pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] MacPyMOL 0.99beta29

[Warren D. <wa...@de...>]

MacPyMOL Users,

For those experiencing performance and/or flicker issues under 10.4.3,
please update to 0.99Beta29 -- this should be the fastest, most stable
MacPyMOL to date (~2-4X faster than betas 26-28).

http://delsci.com/beta

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20

Re: [PyMOL] Superimpose

[Joel T. <joe...@ot...>]

Hi Michael,

I notiuced no-one has posted anything so here goes.

Start with
 align 1abc, 1target
which will superimpose 1abc onto 1target
then from here you can select the non homologous regions (using display 
sequence and highlight from here and colour to your hearts content. I'm 
sure there are other ways to do this but this is one way!

Cheers

J

Michael Morbious wrote:

>Hi everyone,
>I have two similar (closely related) multi-chain
>structures. I want to merge them and highlight the
>regions that do not superimpose. However, I do not
>know how to superimpose these two structures and how
>to select non-intersecting residues. 
>Any help will be appreciated.
>Thanks.  
>
>
>		
>__________________________________ 
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>

-- 
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand                     

Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
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Aotearoa

Ph / Waea               +64 3 4797293 
Fax / Waeawhakaahua     +64 3 4797034

RE: [PyMOL] dna ladders

[Warren D. <wa...@de...>]

Mark,

One of the great things about PyMOL is that you get the code right away.
One of the worst things about it is that you get the code long before
any documentation exists.  Most of that code is new or overhauled as of
yesterday.

Here are some things to try:

set cartoon_ring_mode, 1 (or 2 or 3)
set cartoon_ring_finder, 1 (or 2 or 3 or 4)
set nucleic_acid_mode, 0 (or 1 or 2 or 3 or 4)

set cartoon_side_chain_helper
rebuild

set cartoon_ring_transparency, 0.5

set cartoon_ladder_mode, 0 or 1

set cartoon_ladder_color, color-name
set cartoon_nucleic_acid_color, color-name

cartoon oval
set cartoon_oval_width, 0.8

cartoon rect

cartoon dumbbell
set cartoon_dumbbell_width, 0.4
set cartoon_dumbbell_radius, 0.4

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Mark Wilke
> Sent: Monday, November 07, 2005 3:28 PM
> To: pym...@li...
> Subject: [PyMOL] dna ladders
>=20
> How do I get the dna backbone (currently represented as a=20
> tube) be represented as a fancy helix like in the picture on=20
> the pymol website?
>=20
> - Mark
>=20
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App=20
> Server. Download it for free - -and be entered to win a 42"=20
> plasma tv or your very own Sony(tm)PSP.  Click here to play:=20
> http://sourceforge.net/geronimo.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

Re: [PyMOL] Viewing cavities?

[Andrea S. <and...@gm...>]

what about Caver:
http://loschmidt.chemi.muni.cz/caver/concept.php
very nice and it works very well

