pymol-users Mailing List for PyMOL Molecular Graphics System

I would try the volume visualization tools in PyMOL:
http://pymol.org/volume




Also, you probably want to be careful about "cross-posting" in two
separate forums at the same time...





Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH
 
31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
Office  301-402-0095
Mobile 301-758-3559
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On 5/31/12 9:42 AM, "Bishwa Subedi" <bp...@ut...> wrote:

>Hi all,
>
>I would like to make a figure of my protein-ligand complex for
>publication. I would like to clearly show the density for the ligand in
>the binding cavity. I tried to show it as mesh but the figure is not very
>informative. Can anyone help me with clear steps how to get such
>informative figure with clear density map for the interacting residues
>and with different color for the electron density of ligand.
>
>Any help with coot would also be helpful. (I could not obtain publication
>quality figure with coot in white background, also the representation of
>ball and sticks just for binding residues avoiding other non interacting
>residues were difficult.)
>
>Thanx in advance
>
>Best regards,
>Bishwa
>--------------------------------------------------------------------------
>----
>Live Security Virtual Conference
>Exclusive live event will cover all the ways today's security and
>threat landscape has changed and how IT managers can respond. Discussions
>will include endpoint security, mobile security and the latest in malware
>threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>_______________________________________________
>PyMOL-users mailing list (PyM...@li...)
>Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>Archives: http://www.mail-archive.com/pym...@li...

I found Mike Sawaya's paper to be helpful. 

1.	Mura, C., McCrimmon, C. M., Vertrees, J. & Sawaya, M. R. An introduction to biomolecular graphics. PLoS Comput. Biol. 6, (2010).

F

On May 31, 2012, at 6:42 AM, Bishwa Subedi wrote:

> Hi all,
> 
> I would like to make a figure of my protein-ligand complex for publication. I would like to clearly show the density for the ligand in the binding cavity. I tried to show it as mesh but the figure is not very informative. Can anyone help me with clear steps how to get such informative figure with clear density map for the interacting residues and with different color for the electron density of ligand.
> 
> Any help with coot would also be helpful. (I could not obtain publication quality figure with coot in white background, also the representation of ball and sticks just for binding residues avoiding other non interacting residues were difficult.)
> 
> Thanx in advance
> 
> Best regards,
> Bishwa
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and 
> threat landscape has changed and how IT managers can respond. Discussions 
> will include endpoint security, mobile security and the latest in malware 
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> 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 all,

I would like to make a figure of my protein-ligand complex for publication. I would like to clearly show the density for the ligand in the binding cavity. I tried to show it as mesh but the figure is not very informative. Can anyone help me with clear steps how to get such informative figure with clear density map for the interacting residues and with different color for the electron density of ligand.

Any help with coot would also be helpful. (I could not obtain publication quality figure with coot in white background, also the representation of ball and sticks just for binding residues avoiding other non interacting residues were difficult.)

Thanx in advance

Best regards,
Bishwa

Hi Ritu,

when using the API, you need to quote the text label twice:

cmd.label("chain d and name C1", "'whatever'")

It's a string in a string :)

Cheers,
   Thomas

Rituparna Sengupta wrote, On 05/30/12 22:42:
> Hi,
> 
> Can anyone tell me how to label something using the API. I'm having
> trouble with it and the API usage is not listed in PyMol wiki.
> I use
> 
> label chain d, "whatever"
> 
> from the command line and it works fine. But I want to use it in a
> script. I tried using
> 
> cmd.label("chain d", "whatever")
> 
> but it generates an error; name 'whatever' not defined. Does anyone
> know what I should do? The command I want to use is
> 
> label chain d and name C1, "whatever"
> 
> what is the equivalent of this in API?
> 
> Thanks,
> Ritu

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Hi,

Can anyone tell me how to label something using the API. I'm having trouble with it and the API usage is not listed in PyMol wiki.
I use


label chain d, "whatever"


from the command line and it works fine. But I want to use it in a script. I tried using


cmd.label("chain d", "whatever")


but it generates an error; name 'whatever' not defined. Does anyone know what I should do? The command I want to use is


label chain d and name C1, "whatever"


what is the equivalent of this in API?


