
> 
> Thanks very much for your prompt reply and kindness. I am using VASP
> to do some DFT calculation and want to use pymol to visualize the
> geometry structure (i.e. POSCAR/CONTCAR file) and charge density
> (CHGCAR). The corresponding VASP plugins for VMD has been developed
> and integrated in official VMD. The VASP geometry is always periodic.
> The related files of a simple example (a relax CO molecule,the main
> output file : POSCAR/CONTCAR, CHGCAR/CHG) are enclosed. The
> corresponding help file can be also found at
> http://cms.mpi.univie.ac.at/vasp/vasp/POSCAR_file.html;http://cms.mpi.univie.ac.at/vasp/vasp/CHGCAR_file.html
> 
> Thanks very much for your help again.
> 
> Best wishes
> 
> On 24/04/2015, Thomas Holder <tho...@sc...> wrote:
>> Hi Wei-Bing,
>> 
>> support to load topology files with the vmd plugins was added in PyMOL 1.7.4
>> (previous versions only supported trajectories and maps).
>> 
>> Unfortunately, every supported filetype has to be registered in PyMOL, right
>> now only CMS files (Desmond topology) are registered to be passed to the vmd
>> plugin loader. You could of course modify open-source PyMOL yourself to add
>> a filetype, but you have to edit about 5 files!
>> 
>> If you send me example input files (topology and trajectory) I can register
>> their extensions and check it in to the SVN repo.
>> 
>> Cheers,
>>  Thomas
>> 
>> On 24 Apr 2015, at 06:13, Wei-Bing Zhang <wei...@gm...> wrote:
>> 
>>> Dear all
>>> 
>>> Recently, i plan to use the pymol as my main visualize tools.  I have
>>> complied the latest version successfully and the vmd plugin seems to
>>> be complied as well at least the stage of build (i did not find these
>>> during the install ). However, when i open the pymol and i find i
>>> still can not load some format geometry such as vasp POSCAR which is
>>> included in vmd pludins. Could you tell me how to enable and use the
>>> vmd plugin in pymol.
>>> 
>>> Best
>>> 
>>> Wei-Bing
> 
> -- 
> ----------------------------------------------------------------------
> Dr. Wei-Bing Zhang
> 
> School of Physics and Electronic Sciences
> Changsha University of Science and Technology, Changsha 410004,
> People's Republic of China
> Phone : +86 186 73108538
> E-mail: zh...@cs..., wei...@gm...
> ----------------------------------------------------------------------
> <CHGCAR><POSCAR><XDATCAR><OUTCAR>

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Pymol Users,

I have 2 objects (objects 1 and 2) and I would like to re-orient object 1 so that the distance from either end of object 1 becomes the same to object 2 (see image). Is there a way to achieve this in PyMol?

I have tried using the mouse in edit mode and I have tried using the rotate/translate commands. Neither method can move object 1 without altering the position of the lower end of object 1.

Regards,
Marcelo

Hi,

Did you try with this recipe
<?" rel="nofollow">http://www.pymolwiki.org/index.php/Huge_surfaces>? Did you try doing the
ray-traicing from a script (and not using the GUI)?

Cheers,
Osvaldo.

On Tue, Apr 28, 2015 at 11:46 AM, Rallapalli, Pavithra <
pav...@uc...> wrote:

 Hi all
>
>
>
> I am trying to ray trace my icosahedram viral capsid, a 75 MB .pse file.
>
> I am running this on a 16 GB windows 64 bit machine with 2 GB NVIDEA
> GEFORCE graphics.
>
>
>
> But the memory still seems to be low as for some reason PyMOL’s virtual
> memory is still low.
>
> I have tried set hash_max but does not make a difference.
>
>
>
> Does any one have any suggestions on changing the settings so PyMOL uses
> the full power of the machine?
>
>
>
>
>
> Many Thanks
>
> Pavithra Rallapalli, PhD
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> One dashboard for servers and applications across Physical-Virtual-Cloud
> Widest out-of-the-box monitoring support with 50+ applications
> Performance metrics, stats and reports that give you Actionable Insights
> Deep dive visibility with transaction tracing using APM Insight.
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>
​

Dear Rajib & Yuktimmana

Molecules in PyMOL are stored as .pkl files. Those files are located inside
the

“pymol/data/chempy/fragments” folder.