andrea

2005/11/7, Bingding Huang <bh...@bi...>:
>
> Dear  all,
>
> I download CASTpyMOL.pyc and put it in the right folder.
> Now I want to use it for detecting cavity for 50 proteins. I don't want
> to  do that one after one by hand.
> Is it possible to write a python (pymol) script to do that automatically?
>
> Thanks a lot!
>
> Regards
> Bingding
>
>
>
>
>
> Sebastien Moretti wrote:
>
> Dear Bingding,
> CASTp cavities are pre-computed for most of PDB entries.
>
> So, you could create a PyMOL script (.pml) which could look like that:
>     "call the CASTp plugin for xxxx" ?
>     save xxxx.pdb
>     reinitialize
>     "call the CASTp plugin for yyyy" ?
>     ...
>
> With this kind of script you could be able to get the cavities for your
> 50 proteins with only one PyMOL execution.
> Nevertheless, I don't know how to call the CASTp plugin from a PyMOL
> script. And how to save all cavities as distinct pdb files.
> But I know that that is possible.
>
> Only the PyMOL mailing list or Wiki are able to help you now.
>
>
> >
> > Hi Marcus,
> > You can install the CASTp plugin for PyMOL :
> > http://cast.engr.uic.edu/cast/?mode=3DCASTpyMOL
> >
> > CASTp (http://cast.engr.uic.edu/cast/) is "Computed Atlas of Surface
> > Topography of proteins" and analyzes the "Anatomy of Protein Pockets
> > and Cavities".
> > So, with the plugin, you can get every cavities (pockets), CASTp has
> > predicted, automatically.
> >
> > I hope this will help you.
> >
> >>> Hello all,
> >>>
> >>> The surface rendering in PyMOL is quite nice, but I cannot separate
> >>> the "branches" of the surface.  That is, I would like to view a
> >>> large cavity inside of a protein independently from the outer,
> >>> solvent accessible surface.  Is anyone aware of a means to do this?
> >>>
> >>> Marcus Collins
> >>>
> >>> *********************************************************************=
********
> >>>
> >>>                               Marcus D. Collins
> >>>      Gruner Biophysics Group, Cornell University Dept. of Physics,
> >>> LASSP
> >>>              (h) 607.347.4720 (w) 607.255.8678 (c) 607.351.8650
> >>>        "You have opened a new door, and I share this with you,
> >>>             for I have been where you are now."
> >>> *********************************************************************=
********
> >>
> >>
> >
>
>
> --
> Bingding Huang
> PhD student
> Bioinformatics group
> Biotec & Department of Computing
> Tazberg 47, 01307
> TU Dresden, Germany
>
> Tel:    0049 351 46340064 (Office)
> Tel:    0049 351 4403368  (Home)
> Fax:    0049 351 46340061
> Web:    http://www.biotec.tu-dresden.de/~bhuang
> E-mail: bh...@bi...
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server. Downl=
oad
> it for free - -and be entered to win a 42" plasma tv or your very own
> Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


--
"La conoscenza libera il genere umano dalla superstizione"
J. Watson

[PyMOL] dna ladders

[Mark W. <mw...@in...>]

How do I get the dna backbone (currently represented as a tube) be
represented as a fancy helix like in the picture on the pymol website?

- Mark

[PyMOL] v0.99beta - dna ladder representation

[Mark W. <mw...@in...>]

I'm trying out the new beta version of PyMOL to make a figure with a DNA
ladder cartoon.  I was wondering if there is a setting for connecting the
two DNA strands with a single bar instead of two short bars that don't
quite connect and are not parallel.  I don't need the DNA to be accurate
just look pretty. 

Also, what are the various settings for altering the dna ladder cartoon?

- Mark

Re: [PyMOL] Viewing cavities?

[Bingding H. <bh...@bi...>]

Dear  all,

I download CASTpyMOL.pyc and put it in the right folder.
Now I want to use it for detecting cavity for 50 proteins. I don't want 
to  do that one after one by hand.
Is it possible to write a python (pymol) script to do that automatically?

Thanks a lot!

Regards
Bingding





Sebastien Moretti wrote:

Dear Bingding,
CASTp cavities are pre-computed for most of PDB entries.

So, you could create a PyMOL script (.pml) which could look like that:
    "call the CASTp plugin for xxxx" ?
    save xxxx.pdb
    reinitialize
    "call the CASTp plugin for yyyy" ?
    ...

With this kind of script you could be able to get the cavities for your 
50 proteins with only one PyMOL execution.
Nevertheless, I don't know how to call the CASTp plugin from a PyMOL 
script. And how to save all cavities as distinct pdb files.
But I know that that is possible.

Only the PyMOL mailing list or Wiki are able to help you now.