Thanks,
Ritu

[[ Notes:

   Colin Walker of F5 is confirmed as our Keynote speaker.
   http://www.f5.com

]]

19th Annual Tcl/Tk Conference (Tcl'2012)
http://www.tcl.tk/community/tcl2012/

November 12 - 16, 2012
Holiday Inn Chicago Mart Plaza
350 West Mart Center Drive
Chicago, Illinois, USA

Important Dates:

Abstracts and proposals due   August    27, 2012
Notification to authors       September 10, 2012
WIP and BOF reservations open August     6, 2012
Author materials due          October   29, 2012
Tutorials Start               November  12, 2012
Conference starts             November  14, 2012

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

Submission of Summaries

Tcl/Tk 2012 will be held in Chicago, Illinois, USA from November 12 -
16, 2012. The program committee is asking for papers and presentation
proposals from anyone using or developing with Tcl/Tk (and
extensions). Past conferences 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 <tclconference AT googlegroups DOT com> no later than August 27,
2012. Authors of accepted abstracts will have until October 29, 2012
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

The authors will have 25 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 6, 2012. Specific instructions for reserving WIP
and BOF time slots will be provided in the registration information
available in June 2012. 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 (http://www.tcl.tk/community/tcl2012/) and will be published on
various Tcl/Tk-related information channels.

To keep in touch with news regarding the conference and Tcl events in
general, subscribe to the tcl-announce list. See:
http://code.activestate.com/lists/tcl-announce to subscribe to the
tcl-announce mailing list.


Conference Committee

Clif Flynt              Noumena Corp					General Chair, Website Admin
Andreas Kupries         ActiveState Software Inc.			Program Chair
Cyndy Lilagan           Nat. Museum of Health & Medicine, Chicago	Site/Facilities Chair
Arjen Markus            Deltares
Brian Griffin           Mentor Graphics
Donal Fellows           University of Manchester
Gerald Lester           KnG Consulting, LLC
Jeffrey Hobbs           ActiveState Software Inc.
Kevin Kenny             GE Global Research Center
Larry Virden
Mike Doyle              National Museum of Health & Medicine, Chicago
Ron Fox                 NSCL/FRIB Michigan State University
Steve Landers           Digital Smarties

Contact Information     tcl...@go...


Tcl'2012 would like to thank those who are sponsoring the conference:

ActiveState Software Inc.
Buonacorsi Foundation
Mentor Graphics
Noumena Corp.
SR Technology
Tcl Community Association

Greetings,

Thomas Holder has a webpage on the PyMOLWiki indicating how he
compiled the plugins
(http://pymolwiki.org/index.php/User:Speleo3/VMD_plugins). I suggest
following these directions if you want to try to get the molfile
plugins working. When I get time, I'll make the appropriate changes
and push the code to the open-source project.

Cheers,

-- Jason

On Mon, May 14, 2012 at 4:36 AM, Marius Retegan
<mar...@gm...> wrote:
> I've reported this last week.
> http://sourceforge.net/tracker/?func=detail&aid=3523770&group_id=4546&atid=104546
> For the moment is not assigned.
>
> Marius
>
> On Mon, May 14, 2012 at 10:22 AM, Boris Kheyfets <khe...@gm...> wrote:
>> I use PyMOL 1.4.1 which I have compiled myself. Now I'd like to switch
>> to the latest version, so I checked out the latest svn, have enabled
>> VMD plugins (and have also increased the fonts). I get the following
>> error during compilation:
>>
>> contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c: In function
>> ‘read_basis_metadata’:
>>
>> contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:208:11:
>> error: ‘molfile_qm_metadata_t’ has no member named ‘have_esp’
>>
>> contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:209:11:
>> error: ‘molfile_qm_metadata_t’ has no member named ‘have_npa’
>>
>> contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:211:11:
>> error: ‘molfile_qm_metadata_t’ has no member named ‘have_internals’
>>
>> error: command 'gcc' failed with exit status 1
>>
>>
>> I attach my setup.py if it can be of any help.
>>
>> With great respect,
>> Boris.
>>
>> ------------------------------------------------------------------------------
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond. Discussions
>> will include endpoint security, mobile security and the latest in malware
>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Greetings Priyadarshan,