I guess the only way to get a confident estimation on the feasibility of a
theoretical molecule is to perform quantum chemical computations.
Nevertheless, after building your molecule you could minimize it energy, at
least that will give you a reasonable conformation. The incentive version
of PyMOL is distributed with a built-in minimization feature, if you don’t
have the inventive version you could use the optimize
<" rel="nofollow">http://www.pymolwiki.org/index.php/Optimize> plugin.


Best Regards,

Osvaldo.


On Tue, Apr 28, 2015 at 1:34 PM, bkpsusmitaa <bkp...@gm...> wrote:

Hello, Dr. Thomas and members,
> Is cyclododecene in the database of PyMol? How to search for a
> molecule in Pymol database? How to confirm that any particular we have
> built is feasible?
> Eager to hear,
> Regards
> Rajib & Yuktimmana
>
>
> ------------------------------------------------------------------------------
> One dashboard for servers and applications across Physical-Virtual-Cloud
> Widest out-of-the-box monitoring support with 50+ applications
> Performance metrics, stats and reports that give you Actionable Insights
> Deep dive visibility with transaction tracing using APM Insight.
> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
> _______________________________________________
> 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, Dr. Thomas and members,
Is cyclododecene in the database of PyMol? How to search for a
molecule in Pymol database? How to confirm that any particular we have
built is feasible?
Eager to hear,
Regards
Rajib & Yuktimmana

Yes, now know how to build surface.
But it appears that there is very little activity on the forum.
Anyway, thanks.
Regards

On 23/04/2015, bkpsusmitaa <bkp...@gm...> wrote:
> Corrigendum: Are instead of Is in the title/header.
> as the cases could be(to add a comma)
> Apologies for the typos.
> Regards,
> Rajib
>

Hi all

I am trying to ray trace my icosahedram viral capsid, a 75 MB .pse file.
I am running this on a 16 GB windows 64 bit machine with 2 GB NVIDEA GEFORCE graphics.

But the memory still seems to be low as for some reason PyMOL's virtual memory is still low.
I have tried set hash_max but does not make a difference.

Does any one have any suggestions on changing the settings so PyMOL uses the full power of the machine?


Many Thanks
Pavithra Rallapalli, PhD

Hi,

I am using rms_cur for calculating rmsd for two sets of structures. It
works for the first set but for the second one its gives error:
PyMOL>rms_cur sel1,sel2
ExecutiveRMS-Error: No atoms selected.

Here's the result for set1:

PyMOL>select sel1, native and resid 1:53+56:72 and name P and chain M
 Selector: selection "sel1" defined with 0 atoms.
PyMOL>select sel1, native and resid 142:237 and name P and chain M
 Selector: selection "sel1" defined with 95 atoms.
PyMOL>select sel2, best and resid 142:237 and name P and chain B
 Selector: selection "sel2" defined with 95 atoms.
PyMOL>alter all,segi=""
 Alter: modified 10424 atoms.
PyMOL>alter all,chain=""
 Alter: modified 10424 atoms.
PyMOL>rms_cur sel1,sel2
 Executive: RMS =    7.985 (95 to 95 atoms)


============

Here's the result for set2:
PyMOL>select sel1, 1sj3-1_16715 and chain R and name P and resid 764:835
 Selector: selection "sel1" defined with 72 atoms.
PyMOL>select sel2, 1sj3 and chain R and name P and resid 101:172
 Selector: selection "sel2" defined with 72 atoms.
PyMOL>alter all,segi=""
 Alter: modified 6110 atoms.
PyMOL>alter all,chain=""
 Alter: modified 6110 atoms.
PyMOL>rms_cur sel1,sel2
ExecutiveRMS-Error: No atoms selected.
PyMOL>rms_cur sel1,sel2
ExecutiveRMS-Error: No atoms selected.

What is the reason behind this ??


-- 
*Best Regards*
Bharat

Dear All,

     I'm trying to develop a plugin to Pymol. Do you know about an option
to get value of a map (e.g. electron density) at a particular coordinates?
I would like to know sigma value for a particular atom. Is there any way,
using python, to achieve that?

Best regards,
Filip

Hi Wei-Bing,

support to load topology files with the vmd plugins was added in PyMOL 1.7.4 (previous versions only supported trajectories and maps).