>
> Hi Marcus,
> You can install the CASTp plugin for PyMOL :
> http://cast.engr.uic.edu/cast/?mode=CASTpyMOL
>
> CASTp (http://cast.engr.uic.edu/cast/) is "Computed Atlas of Surface 
> Topography of proteins" and analyzes the "Anatomy of Protein Pockets 
> and Cavities".
> So, with the plugin, you can get every cavities (pockets), CASTp has 
> predicted, automatically.
>
> I hope this will help you.
>
>>> Hello all,
>>>
>>> The surface rendering in PyMOL is quite nice, but I cannot separate 
>>> the "branches" of the surface.  That is, I would like to view a 
>>> large cavity inside of a protein independently from the outer, 
>>> solvent accessible surface.  Is anyone aware of a means to do this?
>>>
>>> Marcus Collins
>>>
>>> ***************************************************************************** 
>>>
>>>                               Marcus D. Collins
>>>      Gruner Biophysics Group, Cornell University Dept. of Physics, 
>>> LASSP
>>>              (h) 607.347.4720 (w) 607.255.8678 (c) 607.351.8650
>>>        "You have opened a new door, and I share this with you,
>>>             for I have been where you are now."
>>> ***************************************************************************** 
>>
>>
>


-- 
Bingding Huang
PhD student
Bioinformatics group
Biotec & Department of Computing
Tazberg 47, 01307
TU Dresden, Germany

Tel:    0049 351 46340064 (Office)
Tel:    0049 351 4403368  (Home)
Fax:    0049 351 46340061
Web:    http://www.biotec.tu-dresden.de/~bhuang
E-mail: bh...@bi...

Re: [PyMOL] Mac Flicker Issue Workaround

[Dirk K. <dir...@ps...>]

Hi Warren,

the new version works fine without flicker on my iBook,1.2 GHz G4,  
ATI Mobility Radeon 9200 with 32 MB.

Thanks a lot!

Cheers,

Dirk.

Am 06.11.2005 um 04:32 schrieb Warren DeLano:

> Mac users:
>
> We lucked out and obtained a little help from an off-duty Apple  
> engineer
> today who figured out how to work around the issue in 10.4.3.  It was
> one of these combined bugs -- we weren't doing things sensibly in  
> PyMOL,
> and the ATI driver wasn't quite complying with normal OpenGL behavior
> with respect to screen updates.
>
> They changes seem to have done the trick, so I have posted an updated
> MacPyMOL build at:
>
> http://delsci.com/beta
>
> Please let me know if this does NOT solve the issue on your machine.
> Also, since I had to change the lighting and draw-buffer code, please
> let me know right away if anything strange or new surfaces.
>
> Cheers,
> Warren
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942  Tech:(650)-872-0834
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:wa...@de...
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server.  
> Download
> it for free - -and be entered to win a 42" plasma tv or your very own
> Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
> _______________________________________________
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> PyM...@li...
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****************************************
Dirk Kostrewa
Paul Scherrer Institut
Life Sciences, OFLC/110
CH-5232 Villigen PSI, Switzerland
Phone:     +41-56-310-4722
Fax:     +41-56-310-5288
E-mail:    dir...@ps...
http://sb.web.psi.ch
****************************************

Re: [PyMOL] Mac Flicker Issue Workaround

[Jianghai Z. <zh...@pu...>]

The new beta works fine on my new Powerbook now.  No flickering anymore.
Thanks.

On Nov 5, 2005, at 11:33 PM, Warren DeLano wrote:

> Hmm...
>
> Working now.
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942  Tech:(650)-872-0834
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:wa...@de...
>
>
>> -----Original Message-----
>> From: Jianghai Zhu [mailto:zh...@pu...]
>> Sent: Saturday, November 05, 2005 7:49 PM
>> To: Warren DeLano
>> Subject: Re: [PyMOL] Mac Flicker Issue Workaround
>>
>> I have problem to uncompress the data.  Anybody has the same problem?
>>
>>
>> On Nov 5, 2005, at 10:32 PM, Warren DeLano wrote:
>>
>>> Mac users:
>>>
>>> We lucked out and obtained a little help from an off-duty Apple
>>> engineer today who figured out how to work around the issue
>> in 10.4.3.
>>> It was one of these combined bugs -- we weren't doing
>> things sensibly
>>> in PyMOL, and the ATI driver wasn't quite complying with
>> normal OpenGL
>>> behavior with respect to screen updates.
>>>
>>> They changes seem to have done the trick, so I have posted
>> an updated
>>> MacPyMOL build at:
>>>
>>> http://delsci.com/beta
>>>
>>> Please let me know if this does NOT solve the issue on your machine.
>>> Also, since I had to change the lighting and draw-buffer
>> code, please
>>> let me know right away if anything strange or new surfaces.
>>>
>>> Cheers,
>>> Warren
>>>
>>> --
>>> Warren L. DeLano, Ph.D.
>>> Principal Scientist
>>>
>>> . DeLano Scientific LLC
>>> . 400 Oyster Point Blvd., Suite 213
>>> . South San Francisco, CA 94080 USA
>>> . Biz:(650)-872-0942  Tech:(650)-872-0834 . Fax:(650)-872-0273
>>> Cell:(650)-346-1154 . mailto:wa...@de...
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> SF.Net email is sponsored by:
>>> Tame your development challenges with Apache's Geronimo App
>> Server.
>>> Download
>>> it for free - -and be entered to win a 42" plasma tv or
>> your very own
>>> Sony(tm)PSP.  Click here to play:
>> http://sourceforge.net/geronimo.php
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> PyM...@li...
>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>
>>
>>
>>
>>
>>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server.  
> Download
> it for free - -and be entered to win a 42" plasma tv or your very own
> Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

[PyMOL] pymol -M ?

[William S. <wg...@ch...>]

Hi Mark:

I just tried the command with -M and it didn't help, but for the  
record, you can use


/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL


or if you are a nerd, you might prefer this shell script, which you  
can call pymol and put in your $path array.  It finds wherever you  
put it, figures out what version you are using, launches it, and puts  
the word pymol in your titlebar or tab of the terminal (or iTerm),  
and whines appropriately if it doesn't work:


#!/bin/zsh -f
getargs=("$@")

if [[ -x /usr/bin/mdfind ]];then
     pymolprefix=($( mdfind MacPyMOL | grep MacPyMOL.app | head -1  ))
else
     pymolprefix=($( locate MacPyMOL.app | head -1 ))
fi

if [[ -x $pymolprefix/Contents/MacOS/PyMOL ]];then
     pymolexec=($pymolprefix/Contents/MacOS/PyMOL)
elif [[ -x $pymolprefix/Contents/MacOS/MacPyMOL ]];then
     pymolexec=($pymolprefix/Contents/MacOS/MacPyMOL)
else
     pymolexec=""
fi


pymolparser=($pymolprefix/pymol/modules/pymol/parser.py )

if [[ -z $pymolprefix ]];then
     print "Can\'t locate MacPyMol in locatedatabase"
     print "If you have MacPyMol, issue sudo /etc/weekly to get this  
to work"
     print "Trying now with X-windows based version..."
     pymolexec='command pymol'
fi

natpymol () {

         $pymolexec -q $getargs
}

# function to settab to show pymol running and then reset with settab

function pymoltab {
     echo -ne "\e]1; pymol \a"; natpymol; settab
}

pymoltab


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


Hope NYC is treating you well.



Bill

RE: [PyMOL] Mac Flicker Issue Workaround

[Warren D. <wa...@de...>]

Hmm...

Working now.