We don't really use slerpy anymore because that functionality is
pretty much built into PyMOL itself. To learn how to easily make
movies check out our Incentive Documentation (http://pymol.org/dsc) if
you're a subscriber or the Movie School tutorial on the PyMOLWiki
(http://pymolwiki.org/index.php/MovieSchool) if not. You can do movie
fades with the movie_fades script
(http://www.pymolwiki.org/index.php/Movie_fade) on the wiki as well.

Cheers,

-- Jason

On Wed, May 30, 2012 at 1:04 AM, ccp4 pymol <ccp...@gm...> wrote:
> Hi
>
> This is my first post to pymol-users lists. I have a problem regarding usage
> of slerpy. Firstly i must admit that i have no clue of how to go about using
> it in the first place. I know the pymol wiki has the list of commands but do
> not know how to exploit them in a real case. If someone can suggest any
> tutorial anywhere it will be great. Second i have been trying to
> 'scrossfade' two ligands (crossfade from substrate to product to animate a
> reaction) in the active site of my molecule. The two ligands are show as
> sticks and exist as separate objects. What is the correct way of going about
> doing this using slerpy (is there any other way)? I tried doing scrossfade
> substrate, product-Nothing happens. Can anyone please suggest the way to go
> about doing this?
>
> Best wishes
> Priyadarshan
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hey,

Of course you can also escape the asterisk (just for the record):

remove resn \*\*\*\*

Cheers,

Tsjerk

On Wed, May 30, 2012 at 8:28 AM, Thomas Holder
<sp...@us...> wrote:
> Hi Martin,
>
>> when visualising data out of a GOLD docking run, where the software
>> has added lone pairs to active site residues and ligands is it
>> possible to remove them post hoc in Pymol?  The "atoms" look like:
>>
>> 62 ****        45.6415  30.9229  12.1185 LP             1 <1>
>> 0.0000
>
> the atom_type field after the x/y/z coordinates says "LP", which will be
> loaded as the element symbol into PyMOL. So this should work:
>
> remove elem LP
>
>> in the output .mol2 files so the **** "atom" names are clearly not
>> going to be helpful in a command line situation. For a single ligand
>> pose it's not too bad doing it by hand but for multiple poses of
>> multiple ligands it gets pretty old pretty fast. Usually I just tell
>> people to rerun the docking with the GOLD software told to turn the
>> LPs off but am after a post hoc solution if possible as people can't
>> always get on to our licenses fast enough to repeat jobs.
>>
>> GOLD also puts the extra  protein LPs into the output ligand file,
>> not into a modded protein file. those lines in the output ligand
>> files look like:
>>
>> 52.0949   25.2031   14.8408 LP  0  0  0  0  0  0  0  0  0  0  0  0  #
>> atno 4332 bound_to 4006
>
> this is a SDF file, right? So you can remove by name:
>
> remove name LP
>
> Cheeres,
>   Thomas
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

