pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] picking discrete coordinates

[Martin W. <Mar...@gm...>]

Hi all!   
I'm trying to pick a discrete coordinate outside of the loaded protein  
structure (something like "create name, coord[x,y,z]") to which I can  
apply the "around" command. Creating an additional atom as a probe  
would be a makeshift solution. Is there a way to use the Fragment Builder 
from the API? 
 
Thanks in advance, 
Martin Weisel 
 
 
------------- 
Martin Weisel 
Diploma Student 
Bioinformatics Group, Frankfurt University 

-- 
10 GB Mailbox, 100 FreeSMS/Monat http://www.gmx.net/de/go/topmail
+++ GMX - die erste Adresse für Mail, Message, More +++

[PyMOL] Re: New user needs help! (Michael Morbious)

[Marc S. <mar...@gm...>]

Michael Morbious wrote:


> Dear All,
> I am a new pymol user. Does anyone know if it is
> possible to merge four units (all units are same) of a
> tetrameric assembly by using pymol? Each unit has the
> same Id and when I load each of them, they overlap. 
> If you please help me, I will be really pleased.

If I understand you correctly, you have four (identical) subunits in
four PDB-files?

The easiest way (sans Pymol) might be:

cat file1.pdb file2.pdb file3.pdb file4.pdb > all.pdb

This assumes, that the coordinates are not (more or less) identical,
because in this case you would end up with all four structures overlaid,
in which case you must do some coordinate transformations to arrange
them properly. If you don't know the orientation of the molecules (from
a template for example) this is non-trivial.

cat is available on all UNIX and Mac OS X systems and can be downloaded
as command-line exe-file for Windows.

There is certainly a more elegang Pymol-only sollution for this.


-- 
Bye,

Marc Saric

Re: [PyMOL] [colors frozen for rendering modes defined in .pymolrc]

[Sebastien M. <seb...@ig...>]

> Sebastien,
>=20
>>I cannot=20
>>change the color for rendering modes I defined.
>=20
> I do not understand what you mean by this.
>=20
> Cheers,
> Warren

I mean that the color, for cartoon view, is unchangeable when 'set=20
cartoon_color' is defined in the $HOME/.pymolrc file.
Thus, when I define 'set cartoon_color' in the $HOME/.pymolrc file, I=20
cannot change the color, for the cartoons, from the GUI.

The color is kept whatever I do.

Thanks

>>Hello,
>>I defined some default colors in the $HOME/.pymolrc file.
>>E.g.:	set cartoon_color, slate
>>
>>It works fine but in PyMOL viewer (version 0.98) I cannot=20
>>change the color for rendering modes I defined.
>>The one I defined is always kept.
>>
>>Is this a normal behavior ?
>>
>>Thanks

--=20
S=E9bastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS
31 chemin Joseph Aiguier
13402 Marseille cedex

[PyMOL] New user needs help!

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

Dear All,
I am a new pymol user. Does anyone know if it is
possible to merge four units (all units are same) of a
tetrameric assembly by using pymol? Each unit has the
same Id and when I load each of them, they overlap. 
If you please help me, I will be really pleased.
Best Wishes,


	
		
__________________________________ 
Yahoo! Mail - PC Magazine Editors' Choice 2005 
http://mail.yahoo.com

Re: [PyMOL] Need testers for new MacPyMOL on Tiger

[Mark A S. <sa...@um...>]

Warren,

Thanks for your hard work in preparing this version.  It will be very  
convenient.  My major use of the upper window is for convenience in  
dragging and dropping commands from other programs into MacPyMOL.   
Because of that I usually kept it behind the main window.  Is it  
possible to hide the top window with a key command?  Also would it  
possible for it to reopen if someone dragged something onto the main  
window?  If not, then I'll just get used to it.

Thanks,
Mark


_________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry
Biophysics Research Division, University of Michigan
Chemistry Building Room 3040
930 N University Ave
Ann Arbor MI 48109-1055 U.S.A.

sa...@um...        (734) 764-3353        fax (734) 764-3323
http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html

RE: [PyMOL] Re: Need testers for new MacPyMOL on Tiger

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

> My only request would be to add a=20
> mechanism to stash the information panel if there isn't one=20
> available --- I've gotten addicted to this capability for=20
> presentations and teaching.