Unfortunately, every supported filetype has to be registered in PyMOL, right now only CMS files (Desmond topology) are registered to be passed to the vmd plugin loader. You could of course modify open-source PyMOL yourself to add a filetype, but you have to edit about 5 files!

If you send me example input files (topology and trajectory) I can register their extensions and check it in to the SVN repo.

Cheers,
  Thomas

On 24 Apr 2015, at 06:13, Wei-Bing Zhang <wei...@gm...> wrote:

> Dear all
> 
> Recently, i plan to use the pymol as my main visualize tools.  I have
> complied the latest version successfully and the vmd plugin seems to
> be complied as well at least the stage of build (i did not find these
> during the install ). However, when i open the pymol and i find i
> still can not load some format geometry such as vasp POSCAR which is
> included in vmd pludins. Could you tell me how to enable and use the
> vmd plugin in pymol.
> 
> Best
> 
> Wei-Bing
> 
> -- 
> ----------------------------------------------------------------------
> Dr. Wei-Bing Zhang
> 
> School of Physics and Electronic Sciences
> Changsha University of Science and Technology, Changsha 410004,
> People's Republic of China
> Phone : +86 186 73108538
> E-mail: zh...@cs..., wei...@gm...
> ----------------------------------------------------------------------

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Gary,

MacPyMOL has SpaceNavigator support.

For Linux, check out http://pymolwiki.org/index.php/Spaceball_plugin

Cheers,
  Thomas

On 24 Apr 2015, at 03:17, Gary J. Hunter <gar...@um...> wrote:

> Is there a way to use 3DConnexion's 3D mice in PyMol?
> Specifically, the space navigator, or space mouse?
> There were some postings once upon a time concerning their mice, I wondered if support had been written into PyMol or if anyone knows of plugin support options.
> thanks
> Gary
> 
> 
> -- 
> Prof. Gary J. Hunter,
> 
> Department of Physiology and Biochemistry
> 
> University of Malta, Msida, MSD 2080, Malta.
> 
> phone: +356 2340 2917
> 
> phone: +356 21316655 (secretary),  Fax: +356 21310577
> 
> http://www.um.edu.mt/ms/physbiochem
> 
> There may be confidential information within the contents of this email meant only for the person addressed. This email must not be forwarded to third parties without the express consent of the sender. If you believe you have received this email in error please inform the sender and remove it from your system. 

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear all

Recently, i plan to use the pymol as my main visualize tools.  I have
complied the latest version successfully and the vmd plugin seems to
be complied as well at least the stage of build (i did not find these
during the install ). However, when i open the pymol and i find i
still can not load some format geometry such as vasp POSCAR which is
included in vmd pludins. Could you tell me how to enable and use the
vmd plugin in pymol.

Best

Wei-Bing

-- 
----------------------------------------------------------------------
Dr. Wei-Bing Zhang

School of Physics and Electronic Sciences
Changsha University of Science and Technology, Changsha 410004,
People's Republic of China
Phone : +86 186 73108538
E-mail: zh...@cs..., wei...@gm...
----------------------------------------------------------------------

Is there a way to use 3DConnexion's 3D mice in PyMol?
Specifically, the space navigator, or space mouse?
There were some postings once upon a time concerning their mice, I wondered
if support had been written into PyMol or if anyone knows of plugin support
options.
thanks
Gary


-- 

Prof. Gary J. Hunter,

Department of Physiology and Biochemistry

University of Malta, Msida, MSD 2080, Malta.

phone: +356 2340 2917

phone: +356 21316655 (secretary),  Fax: +356 21310577

http://www.um.edu.mt/ms/physbiochem

There may be confidential information within the contents of this email
meant only for the person addressed. This email must not be forwarded to
third parties without the express consent of the sender. If you believe you
have received this email in error please inform the sender and remove it
from your system.

preset.ball_and_stick('r. STI’)