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: Jianghai Zhu [mailto:zh...@pu...]=20
> Sent: Saturday, November 05, 2005 7:49 PM
> To: Warren DeLano
> Subject: Re: [PyMOL] Mac Flicker Issue Workaround
>=20
> I have problem to uncompress the data.  Anybody has the same problem?
>=20
>=20
> On Nov 5, 2005, at 10:32 PM, Warren DeLano wrote:
>=20
> > Mac users:
> >
> > We lucked out and obtained a little help from an off-duty Apple=20
> > engineer today who figured out how to work around the issue=20
> in 10.4.3. =20
> > It was one of these combined bugs -- we weren't doing=20
> things sensibly=20
> > in PyMOL, and the ATI driver wasn't quite complying with=20
> normal OpenGL=20
> > behavior with respect to screen updates.
> >
> > They changes seem to have done the trick, so I have posted=20
> an updated=20
> > MacPyMOL build at:
> >
> > http://delsci.com/beta
> >
> > Please let me know if this does NOT solve the issue on your machine.
> > Also, since I had to change the lighting and draw-buffer=20
> code, please=20
> > let me know right away if anything strange or new surfaces.
> >
> > Cheers,
> > Warren
> >
> > --
> > Warren L. DeLano, Ph.D.
> > Principal Scientist
> >
> > . DeLano Scientific LLC
> > . 400 Oyster Point Blvd., Suite 213
> > . South San Francisco, CA 94080 USA
> > . Biz:(650)-872-0942  Tech:(650)-872-0834 . Fax:(650)-872-0273 =20
> > Cell:(650)-346-1154 . mailto:wa...@de...
> >
> >
> >
> > -------------------------------------------------------
> > SF.Net email is sponsored by:
> > Tame your development challenges with Apache's Geronimo App=20
> Server. =20
> > Download
> > it for free - -and be entered to win a 42" plasma tv or=20
> your very own=20
> > Sony(tm)PSP.  Click here to play:=20
> http://sourceforge.net/geronimo.php
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
>=20
>=20
>=20
>=20
>=20

RE: [PyMOL] Discreet cartoon representation for overlapping secondary structure ?

[Warren D. <wa...@de...>]

Indraneel,

PyMOL's cartoon generation code is some of the worst "production" code I
have ever written in my life.  It consists of one huge 2,000 line
function with numerous one or two-letter variables and all kinds of
implicit assumptions about the linear structure of the protein and the
discrete nature of secondary structure elements.  It would requires
tremendous effort to make changes to it safely, and as such, it serves
as a classic example of how NOT to write important code.
[layer2/RepCartoon.c, RepCartoonNew()]

My only defense for that mess it is that it has performed
extraordinarily well over a period of years with all kinds of
structures, from small peptides up to million-atom virus particles.
Despite is ugliness, is fast, stable, and functional.
=20
Eventually it will be overhauled and we'll probably switch over nicer
looking to Bezier curves at that point -- but until then, I am loath to
make any significant modifications to it.  Since PyMOL is open-source
you are welcome to try, but I think your time would be better spent
constructing an alternate implementation that meets your specific needs.


Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Indraneel Majumdar
> Sent: Saturday, November 05, 2005 7:29 PM
> To: pym...@li...
> Cc: Warren DeLano
> Subject: [PyMOL] Discreet cartoon representation for=20
> overlapping secondary structure ?
>=20
> Hi,
>=20
> Is changing cartoon representation a major work? My program=20
> PALSSE defines overlapping Secondary Structural Elements and=20
> it would be nice if I could see cartoons without having=20
> consecutive elements merged.
>=20
> It is technically possible for consecutive helices or=20
> consecutive strands or helices and strands to have upto 2=20
> common residues.
>=20
> I was wondering if the start and ends could somehow be=20
> distinguished, eg. by changing or adding another "more_fancy"=20
> option to not remove the head arrow of any SSE (also add=20
> arrow to helices) and modify the base of all SSE so they are=20
> visible at all times (probably show the base as a circle?).=20
> The SS merge feature would probably have to be switched off=20
> before this though.
>=20
> Which is the best place to start modifications?
>=20
> An example arrow:
>=20
>     __                  *
>   *    *                *  *
>  *      *****************    *
>  *                             *
>  *      *****************    *
>   * __ *                *  *
>                         *
>=20
>  1      2               3      4
>=20
> The head should be visible even if 1-2 overlaps on 3-4.
>=20
>=20
> Thanks,
> Indraneel
>=20
> --
> http://prodata.swmed.edu
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App=20
> Server. Download
> it for free - -and be entered to win a 42" plasma tv or your very own
> Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

[PyMOL] Mac Flicker Issue Workaround

[Warren D. <wa...@de...>]

Mac users:

We lucked out and obtained a little help from an off-duty Apple engineer
today who figured out how to work around the issue in 10.4.3.  It was
one of these combined bugs -- we weren't doing things sensibly in PyMOL,
and the ATI driver wasn't quite complying with normal OpenGL behavior
with respect to screen updates.