You can manually collapse it by dragging the separator bar up to the
top.  Cocoa doesn't seem to provide a way to do this programatically,
yet, but there are several ways to start without this portion of the
window, just like with regular pymol:

(1) launch MacPyMOL with a ".psw" file, in which case you get
full-screen GUI-less PyMOL

(2) launch ./MacPyMOL.app/Contents/MacOS/MacPyMOL -x in which case you
get something that behaves very much like the old GLUT viewer window.

(3) launch ./MacPyMOL.app/Contents/MacOS/MacPyMOL -e which starts
full-screen, or if you are using a session file that contains window
information, use: ./MacPyMOL.app/Contents/MacOS/MacPyMOL sessionfile -d
full_screen%on

Cheers,
Warren
=20

--
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
> Kevin Gardner
> Sent: Saturday, October 15, 2005 5:01 AM
> To: pym...@li...
> Subject: [PyMOL] Re: Need testers for new MacPyMOL on Tiger
>=20
> Hi Warren:
>=20
> > For cutting-edge Mac users, there is a new MacPyMOL for Tiger that=20
> > integrates into a single window and links to the system=20
> Python instead=20
> > of bringing its own copy (in part this is necessary preparation for=20
> > Intel...).
> >
> > http://delsci.com/beta
>=20
> Works great here, too.  My only request would be to add a=20
> mechanism to stash the information panel if there isn't one=20
> available --- I've gotten addicted to this capability for=20
> presentations and teaching.
>=20
> Sincerely,
> Kevin
>=20
> --
> **********************************************************************
> Kevin Gardner, Ph.D.                  Kev...@ut...
> Associate Professor - Dept. of Biochemistry - UT Southwestern Med Ctr
> 214-645-6365/FAX: -6353                      http://freedom7.swmed.edu
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads,=20
> discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

[PyMOL] Re: Need testers for new MacPyMOL on Tiger

[Kevin G. <Kev...@ut...>]

Hi Warren:

> For cutting-edge Mac users, there is a new MacPyMOL for Tiger that
> integrates into a single window and links to the system Python instead
> of bringing its own copy (in part this is necessary preparation for
> Intel...).
>
> http://delsci.com/beta

Works great here, too.  My only request would be to add a mechanism to
stash the information panel if there isn't one available --- I've gotten
addicted to this capability for presentations and teaching.

Sincerely,
Kevin

--
**********************************************************************
Kevin Gardner, Ph.D.                  Kev...@ut...
Associate Professor - Dept. of Biochemistry - UT Southwestern Med Ctr
214-645-6365/FAX: -6353                      http://freedom7.swmed.edu

Re: [PyMOL] ugly font in GUI, FAQ wrong

[Alan <ala...@gm...>]

Thanks Renato.

My distribution is Ubuntu. But, what I want is independent of distribution.

There's a default font being used by Pymol and I want to change it,
like you do in nedit, for instance.

Cheers,
Alan

On 14/10/05, Joao Renato Carvalho Muniz <jrc...@if...> wrote:
> Hey Alan
>
> What's your linux distro?
>
> Sometimes is not a pymol problem... but the right configuration of
> Qt/Gtk apps..
>
> Joao Renato.
>
> Alan wrote:
>
> >Hi List
> >
> >I want to change the font in GUI of PyMOL. However, reading the FAQ:
> >
> >http://pymol.sourceforge.net/faq.html#FONT
> >
> >Such instructions were lost in time, maybe for another old version of Py=
mol.
> >
> >So, I would ask help in how to change the Font for the TK/Tcl external
> >GUI of pymol (menu). In my computer it is really bad.
> >
> >I'd thank any help here.
> >
> >Cheers,
> >Alan
> >--
> >Alan Wilter S. da Silva, D.Sc.
> >
> >
> >-------------------------------------------------------
> >This SF.Net email is sponsored by:
> >Power Architecture Resource Center: Free content, downloads, discussions=
,
> >and more. http://solutions.newsforge.com/ibmarch.tmpl
> >_______________________________________________
> >PyMOL-users mailing list
> >PyM...@li...
> >https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> >
> >
>
> --
> ------------------------------------------------------------
> Joao Renato Carvalho Muniz < e-mail: jrc...@if... >
> PhD. Student.
> Sao Paulo University - Sao Carlos Physics Institute
> Protein Crystallography Department
> Address: Av. do Trabalhador Saocarlense, 400
> Centro - Caixa Postal 369, CEP 13560-970 - Sao Carlos - SP
> BRASIL
> Phone: ++55 16 3373.9868
> FAX:   ++55 16 3373.9881
> ------------------------------------------------------------
>
>