Hi Martin,

> when visualising data out of a GOLD docking run, where the software
> has added lone pairs to active site residues and ligands is it
> possible to remove them post hoc in Pymol?  The "atoms" look like:
> 
> 62 ****        45.6415  30.9229  12.1185 LP             1 <1>
> 0.0000

the atom_type field after the x/y/z coordinates says "LP", which will be 
loaded as the element symbol into PyMOL. So this should work:

remove elem LP

> in the output .mol2 files so the **** "atom" names are clearly not
> going to be helpful in a command line situation. For a single ligand
> pose it's not too bad doing it by hand but for multiple poses of
> multiple ligands it gets pretty old pretty fast. Usually I just tell
> people to rerun the docking with the GOLD software told to turn the
> LPs off but am after a post hoc solution if possible as people can't
> always get on to our licenses fast enough to repeat jobs.
> 
> GOLD also puts the extra  protein LPs into the output ligand file,
> not into a modded protein file. those lines in the output ligand
> files look like:
> 
> 52.0949   25.2031   14.8408 LP  0  0  0  0  0  0  0  0  0  0  0  0  #
> atno 4332 bound_to 4006

this is a SDF file, right? So you can remove by name:

remove name LP

Cheeres,
   Thomas

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Hi folks,

when visualising data out of a GOLD docking run, where the software has added lone pairs to active site residues and ligands is it possible to remove them post hoc in Pymol?  The "atoms" look like:

     62 ****        45.6415  30.9229  12.1185 LP             1 <1>                0.0000

in the output .mol2 files so the **** "atom" names are clearly not going to be helpful in a command line situation. For a single ligand pose it's not too bad doing it by hand but for multiple poses of multiple ligands it gets pretty old pretty fast. Usually I just tell people to rerun the docking with the GOLD software told to turn the LPs off but am after a post hoc solution if possible as people can't always get on to our licenses fast enough to repeat jobs.

GOLD also puts the extra  protein LPs into the output ligand file, not into a modded protein file. those lines in the output ligand files look like:

   52.0949   25.2031   14.8408 LP  0  0  0  0  0  0  0  0  0  0  0  0  # atno 4332 bound_to 4006


Any ideas? Thanks,
Martin

Hi

This is my first post to pymol-users lists. I have a problem regarding
usage of slerpy. Firstly i must admit that i have no clue of how to go
about using it in the first place. I know the pymol wiki has the list of
commands but do not know how to exploit them in a real case. If someone can
suggest any tutorial anywhere it will be great. Second i have been trying
to 'scrossfade' two ligands (crossfade from substrate to product to animate
a reaction) in the active site of my molecule. The two ligands are show as
sticks and exist as separate objects. What is the correct way of going
about doing this using slerpy (is there any other way)? I tried doing
scrossfade substrate, product-Nothing happens. Can anyone please suggest
the way to go about doing this?

Best wishes
Priyadarshan

Hi Jen,

We need more information before we can try to help.

When you create a session on computer A and try to load it on computer B
the visualization is incorrect, right? Does this also happen when you
create the session on computer B and try to load it on computer A? What
versions of PyMOL are used on each computer? What types of computers are
these? What video cards?

Cheers,

-- Jason

On Fri, May 25, 2012 at 7:36 PM, zwangnju <zwa...@gm...> wrote:

> Greetings!
>
> I have a problem with loading pse (session files) in a different computer
> than the one where the pse was created. I cannot see most of the
> structure,--it appears as if there is too much light...I'm copying the view
> from Pymol. Any idea why this happens? How can I fix it?
>
>
> I've seen many complains about pse files (e.g. takes up a lot of memory),
> but I need to use them a lot just for graphical purposes. For example, if I
> save a Pymol session with a beautiful view for a publication figure, next
> time if I need to change a label etc., I can simply load the session and
> modify it. But is there an alternate way to do this, probably by using
> scripts?
>
> Thanks!!!
> Jen
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Xinghua,

you can install the "psico" module which provides commands for both of 
your tasks:

  * angle_between_helices
  * angle_between_domains

PyMOLWiki page:
http://pymolwiki.org/index.php/Psico

Direct download link:
https://github.com/speleo3/pymol-psico/zipball/master

After having installed psico, read the help pages for both commands:

PyMOL>help angle_between_helices
PyMOL>help angle_between_domains

An older version of the "angle_between_helices" command is also 
available as a separate script:
http://pymolwiki.org/index.php/AngleBetweenHelices

Cheers,
   Thomas

On 05/29/2012 04:45 AM, Xinghua Qin wrote:
> hi,
> how do I calculate the rotation angle of a certain helix in structures
> with different ATP analogues?
> and how if it is a domain ?
> Best wishes
> Xinghua Qin
>
> --
> Xinghua Qin
> State Key Laboratory of Plant Physiology and biochemistry
> College of Biological Sciences
> China Agricultural University
> No.2, Yuan Ming Yuan West Road
> Haidian District, Beijing, China 100193
> Tel: +86-10-62732672
> E-mail: xin...@12...