They changes seem to have done the trick, so I have posted an updated
MacPyMOL build at:

http://delsci.com/beta

Please let me know if this does NOT solve the issue on your machine.
Also, since I had to change the lighting and draw-buffer code, please
let me know right away if anything strange or new surfaces.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20

[PyMOL] Discreet cartoon representation for overlapping secondary structure ?

[Indraneel M. <ind...@sm...>]

Hi,

Is changing cartoon representation a major work? My program PALSSE
defines overlapping Secondary Structural Elements and it would be nice
if I could see cartoons without having consecutive elements merged.

It is technically possible for consecutive helices or consecutive
strands or helices and strands to have upto 2 common residues.

I was wondering if the start and ends could somehow be distinguished,
eg. by changing or adding another "more_fancy" option to not remove
the head arrow of any SSE (also add arrow to helices) and modify the
base of all SSE so they are visible at all times (probably show the base
as a circle?). The SS merge feature would probably have to be switched
off before this though.

Which is the best place to start modifications?

An example arrow:

    __                  *
  *    *                *  *
 *      *****************    *
 *                             *
 *      *****************    *
  * __ *                *  *
                        *

 1      2               3      4

The head should be visible even if 1-2 overlaps on 3-4.


Thanks,
Indraneel

-- 
http://prodata.swmed.edu

RE: [PyMOL] Loading tetramer

[Warren D. <wa...@de...>]

Multiple ways to go:

load tetramer.pdb1
set all_states

is most memory-efficient

However,=20

load tetramer.pdb1
split_states tetramer
delete tetramer

Would give you the ability to manipulate each subunit independently.

Cheers,
Warren


--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Michael Morbious
> Sent: Saturday, November 05, 2005 10:57 AM
> To: pym...@li...
> Subject: [PyMOL] Loading tetramer
>=20
> Hi everyone,
> I want to load a biological assembly (tetramer) in
> pdb1 format. However, when I load it, I can only see one=20
> chain not the tetramer.
> On Command Line:=20
>  ObjectMolecule: Read secondary structure assignments.
>  ObjectMolecule: Read crystal symmetry information.
>  Symmetry: Found 8 symmetry operators.
>  ObjectMolReadPDBStr: read MODEL 1
>  ObjectMolReadPDBStr: read MODEL 2
>  ObjectMolReadPDBStr: read MODEL 3
>  ObjectMolReadPDBStr: read MODEL 4
>  CmdLoad: "2a79.pdb1" loaded as "2a79".
> is written.
> Any help would be appreciated.
>=20
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection=20
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>=20
>=20
> -------------------------------------------------------
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> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

[PyMOL] Loading tetramer

[Michael M. <dwa...@ya...>]

Hi everyone,
I want to load a biological assembly (tetramer) in
pdb1 format. However, when I load it, I can only see
one chain not the tetramer.
On Command Line: 
 ObjectMolecule: Read secondary structure assignments.
 ObjectMolecule: Read crystal symmetry information.
 Symmetry: Found 8 symmetry operators.
 ObjectMolReadPDBStr: read MODEL 1
 ObjectMolReadPDBStr: read MODEL 2
 ObjectMolReadPDBStr: read MODEL 3
 ObjectMolReadPDBStr: read MODEL 4
 CmdLoad: "2a79.pdb1" loaded as "2a79".
is written.
Any help would be appreciated.

__________________________________________________
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Tired of spam?  Yahoo! Mail has the best spam protection around 
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RE: [PyMOL] OS 10.4.3

[Warren D. <wa...@de...>]

MacPyMOL users:

Just to let everyone know, we are aware of the screen fliker problem
with the 10.4.3 update and working with Apple to resolve it ASAP.  I
have a favor to ask though:

Could those who are expericing this issue please send me their machine
info?  Mac OS X has a comprehensive system profile built-in that can be
accessed as follows:

Go to "About this Mac" under the Apple menu and click on "More Info...".
Then, from the File menu, Save your system file out to a file which you
then email to me at wa...@de....  The default XML format is fine.