--
Alan Wilter S. da Silva, D.Sc.

[PyMOL] Pharmacophore visualizations

[Andrew D. F. <and...@tu...>]

Has anyone done anything with with making PyMol able to display pharmacophores 
as CGOs?  Being able to align molecules in pymol with a defined pharmacophore 
would be nice too, but I realize that doing that would require much more effort 
from some developer. For the time being, it would be good to have a predefined 
rendering solution that I can manually align structures to for visualization.

Thanks,
	Andy

-- 
Andrew Fant           | The lion and the calf shall lie   | Disclaimer:
and...@tu... | down together, but the calf won't | Do you REALLY
TCCS/USG              | get much sleep.                   | think I can
Tufts University      |                  W. Allen         | speak for Tufts?

[PyMOL] script feedback: how print out distance and not average

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

Hi all,
this script below runs well in pymol. It loads pdb files and
calculates the distance of some atoms contained in the fileAmb whose
format is:
26,O11:HN
28,*:HE1
...............
With * I select whole ligand (segi B) and pymol returns only one
value, the average distance for all atoms to the HE1 atoms. I need to
print out all the distances, atom by atom.
any helps??
thanks a lot
andrea

----------------------
from pymol import cmd
import string, sys, os

def viol(fileAmb,deep):
    cmd.reinitialize()
    if ("dist.out"):
        os.system("rm -f dist.out")
    nam =3D open("file.nam",'r')
    KeepStruc =3D []
    readnam =3D nam.readlines()
    deep =3D int(deep)
    for j in range(0,deep):
        readnam[j] =3D string.strip(readnam[j])
        KeepStruc.append(readnam[j])

    for i in KeepStruc:
        cmd.load(i,i)
        cmd.select("lig","segi B")
        cmd.select("pro","all and not segi B")
        amb =3D open(fileAmb,'r')
        out =3D open("dist.out","a")
        out.write("%4s\n"%(i))
        for lines in amb.readlines():
            lines =3D string.strip(lines)
            tmp =3D string.split(lines,",")
            resname =3D tmp[0]
            atomtypes =3D tmp[1]
            tmp1 =3Dstring.split(atomtypes,":")
            atomlig =3D tmp1[0]
            atompro =3D tmp1[1]
            p =3D cmd.select("p","resi "+resname+" and name "+atompro+" and=
 "+i)
            l =3D cmd.select("l","name "+atomlig+" and segi B and "+i)
            d =3D cmd.distance("dist_"+str(i),"p","l")
            if (d > 5):
                print resname,":",atompro,"->",atomlig,d
                out.write("%4s%8s%8s%8.3f\n"%(resname,atompro,atomlig,d))

    out.close()

cmd.extend('viol',viol)

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

Re: [PyMOL] Need testers for new MacPyMOL on Tiger

[Gilleain T. <gil...@gm...>]

Hi,

Works great for me!

Very nice to have access to the system python.

gilleain torrance

On 14 Oct 2005, at 16:50, Warren DeLano wrote:

> For cutting-edge Mac users, there is a new MacPyMOL for Tiger that
> integrates into a single window and links to the system Python instead
> of bringing its own copy (in part this is necessary preparation for
> Intel...).
>
> http://delsci.com/beta
>
> Please let me know how it works for you!
>
> 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...
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads,  
> discussions,
> and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

[PyMOL] Need testers for new MacPyMOL on Tiger

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

For cutting-edge Mac users, there is a new MacPyMOL for Tiger that
integrates into a single window and links to the system Python instead
of bringing its own copy (in part this is necessary preparation for
Intel...).

http://delsci.com/beta

Please let me know how it works for you!