> On Apr 23, 2015, at 12:52 PM, Brenton Horne <bre...@ym...> wrote:
> 
> Hi, 
> 
> I recently read this reply (http://www.mail-archive.com/pym...@li.../msg13248.html <)" rel="nofollow">http://www.mail-archive.com/pym...@li.../msg13248.html>) to another users' query on this list so I went to the PyMOL Wiki page hyperlinked in the answer and found this piece of code:
> 
> preset.ball_and_stick(selection='all', mode=1)
> set_bond stick_color, white, selection, selection
> set_bond stick_radius, 0.14, selection, selection
> set sphere_scale, 0.25, selection
> show sticks, selection
> show spheres, selection
> 
> I want to customize it such that the selection that is changed in representation from the cartoon style (which is the present style for the macromolecule & I'd like it to stay the representation style for the macromolecule) to ball-and-stick style, is just het ID STI (i.e., the imatinib ligand) in 2HYY. Any ideas of how I might achieve this? 
> 
> Thanks for your time,
> Brenton
> 
> ------------------------------------------------------------------------------
> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
> Develop your own process in accordance with the BPMN 2 standard
> Learn Process modeling best practices with Bonita BPM through live exercises
> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF_______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Hi,

I recently read this reply 
(http://www.mail-archive.com/pym...@li.../msg13248.html) 
to another users' query on this list so I went to the PyMOL Wiki page 
hyperlinked in the answer and found this piece of code:

preset.ball_and_stick(selection='all',  mode=1)
set_bond stick_color,  white,  selection,  selection
set_bond stick_radius,  0.14,  selection,  selection
set  sphere_scale,  0.25,  selection
show sticks,  selection
show spheres,  selection


I want to customize it such that the selection that is changed in 
representation from the cartoon style (which is the present style for 
the macromolecule & I'd like it to stay the representation style for the 
macromolecule) to ball-and-stick style, is just het ID STI (i.e., the 
imatinib ligand) in 2HYY. Any ideas of how I might achieve this?

Thanks for your time,
Brenton

Corrigendum: Are instead of Is in the title/header.
as the cases could be(to add a comma)
Apologies for the typos.
Regards,
Rajib

Dear all,

we just published the Protein-Ligand Interaction Profiler (PLIP), a web 
service and open source command line tool for characterizing and 
visualizing all relevant non-covalent interactions between proteins and 
ligands in PDB structures.

Web Service: _https://projects.biotec.tu-dresden.de/plip-web_
Code: _https://github.com/ssalentin/plip
_Publication: 
_http://nar.oxfordjournals.org/content/early/2015/04/14/nar.gkv315
_
The code is written in Python and makes use of PyMOL for visualization, 
including generation of session files for further processing and 
rendering high-quality images showing the interactions.

Best
Sebastian

-- 
Sebastian Salentin, PhD student
Bioinformatics Group

Technische Universität Dresden
Biotechnology Center (BIOTEC)
Tatzberg 47/49
01307 Dresden, Germany

Hi Rajib & Yuktimmana,

For the question about ball & stick see this page on the wiki:

http://www.pymolwiki.org/index.php/Ball_and_Stick


HTH,
Folmer


2015-04-23 7:41 GMT+02:00 bkpsusmitaa <bkp...@gm...>:

> Hi!
>
> So far we have been able to make only stick models for molecules.
>
> We now wish to build both solid (based on electronic clouds) and Ball
> & stick models.
>
> Can we have several molecules of identical types to build crystal
> structures, amorphous structures or fluide models, as the cases could
> be for specific molecules?
>
> Eager for your inputs.
>
> Rajib & Yuktimmana
>
>
> ------------------------------------------------------------------------------
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> exercises
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-- 
Folmer Fredslund

Hi!

So far we have been able to make only stick models for molecules.

We now wish to build both solid (based on electronic clouds) and Ball
& stick models.

Can we have several molecules of identical types to build crystal
structures, amorphous structures or fluide models, as the cases could
be for specific molecules?

Eager for your inputs.

Rajib & Yuktimmana

Thanks, it was indeed due to the autodock plugin setting retain_order. That
would have taken me quite a while to debug on my own!