Having files will help us identify the exact system configurations that
are experiencing the issue so that we can troubleshoot the problem on
equivalent hardware at Apple's nearby Compatibility Labs.  (All of the
G4 and G5 Macs we have access to for testing here at DeLano Scientific
work just fine -- only certain hardware seems to be affected).

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Mark Collins
> Sent: Saturday, November 05, 2005 10:09 AM
> To: pym...@li...
> Subject: [PyMOL] OS 10.4.3
>=20
> Hi
>=20
> I also have the flickering problem with my 15" g4 powerbook=20
> (ATI Radeon 9700 card).  Some mentioned a pymol -M command=20
> but I don't use the x11 window to open pymol...I just click=20
> on a pdb file.  Anybody know how to setup the pymol command (alias) ?
>=20
> Thanks,
> Mark Collins
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App=20
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> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

RE: [PyMOL] get color of atom ?

[Warren D. <wa...@de...>]

Indraneel,

iterate sele-name, print color

Will dump out the color name.  If you need this in a Python variable,
the process is a bit more convoluted:

from pymol import cmd, stored

stored.list =3D []
cmd.iterate(sele-str, "stored.list.append(color)")
print stored.list

Cheers,
Warren


--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Indraneel Majumdar
> Sent: Saturday, November 05, 2005 10:21 AM
> To: pym...@li...
> Cc: Warren DeLano
> Subject: [PyMOL] get color of atom ?
>=20
> Hi,
>=20
> How can I find out the color of an atom?
> Also, how should I call it from a python script?
>=20
> (Is there a function that will let me access the C variables?)
>=20
> get <color>, /x///1/CA
>=20
> does not work. (where <color> is any item in settings.py that=20
> has anything to do with color)
>=20
> TIA,
> Indraneel
>=20
> --
> http://prodata.swmed.edu
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App=20
> Server. Download
> it for free - -and be entered to win a 42" plasma tv or your very own
> Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

[PyMOL] New PyMOL plugin

[Jerome P. <j.p...@pa...>]

Hi,

I've develop a new plugin. It offers the ability to do a PDB advance sear=
ch.
You can search directly keywords into the PDB entries file. For this, the
PDB entries file is downloaded (the file is stored into the home
directory).
The results are diplayed into a spreadsheet. By a double click on a resul=
t
line, the structure is open into the PyMOL visualization window.

You can find the plugin at this address:
http://www.pansanel.net/chemistry/resources/pymol_pdbsearch.tar.gz

I'm waiting for your comments !

Thanks

Jerome Pansanel

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Re: [PyMOL] Mac OS X 10.4.3

[Morri F. <mor...@gm...>]

I see the same flickering problem (iMac G5, OSX 10.4.3).  Opening as
pymol -M doesn't help.

Best,
Morri

On 11/3/05, Sabuj Pattanayek <sab...@va...> wrote:
> I don't know if it will make a difference (I don't even have a Mac) but
> try opening it from a console using:
>
> pymol -M
>
>

--
Morri Feldman
Shokat Lab
UCSF Biophysics Graduate Program

[PyMOL] Superimpose

[Michael M. <dwa...@ya...>]

Hi everyone,
I have two similar (closely related) multi-chain
structures. I want to merge them and highlight the
regions that do not superimpose. However, I do not
know how to superimpose these two structures and how
to select non-intersecting residues. 
Any help will be appreciated.
Thanks.  


		
__________________________________ 
Yahoo! FareChase: Search multiple travel sites in one click.
http://farechase.yahoo.com

[PyMOL] get color of atom ?

[Indraneel M. <ind...@sm...>]

Hi,

How can I find out the color of an atom?
Also, how should I call it from a python script?