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] Missing parts in cartoon mode

[Gilleain T. <gil...@gm...>]

Which parts are missing? Looks fine to me...

Although the pdb file has some horrible features. Some residues are  
multiply defined (eg 170 in chain H) and there is some kind of poly- 
calcium binding tail in chain L.

gilleain torrance

On 14 Oct 2005, at 10:43, <ran...@ic...>  
<ran...@ic...> wrote:

> Hi everybody
> I am getting quite desperate! For some strange reason PyMol do not  
> display certain areas (several loops) of my .pdb file (1DAN) when  
> in cartoon display mode. When I display the structure in "lines" or  
> "sticks" everything is ok. Other pdb-viewers dont have this problem  
> with the same .pdb file. I have tried several things:
> 1. Upgraded to the newest version og PyMol.
> 2. Redefined secondary structure using the "alter" command.
> 3. Imported the .pdb file into SwissViewer, saved as the imported  
> structure as a .pdb file, and then imported into PyMOl.
> None of these things have solved the problem. Help please! (I would  
> hate to have to start using another pdb-viewer!!) Cheers Kasper
>
> _______________________________________________________________
> ICQ - You get the message, anywhere!
> Get it @ http://www.icq.com
>
>

[PyMOL] [colors frozen for rendering modes defined in .pymolrc]

[Sebastien M. <seb...@ig...>]

Hello,
I defined some default colors in the $HOME/.pymolrc file.
E.g.:	set cartoon_color, slate

It works fine but in PyMOL viewer (version 0.98) I cannot change the=20
color for rendering modes I defined.
The one I defined is always kept.

Is this a normal behavior ?

Thanks

--=20
S=E9bastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS
31 chemin Joseph Aiguier
13402 Marseille cedex

[PyMOL] Missing parts in cartoon mode

[<ran...@ic...>]

Hi everybody
I am getting quite desperate! For some strange reason PyMol do not
display certain areas (several loops) of my .pdb file (1DAN) when in
cartoon display mode. When I display the structure in "lines" or
"sticks" everything is ok. Other pdb-viewers dont have this problem with
the same .pdb file. I have tried several things: 
1. Upgraded to the newest version og PyMol. 
2. Redefined secondary structure using the "alter" command. 
3. Imported the .pdb file into SwissViewer, saved as the imported
structure as a .pdb file, and then imported into PyMOl. 

None of these things have solved the problem. Help please! (I would hate
to have to start using another pdb-viewer!!) Cheers Kasper 



<P><font face="Arial, Helvetica, sans-serif" size="2" style="font-size:13.5px">_______________________________________________________________<BR><font face="Arial, Helvetica, sans-serif" size="2" style="font-size:13.5px">ICQ - You get the message, anywhere!<br>Get it @ <a href="http://www.icq.com" target=new>http://www.icq.com</a></font><br><br>&nbsp;</font></font>

[PyMOL] ugly font in GUI, FAQ wrong

[Alan <ala...@gm...>]

Hi List

I want to change the font in GUI of PyMOL. However, reading the FAQ:

http://pymol.sourceforge.net/faq.html#FONT

Such instructions were lost in time, maybe for another old version of Pymol=
.

So, I would ask help in how to change the Font for the TK/Tcl external
GUI of pymol (menu). In my computer it is really bad.

I'd thank any help here.

Cheers,
Alan
--
Alan Wilter S. da Silva, D.Sc.