-Spencer

On Wed, Apr 22, 2015 at 6:03 PM, Matthew Baumgartner <mp...@pi...> wrote:

> Hi,
>
> I had problems with the retain order setting as well. The autodock vina
> pulgin turns it on. Unload the plugin to fix it, or manually set it
> after plugins are loaded.
>
> Matt
>
> On 4/22/15 8:56 PM, Thomas Holder wrote:
> > Hi Spencer,
> >
> > please check your retain_order setting, it should be off (default). If
> it's on, also check your pymolrc if you're setting it there.
> >
> > http://www.pymolwiki.org/index.php/Retain_order
> > http://www.pymolwiki.org/index.php/Pymolrc
> >
> > Cheers,
> >    Thomas
> >
> > On 22 Apr 2015, at 20:39, Spencer Bliven <sb...@uc...> wrote:
> >
> >> I'm working on a script which involves joining two objects together,
> which I do using the create command. The input objects have different chain
> identifiers, but identical residue numbers. When I create the joined
> object, I would expect all atoms from the first object to be added,
> followed by all atoms from the second object (with atom IDs being unchanged
> for the first object, and then continuing sequentially for the second
> object). Instead, the produced object alternates between atoms of each of
> the input objects:
> >>
> >> PyMOL>iterate joined, print (ID,chain,name)
> >> (0, 'A', 'N')
> >> (1, 'B', 'N')
> >> (2, 'A', 'CA')
> >> (3, 'B', 'CA')
> >> (4, 'A', 'C')
> >> (5, 'B', 'C')
> >> (6, 'A', 'O')
> >> (7, 'B', 'O')
> >> ...
> >>
> >>
> >> This order breaks cartoon and ribbon representations, as well as makes
> the sequence view display each atom individually rather than combining
> residues.
> >>
> >> A somewhat convoluted but reproducible case follows (Using MacPyMOL
> 1.7.4):
> >>
> >> fetch 4rp9, type=pdb1
> >> split_states 4rp9
> >> alter 4rp9_0002, chain = 'B'
> >> create joined, 4rp9_* and resi 282
> >>
> >> I've tried various combinations of the rebuild and sort commands, as
> well as manually changing the IDs of the objects, but I haven't been able
> to find a workaround yet. Sort seems to operate on the resi and ignores the
> ID & chain.
> >>
> >> Is this a bug or am I doing something wrong?
> >>
> >> Thanks,
> >> Spencer
> >
>
>
>
> ------------------------------------------------------------------------------
> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
> Develop your own process in accordance with the BPMN 2 standard
> Learn Process modeling best practices with Bonita BPM through live
> exercises
> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual-
> event?utm_
> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi,

I had problems with the retain order setting as well. The autodock vina 
pulgin turns it on. Unload the plugin to fix it, or manually set it 
after plugins are loaded.

Matt

On 4/22/15 8:56 PM, Thomas Holder wrote:
> Hi Spencer,
>
> please check your retain_order setting, it should be off (default). If it's on, also check your pymolrc if you're setting it there.
>
> http://www.pymolwiki.org/index.php/Retain_order
> http://www.pymolwiki.org/index.php/Pymolrc
>
> Cheers,
>    Thomas
>
> On 22 Apr 2015, at 20:39, Spencer Bliven <sb...@uc...> wrote:
>
>> I'm working on a script which involves joining two objects together, which I do using the create command. The input objects have different chain identifiers, but identical residue numbers. When I create the joined object, I would expect all atoms from the first object to be added, followed by all atoms from the second object (with atom IDs being unchanged for the first object, and then continuing sequentially for the second object). Instead, the produced object alternates between atoms of each of the input objects:
>>
>> PyMOL>iterate joined, print (ID,chain,name)
>> (0, 'A', 'N')
>> (1, 'B', 'N')
>> (2, 'A', 'CA')
>> (3, 'B', 'CA')
>> (4, 'A', 'C')
>> (5, 'B', 'C')
>> (6, 'A', 'O')
>> (7, 'B', 'O')
>> ...
>>
>>
>> This order breaks cartoon and ribbon representations, as well as makes the sequence view display each atom individually rather than combining residues.
>>
>> A somewhat convoluted but reproducible case follows (Using MacPyMOL 1.7.4):
>>
>> fetch 4rp9, type=pdb1
>> split_states 4rp9
>> alter 4rp9_0002, chain = 'B'
>> create joined, 4rp9_* and resi 282
>>
>> I've tried various combinations of the rebuild and sort commands, as well as manually changing the IDs of the objects, but I haven't been able to find a workaround yet. Sort seems to operate on the resi and ignores the ID & chain.
>>
>> Is this a bug or am I doing something wrong?
>>
>> Thanks,
>> Spencer
>