(Is there a function that will let me access the C variables?)

get <color>, /x///1/CA

does not work. (where <color> is any item in settings.py that has
anything to do with color)

TIA,
Indraneel

-- 
http://prodata.swmed.edu

[PyMOL] OS 10.4.3

[Mark C. <mco...@co...>]

Hi

I also have the flickering problem with my 15" g4 powerbook (ATI  
Radeon 9700 card).  Some mentioned a pymol -M command but I don't use  
the x11 window to open pymol...I just click on a pdb file.  Anybody  
know how to setup the pymol command (alias) ?

Thanks,
Mark Collins

RE: [PyMOL] Independent Rotation axis...

[Warren D. <wa...@de...>]

The "rotate" and "translate" commands can do this *if* you append the
object=3Dobject-name to the command:

Try typing in the following sequence of commands:

fragment arg
fragment glu

translate [5,0,0], object=3Darg
translate [-5,0,0], object=3Dglu

origin arg, object=3Darg
origin glu, object=3Dglu

rotate y, 10, object=3Darg
rotate y, -10, object=3Dglu

Note that these movements are accomplished via matrix and not coordinate
transformations, so interacting with the molecules after they have been
moved is currently a bit problematic (bugs to fix...).  However, you can
move complex geometries like surfaces without forcing recalcuation using
this approach.

Normally for movies, you'd embed commands like the above into movie
commands.  For that to work, you'll also need commands like:

reset object=3Darg
reset object=3Dglu

in the first movie frame.

Cheers,
Warren

PS. Coming down the pipe: automatic 'tweening for object motion!

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Nathaniel G. Butlin
> Sent: Friday, November 04, 2005 6:34 AM
> To: PyM...@li...
> Subject: [PyMOL] Independent Rotation axis...
>=20
> Hi All,
>=20
> I was wondering if anyone know if there is anyway to assign=20
> independent rotation axis to two different proteins within=20
> Pymol.  Specifically, I amintersted in having two molecules=20
> rotate about individual axis in a movie sequence.
>=20
> Thanks,
>=20
> Nate Butlin
>=20
> UCDavis - Chemistry
> ngb...@uc...
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App=20
> Server. Download it for free - -and be entered to win a 42"=20
> plasma tv or your very own Sony(tm)PSP.  Click here to play:=20
> http://sourceforge.net/geronimo.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

RE: [PyMOL] .xyz file loading problem from chempy module

[Warren D. <wa...@de...>]

Dmitriy,

The very latest beta versions of PyMOL can read .xyz files directly (via
the "load" or "load_raw" commands). =20

http://delsci.com/beta

load_raw usage:

my_xyz=3Dopen("some.xyz").read()
cmd.load_raw(my_xyz, 'xyz', "my_xyz")

I suspect the chempy XYZ file is limited to reading Tinker's
fixed-column XYZ format.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of Dmitriy
> Sent: Friday, November 04, 2005 6:34 AM
> To: pym...@li...
> Subject: [PyMOL] .xyz file loading problem from chempy module
>=20
> Hello everyone
>=20
> It seems to be a problem with loading an .xyz file as a chempy model.
> For example doing
>=20
> from chempy import io
> m =3D io.xyz.fromFile("some.xyz")
>=20
> gives:
>=20
> chempy: reading "some.xyz".
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   File=20
> "/home/dmitriy/pymol/lib/python2.4/site-packages/chempy/__init__.py",
> line 185, in fromFile
> TypeError: fromList() takes exactly 1 argument (2 given)
>=20
> If I've got the right idea whats going on, there should be
> fromList(self,list)  function in xyz.py which will hide the=20
> Storage one.
> Like it's done in pdb.py (it works fine for io.pdb.fromFile)
>=20
> I'm trying to establish a communication between my program=20
> and pymol in a simple .xyz format. Sending a list of strings,=20
> creating a chempy model and loading it into pymol will work.=20
> If there is some workaround or a fix for problem mention above.
>=20
> Warren, Is it possible to implement a way of passing .xyz=20
> file as a string, not as a list of strings or a file? I've=20
> seen molstr, pdbstr etc. but not xyzstr.=20
> And a short description how to load pdbstr for example it in=20
> this way will be great.
>=20
> Thanks
>   Dmitriy
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App=20
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>=20
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>=20
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