RE: [PyMOL] lcd stereo

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

PyMOL can indeed drive this monitor, but a special build is required
which includes Sharp's drivers. In fact, I just updated the Windows
build for this product yesterday http://www.delsci.com/sharp3d
=20
For $600, I think this is defiinitely worth it -- but don't expect this
product to replace your 21" glasses--equipped stereo CRT. =20
=20
Cheers,
Warren
=20
--
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


________________________________

	From: pym...@li...
[mailto:pym...@li...] On Behalf Of Schubert,
Carsten [PRDUS]
	Sent: Wednesday, October 12, 2005 6:01 AM
	To: wg...@ch...;
pym...@li...
	Subject: RE: [PyMOL] lcd stereo
=09
=09

	Bill,=20

	the Linux NVidia driver does not (yet) seem to support this
option. Lets hope for future releases.=20

	Carsten=20

	-----Original Message-----=20
	From: pym...@li...=20
	[mailto:pym...@li...]On Behalf Of
William=20
	Scott=20
	Sent: Tuesday, October 11, 2005 11:03 PM=20
	To: pym...@li...=20
	Subject: [PyMOL] lcd stereo=20


	I just noticed that the price on the Sharp LCD stereo monitor is
now =20
	$600.=20

	http://store.sharpsystems.com/product.asp?sku=3D2555920=20

	Is it possible to run pymol on linux in stereo on this?=20


	-------------------------------------------------------=20
	This SF.Net email is sponsored by:=20
	Power Architecture Resource Center: Free content, downloads,
discussions,=20
	and more. http://solutions.newsforge.com/ibmarch.tmpl=20
	_______________________________________________=20
	PyMOL-users mailing list=20
	PyM...@li...=20
	https://lists.sourceforge.net/lists/listinfo/pymol-users=20

RE: [PyMOL] lcd stereo

[Schubert, C. [PRDUS] <CSC...@pr...>]

Bill,

the Linux NVidia driver does not (yet) seem to support this option. Lets
hope for future releases. 

Carsten

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...]On Behalf Of William
Scott
Sent: Tuesday, October 11, 2005 11:03 PM
To: pym...@li...
Subject: [PyMOL] lcd stereo


I just noticed that the price on the Sharp LCD stereo monitor is now  
$600.

http://store.sharpsystems.com/product.asp?sku=2555920

Is it possible to run pymol on linux in stereo on this?


-------------------------------------------------------
This SF.Net email is sponsored by:
Power Architecture Resource Center: Free content, downloads, discussions,
and more. http://solutions.newsforge.com/ibmarch.tmpl
_______________________________________________
PyMOL-users mailing list
PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users

Antw: Re: [PyMOL] lcd stereo

[Manfred B. <Man...@un...>]

All of these =22ultra fast 8=B5s=22 LCD screens I have seen do not support
horizontal scan frequencies above 75 or 80Hz. No idea why...

Currently I use a dual head setup with a CRT and a LCD monitor
connected to a FX1400 card. This way I have the best of both worlds
simultaneosly.

Best regards
Manfred

>>> Dirk Kostrewa <dirk.kostrewa=40psi.ch> 12.10.2005 9:02 >>>
And what about the ever faster LCD screens designed for gamers? With=20
refresh times appraching 8 microseconds, hardware stereo with 2x 60 Hz

on LCD screens seems to come into reach.

Best regards,

Dirk.

William Scott wrote:

> I just noticed that the price on the Sharp LCD stereo monitor is now=20

> =24600.
>
> http://store.sharpsystems.com/product.asp?sku=3D2555920=20
>
> Is it possible to run pymol on linux in stereo on this?
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads,
discussions,
> and more. http://solutions.newsforge.com/ibmarch.tmpl=20
> _______________________________________________
> PyMOL-users mailing list
> PyMOL-users=40lists.sourceforge.net=20
> https://lists.sourceforge.net/lists/listinfo/pymol-users=20



--=20

****************************************
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:	dirk.kostrewa=40psi.ch=20
http://sb.web.psi.ch=20
****************************************



-------------------------------------------------------
This SF.Net email is sponsored by:
Power Architecture Resource Center: Free content, downloads,
discussions,
and more. http://solutions.newsforge.com/ibmarch.tmpl=20
_______________________________________________
PyMOL-users mailing list
PyMOL-users=40lists.sourceforge.net=20
https://lists.sourceforge.net/lists/listinfo/pymol-users

Re: [PyMOL] lcd stereo

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

And what about the ever faster LCD screens designed for gamers? With 
refresh times appraching 8 microseconds, hardware stereo with 2x 60 Hz 
on LCD screens seems to come into reach.