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

hi,
how do I calculate the rotation angle of a certain helix  in structures with different ATP analogues?
and how if it is a domain ?
 
Best wishes
Xinghua Qin


--
Xinghua Qin
State Key Laboratory of Plant Physiology and biochemistry 
College of Biological Sciences
China Agricultural University
No.2, Yuan Ming Yuan West Road
Haidian District, Beijing, China 100193
Tel: +86-10-62732672
E-mail: xin...@12...

Hi,

You can use get_raw_distances script
http://pymolwiki.org/index.php/Get_raw_distances

Best regards,

Takanori Nakane

Hi,

I am examining electrostatic interactions between residues of two different
molecules, based on a large number of models generated. I have distance
objects created between proximal basic and acidic side chains, but because
of the number of models and amount of interactions per model, recording the
particular donor and acceptor atoms and corresponding distance between them
isn't very feasible to do manually. How would I go about exporting the
atoms and corresponding distances of a distance object in text? I did find
the following message...

http://www.mail-archive.com/pym...@li.../msg05072.html

But that would require manually entering each atom of each interaction of
each model.

Thank you,
Spencer

Greetings!

I have a problem with loading pse (session files) in a different computer
than the one where the pse was created. I cannot see most of the
structure,--it appears as if there is too much light...I'm copying the view
from Pymol. Any idea why this happens? How can I fix it?


I've seen many complains about pse files (e.g. takes up a lot of memory),
but I need to use them a lot just for graphical purposes. For example, if I
save a Pymol session with a beautiful view for a publication figure, next
time if I need to change a label etc., I can simply load the session and
modify it. But is there an alternate way to do this, probably by using
scripts?

Thanks!!!
Jen

regarding CONECT records and whether to use them, try:

set connect_mode, 1
load youfile.pdb

See also:
http://www.pymolwiki.org/index.php/Connect_mode
http://www.mail-archive.com/pym...@li.../msg10413.html

Cheers,
   Thomas

Nat Echols wrote, On 05/23/12 20:01:
> On Wed, May 23, 2012 at 10:20 AM, Rituparna Sengupta <rse...@wi...> wrote:
>> Sorry about the lack of description in the previous post.
>> The chemicals show incorrect bond connections. Some of the rings go missing. In all, the structure changes and just by looking at it, its possible to tell that the structure is not right. I didn't see much details though, except that the atom connections seem to be wrong.
> 
> A screenshot would be helpful here, but my guess is that PyMOL's
> automatic detection of bond's didn't work for your input structure.
> This can happen for non-standard chemistries or distorted geometries;
> the most frequent artifact is more bonds than are appropriate.  The
> reason it happens is that instead of applying some chemically sensible
> rules and/or prior knowledge to determine bonding (which would be
> relatively slow), PyMOL simply bonds every atom pair within some
> radius (probably excluding certain obvious cases, although I'm not
> sure).  This is very fast, simple, and easily confused.
> 
> I thought perhaps PyMOL can understand CONECT records in the PDB file
> - adding these might fix your problem, although I'm not sure how to
> generate them.  Alternately, you can use the 'bond' and 'unbond'
> commands, but this can be non-trivial to do on a large scale.
> 
> -Nat

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Thanks kpwu. That's the secret! I did not know that I could do that!