Best regards,

Dirk.

William Scott wrote:

> I just noticed that the price on the Sharp LCD stereo monitor is now  
> $600.
>
> http://store.sharpsystems.com/product.asp?sku=2555920
>
> Is it possible to run pymol on linux in stereo on this?
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads, discussions,
> and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users



-- 

****************************************
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
****************************************

[PyMOL] PmgTk/Pmw Problem?

[tree <jav...@ut...>]

I just rebuilt from CVS on my SuSe x86-64 box.  Anyone know why keyboard
input isn't working in the Pmw command line?  The internal GUI command
line still works.  One quirk though, if I select
  Setting -> Edit All
I can edit entries in there using the keyboard/mouse.

I have python2.4 now & used the same build process I always do (through
Python distutils).

Thanks,

-- Jason

-- 
Jason Vertrees (jav...@ut...)
BSCB Graduate Student @ UTMB, Galveston
http://www.bscb.utmb.edu :: BSCB @ UTMB
http://best.utmb.edu :: B.E.S.T. @ UTMB
http://pymolwiki.org :: PyMol Wiki

Re: [PyMOL] align selected regions

[tree <jav...@ut...>]

Jie,

The PyMolWiki can help you here!

First, the PyMol tricks, that you need, for aligning are described here
  http://www.pymolwiki.org/index.php/Intra_Rms

But, if you already know what you want to align, the Kabsch algorithm
can do the job (optimally well)
  http://www.pymolwiki.org/index.php/Kabsch
(and it now works for Windows users, too).

HTH,

-- Jason


On Tue, 2005-10-11 at 20:22 -0700,
pym...@li... wrote:
> Message: 4
> Date: Tue, 11 Oct 2005 10:48:25 -0700
> From: jy-ucsd <ji...@uc...>
> To:  pym...@li...
> Subject: Re: [PyMOL] align selected regions
> 
> Hi, all
> I am trying to align two proteins, but I would like to specify
> different 
> regions for different alignment, since the two proteins that I wish
> to 
> align has a hinge region. 
> I tried the fit command, as the following:
> fit (protein1 and chain A and resi 200-300 and name ca), (protein 2
> and 
> chain B and resi 200-300 and name ca)
> 
> and it did not work, "no atoms selected".
> 
> can someone tell me the best way to do it?
> 
> Thank you
> 
> Jie
-- 
Jason Vertrees (jav...@ut...)
BSCB Graduate Student @ UTMB, Galveston
http://www.bscb.utmb.edu :: BSCB @ UTMB
http://best.utmb.edu :: B.E.S.T. @ UTMB
http://pymolwiki.org :: PyMol Wiki

[PyMOL] lcd stereo

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

I just noticed that the price on the Sharp LCD stereo monitor is now  
$600.

http://store.sharpsystems.com/product.asp?sku=2555920

Is it possible to run pymol on linux in stereo on this?

RE: [PyMOL] PyMol segmentation fault while starting from external python program

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

Update:

With respect to "import pymol", I think all of the reported segmentation
fault and race conditions have now been eliminated from the very latest
source code.  Since everyone doesn't have CVS access, I have posted a
source tar-gz file on http://delsci.com/beta with updated instructions
on building and usage.

So if you are a unix-based Python developer with an interest in calling
PyMOL from you own stadalone applications, then this would be a good
time to try building from source into your own Python environment in
order to see whether or not it can work for you.  Windows is a
possibility too, but getting all the dependencies satisfied under Win32
is a bit of a chore.

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

Re: [PyMOL] align selected regions

[jy-ucsd <ji...@uc...>]

Hi, all
I am trying to align two proteins, but I would like to specify different 
regions for different alignment, since the two proteins that I wish to 
align has a hinge region. 
I tried the fit command, as the following:
fit (protein1 and chain A and resi 200-300 and name ca), (protein 2 and 
chain B and resi 200-300 and name ca)

and it did not work, "no atoms selected".

can someone tell me the best way to do it?

Thank you

Jie