DMS
On May 23, 2012, at 8:37 PM, homespuner wrote:

> Hello DMS,
> 
> I think you have to do 3 steps like:
> 
> select all_A, resn A
> set cartoon_ring_color, red, all_A
> color red, all_A
> 
> and then do other 3 groups in the same way.
> 
> It works for me to show different colors for different types of nucleotides while the color of "ring and bond" in "single" nucleotide is same.
> 
> kpwu
> 
> On Wed, May 23, 2012 at 7:26 PM, Daron Standley <sta...@if...> wrote:
> Thank you Jason,
> 
> Actually this is exactly where I got stuck. With the commands below, each of the
> bases is colored differently *except* the center of the ring, which is set to a
> constant value (green in this case).  What I'm wanting is to have each base
> appear as a single solid color.
> 
> DMS
> 
> On May 23, 2012, at 2:16 PM, Jason Vertrees wrote:
> 
> > Hi DMS,
> >
> > fetch 3r8t, async=0
> > as cartoon
> >
> > set cartoon_ring_mode, 3
> >
> > set cartoon_nucleic_acid_color, magenta
> >
> > # use 'resn' and the one letter nucleotide codes
> >
> > color blue, resn A
> > color green, resn C
> > color yellow, resn T+U
> > color orange, resn G
> >
> > Cheers,
> >
> > -- Jason
> >
> > On Wed, May 23, 2012 at 12:44 PM, Daron Standley
> > <sta...@if...> wrote:
> >> Hi. I want to make a figure of an RNA molecules similar to the DNA
> >> molecule shown here:
> >>
> >> http://kpwu.files.wordpress.com/2011/07/2l8q-cartoon-ring-v1.png
> >>
> >> However, I want each nucleotide type (A,T/U,G,C) colored differently. I
> >> managed to get everything but the center of the ring colored the way I wanted.
> >> I can set the "cartoon_ring_color" to a given color but I don't know how
> >> to give each nucleotide its own ring color.  Can anyone help?
> >>
> >> Thanks
> >>
> >> DMS
> >> ------------------------------------------------------------------------------
> >> Live Security Virtual Conference
> >> Exclusive live event will cover all the ways today's security and
> >> threat landscape has changed and how IT managers can respond. Discussions
> >> will include endpoint security, mobile security and the latest in malware
> >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> >> _______________________________________________
> >> PyMOL-users mailing list (PyM...@li...)
> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> Archives: http://www.mail-archive.com/pym...@li...
> >
> >
> >
> > --
> > Jason Vertrees, PhD
> > PyMOL Product Manager
> > Schrödinger, LLC
> >
> > (e) Jas...@sc...
> > (o) +1 (603) 374-7120
> 
> 
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> 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 DMS,

I think you have to do 3 steps like:

select all_A, resn A
set cartoon_ring_color, red, all_A
color red, all_A

and then do other 3 groups in the same way.

It works for me to show different colors for different types of nucleotides
while the color of "ring and bond" in "single" nucleotide is same.

kpwu

On Wed, May 23, 2012 at 7:26 PM, Daron Standley <
sta...@if...> wrote:

> Thank you Jason,
>
> Actually this is exactly where I got stuck. With the commands below, each
> of the
> bases is colored differently *except* the center of the ring, which is set
> to a
> constant value (green in this case).  What I'm wanting is to have each base
> appear as a single solid color.
>
> DMS
>
> On May 23, 2012, at 2:16 PM, Jason Vertrees wrote:
>
> > Hi DMS,
> >
> > fetch 3r8t, async=0
> > as cartoon
> >
> > set cartoon_ring_mode, 3
> >
> > set cartoon_nucleic_acid_color, magenta
> >
> > # use 'resn' and the one letter nucleotide codes
> >
> > color blue, resn A
> > color green, resn C
> > color yellow, resn T+U
> > color orange, resn G
> >
> > Cheers,
> >
> > -- Jason
> >
> > On Wed, May 23, 2012 at 12:44 PM, Daron Standley
> > <sta...@if...> wrote:
> >> Hi. I want to make a figure of an RNA molecules similar to the DNA
> >> molecule shown here:
> >>
> >> http://kpwu.files.wordpress.com/2011/07/2l8q-cartoon-ring-v1.png
> >>
> >> However, I want each nucleotide type (A,T/U,G,C) colored differently. I
> >> managed to get everything but the center of the ring colored the way I
> wanted.
> >> I can set the "cartoon_ring_color" to a given color but I don't know how
> >> to give each nucleotide its own ring color.  Can anyone help?
> >>
> >> Thanks
> >>
> >> DMS
> >>
> ------------------------------------------------------------------------------
> >> Live Security Virtual Conference
> >> Exclusive live event will cover all the ways today's security and
> >> threat landscape has changed and how IT managers can respond.
> Discussions
> >> will include endpoint security, mobile security and the latest in
> malware
> >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> >> _______________________________________________
> >> PyMOL-users mailing list (PyM...@li...)
> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> Archives: http://www.mail-archive.com/pym...@li...
> >
> >
> >
> > --
> > Jason Vertrees, PhD
> > PyMOL Product Manager
> > Schrödinger, LLC
> >
> > (e) Jas...@sc...
> > (o) +1 (603) 374-7120
>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Thank you Jason,

Actually this is exactly where I got stuck. With the commands below, each of the 
bases is colored differently *except* the center of the ring, which is set to a
constant value (green in this case).  What I'm wanting is to have each base 
appear as a single solid color.

DMS

On May 23, 2012, at 2:16 PM, Jason Vertrees wrote:

> Hi DMS,
> 
> fetch 3r8t, async=0
> as cartoon
> 
> set cartoon_ring_mode, 3
> 
> set cartoon_nucleic_acid_color, magenta
> 
> # use 'resn' and the one letter nucleotide codes
> 
> color blue, resn A
> color green, resn C
> color yellow, resn T+U
> color orange, resn G
> 
> Cheers,
> 
> -- Jason
> 
> On Wed, May 23, 2012 at 12:44 PM, Daron Standley
> <sta...@if...> wrote:
>> Hi. I want to make a figure of an RNA molecules similar to the DNA
>> molecule shown here:
>> 
>> http://kpwu.files.wordpress.com/2011/07/2l8q-cartoon-ring-v1.png
>> 
>> However, I want each nucleotide type (A,T/U,G,C) colored differently. I
>> managed to get everything but the center of the ring colored the way I wanted.
>> I can set the "cartoon_ring_color" to a given color but I don't know how
>> to give each nucleotide its own ring color.  Can anyone help?
>> 
>> Thanks
>> 
>> DMS
>> ------------------------------------------------------------------------------
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond. Discussions
>> will include endpoint security, mobile security and the latest in malware
>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
> 
> 
> 
> -- 
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrödinger, LLC
> 
> (e) Jas...@sc...
> (o) +1 (603) 374-7120

Hi DMS,

fetch 3r8t, async=0
as cartoon

set cartoon_ring_mode, 3

set cartoon_nucleic_acid_color, magenta

# use 'resn' and the one letter nucleotide codes

color blue, resn A
color green, resn C
color yellow, resn T+U
color orange, resn G

Cheers,

-- Jason

On Wed, May 23, 2012 at 12:44 PM, Daron Standley
<sta...@if...> wrote:
> Hi. I want to make a figure of an RNA molecules similar to the DNA
> molecule shown here:
>
> http://kpwu.files.wordpress.com/2011/07/2l8q-cartoon-ring-v1.png
>
> However, I want each nucleotide type (A,T/U,G,C) colored differently. I
> managed to get everything but the center of the ring colored the way I wanted.
> I can set the "cartoon_ring_color" to a given color but I don't know how
> to give each nucleotide its own ring color.  Can anyone help?
>
> Thanks
>
> DMS
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Ritu,

 

just an idea. It could be that your PDB files contains CONECT records
for your ligands. Those bonds are defined by atom number or atom index I
believe. There could be a conflict between the different files you are
loading. Try stripping the CONECT records and see if that helps.

 

HTH 

 

Carsten 

 

From: Folmer Fredslund [mailto:fo...@gm...] 
Sent: Wednesday, May 23, 2012 1:53 PM
To: Rituparna Sengupta
Cc: PyMol Users Mailing List
Subject: Re: [PyMOL] Messed up structures in movie

 

Hi again Ritu,

This does seem odd. I have no idea what might be wrong, but could you
provide an example pdb, or a png of the output you see?

I would personally try to strip all extra information from the ligand
pdb (so only ATOM and HETATM records is included) and then try loading
that pdb.

Best regards,
Folmer

2012/5/23 Rituparna Sengupta <rse...@wi...>

Hi,

Sorry about the lack of description in the previous post.
The chemicals show incorrect bond connections. Some of the rings go
missing. In all, the structure changes and just by looking at it, its
possible to tell that the structure is not right. I didn't see much
details though, except that the atom connections seem to be wrong.


Thanks,
Ritu

On 05/23/12, Folmer Fredslund

 wrote:
> Hi Ritu,
>
> Could you elaborate on "some of the ligand structures get completely
messed up when viewed as sticks or lines"?
>
> To get the best possible answer a few more details would help.
>
> Best regards,
> Folmer
>

> 2012/5/23 Rituparna Sengupta <PyM...@li...
<rse...@wi...')" target="1">rse...@wi...>
>
> > Hi,
> >
> > Just observed something weird. When I try loading protein -ligand
complexes as frames of a movie (same protein but different ligands for
different frames), some of the ligand structures get completely messed
up when viewed as sticks or lines. Right now I&#39;m using spheres
instead, but wondering if there&#39;s a way to work around the problem
and still view the ligands as sticks/lines.

> >
> >
> > Thanks,
> > Ritu
> >
> >
------------------------------------------------------------------------
------
> > Live Security Virtual Conference

> > Exclusive live event will cover all the ways today&#39;s security
and

> > threat landscape has changed and how IT managers can respond.
Discussions
> > will include endpoint security, mobile security and the latest in
malware
> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> > _______________________________________________

> > PyMOL-users mailing list
(https://lists.sourceforge.net/lists/listinfo/pymol-users(javascript:mai
n.compose('new
<https://lists.sourceforge.net/lists/listinfo/pymol-users%28javascript:m
ain.compose%28%27new> ', 't=P...@li...>)
> > Info Page: <a href=)

> > Archives:
http://www.mail-archive.com/pym...@li...
> >
>
>
>
>
> --
> Folmer Fredslund

------------------------------------------------------------------------
------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond.
Discussions
will include endpoint security, mobile security and the latest in
malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
PyMOL-users mailing list (PyM...@li...)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pym...@li...




-- 
Folmer Fredslund

On Wed, May 23, 2012 at 10:20 AM, Rituparna Sengupta <rse...@wi...> wrote:
> Sorry about the lack of description in the previous post.
> The chemicals show incorrect bond connections. Some of the rings go missing. In all, the structure changes and just by looking at it, its possible to tell that the structure is not right. I didn't see much details though, except that the atom connections seem to be wrong.

A screenshot would be helpful here, but my guess is that PyMOL's
automatic detection of bond's didn't work for your input structure.
This can happen for non-standard chemistries or distorted geometries;
the most frequent artifact is more bonds than are appropriate.  The
reason it happens is that instead of applying some chemically sensible
rules and/or prior knowledge to determine bonding (which would be
relatively slow), PyMOL simply bonds every atom pair within some
radius (probably excluding certain obvious cases, although I'm not
sure).  This is very fast, simple, and easily confused.

I thought perhaps PyMOL can understand CONECT records in the PDB file
- adding these might fix your problem, although I'm not sure how to
generate them.  Alternately, you can use the 'bond' and 'unbond'
commands, but this can be non-trivial to do on a large scale.

-Nat