pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] MacPyMOL command entry

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

Hi,

Happy Holidays everyone.  This is actually a bug report for Warren.   
If you have time, could you work on the implementation of the command  
recall option (up and down arrow) in the command text input field in  
the OS X-specific part of the window.  It often forgets what the  
previous commands are.

Many thanks,
Mark
_________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry
Associate Research Scientist in Biophysics

Biophysics Research Division, University of Michigan
Chemistry Building Room 3040
930 North 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] Has anyone got apbs 0.4 to work with the pymol apbs plugin?

[Michael G. L. <ml...@um...>]

On Wed, 21 Dec 2005, William Scott wrote:

>
> Dear Michael:
>
> Thanks.
>
> It works great.  Sorry that I stupidly didn't think to check it.

No problem.  I'm glad it works.  Almost everything should be the same. 
APBS has a new required parameter, sdens (Vacc sphere density) that I've 
added to the configuration pane.  As far as I've heard, the default 
setting of 10.0 should be fine for most uses.

> If you permit me one whine, I still need to use pdb2pqr (new version of 
> that too) in order to do this with nucleic acids.

Allowing the plugin to use pdb2pqr is at the top of my PyMOL-related todo 
list.

-michael

--
www.umich.edu/~mlerner |                        _  |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) |   Michigan
it's a cheer-ocracy.   |  - against HTML email  X  |  Biophysics
-Torrence,  Bring It On|                       / \ | mlerner@umich

>
>
> On Tue, 20 Dec 2005, Michael George Lerner wrote:
>
>>
>> There's a new version on my website
>> (http://www.umich.edu/~mlerner/PyMOL/).  Please feel free to try it out
>> and let me know if it works.  I've tested it on a few systems that I work
>> with, and it seems fine.  One person has reported some difficulties, but
>> these may not be related to my plugin.
>>
>> Thanks,
>>
>> -michael
>>
>> --
>> www.umich.edu/~mlerner |                        _  |Michael Lerner
>> This isn't a democracy;| ASCII ribbon campaign ( ) |   Michigan
>> it's a cheer-ocracy.   |  - against HTML email  X  |  Biophysics
>> -Torrence,  Bring It On|                       / \ | mlerner@umich
>>
>> On Tue, 20 Dec 2005, William Scott wrote:
>>
>>> I'm not getting very far...
>>>
>>> parsePBE:  Warning -- parsed deprecated "calcforce 0" statement.
>>> parsePBE:  Please use "calcforce no" instead.
>>> PBEparm_check: SDENS not set!
>>> NOsh:  MG parameters not set correctly!
>>> Error while parsing input file.
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
>>> for problems?  Stop!  Download the new AJAX search engine that makes
>>> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
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>>> _______________________________________________
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>>>
>>>
>>>
>>
>
>
>

Re: [PyMOL] Has anyone got apbs 0.4 to work with the pymol apbs plugin?

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

Dear Michael:

Thanks.

It works great.  Sorry that I stupidly didn't think to check it. If you
permit me one whine, I still need to use pdb2pqr (new version of that too)
in order to do this with nucleic acids.

All the best,

Bill



On Tue, 20 Dec 2005, Michael George Lerner wrote:

>
> There's a new version on my website
> (http://www.umich.edu/~mlerner/PyMOL/).  Please feel free to try it out
> and let me know if it works.  I've tested it on a few systems that I work
> with, and it seems fine.  One person has reported some difficulties, but
> these may not be related to my plugin.
>
> Thanks,
>
> -michael
>
> --
> www.umich.edu/~mlerner |                        _  |Michael Lerner
> This isn't a democracy;| ASCII ribbon campaign ( ) |   Michigan
> it's a cheer-ocracy.   |  - against HTML email  X  |  Biophysics
> -Torrence,  Bring It On|                       / \ | mlerner@umich
>
> On Tue, 20 Dec 2005, William Scott wrote:
>
> > I'm not getting very far...
> >
> > parsePBE:  Warning -- parsed deprecated "calcforce 0" statement.
> > parsePBE:  Please use "calcforce no" instead.
> > PBEparm_check: SDENS not set!
> > NOsh:  MG parameters not set correctly!
> > Error while parsing input file.
> >
> >
> > -------------------------------------------------------
> > This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
> > for problems?  Stop!  Download the new AJAX search engine that makes
> > searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> >
> >
>

[PyMOL] Correction: X server to crashes, when working with pymol

[bgbg bg <bg...@gm...>]

Correction, the X server crashes on each attempt to resize the pymol window
On 12/21/05, bgbg bg <bg...@gm...> wrote:
>
> Hello, list.
> This is my setup:
> Mandriva Linux 2006.0,
> X Window System Version 6.8.99.900 (6.9.0 RC 0)
> X Protocol Version 11, Revision 0, Release 6.8.99.900
> Build Operating System: Linux 2.6.12-12mdksmp i686 [ELF]
>
> I used PyMol 0.98 both installed from Mandriva's rpm's and from sources.
> The problem is as follows: when resizing pymol window (not always
> though), the X server crashes. I've redirected the stderr of pymol to
> a file and this is the output:
> <OUTPUT>
> Loading required GL library /usr/X11R6/lib/libGL.so.1.2
> X connection to :0.0 broken (explicit kill or server shutdown).
> </OUTPUT>
>
> I haven't experienced the X crash with any other program on this computer=
.
>
> Can anyone give a hint on what might be a problem?
> Thank you very much
>

[PyMOL] X server to crashes, when working with pymol

[bgbg bg <bg...@gm...>]

Hello, list.
This is my setup:
Mandriva Linux 2006.0,
X Window System Version 6.8.99.900 (6.9.0 RC 0)
X Protocol Version 11, Revision 0, Release 6.8.99.900
Build Operating System: Linux 2.6.12-12mdksmp i686 [ELF]

I used PyMol 0.98 both installed from Mandriva's rpm's and from sources.
The problem is as follows: when resizing pymol window (not always
though), the X server crashes. I've redirected the stderr of pymol to
a file and this is the output:
<OUTPUT>
Loading required GL library /usr/X11R6/lib/libGL.so.1.2
X connection to :0.0 broken (explicit kill or server shutdown).
</OUTPUT>

I haven't experienced the X crash with any other program on this computer.

Can anyone give a hint on what might be a problem?
Thank you very much

[PyMOL] Re: PyMOL-users digest, Vol 1 #1088 - 1 msg

[Stephen G. <ste...@us...>]

It worked for me just yesterday.  You should download the new version
of the plugin (http://www-personal.umich.edu/~mlerner/PyMOL/apbs_tools.py)
and replace the old (it should be located in
$PYMOL_PATH/modules/pmg_tk/startup/ but on my Debian sarge system it
can be found in found at
/usr/lib/python2.3/site-packages/pmg_tk/startup/).

Cheers,

Stephen

> Message: 1
> To: pym...@li...
> From: William Scott <wg...@ch...>
> Date: Tue, 20 Dec 2005 14:50:36 -0800
> Subject: [PyMOL] Has anyone got apbs 0.4 to work with the pymol apbs plug=
in?
>
> I'm not getting very far...
>
> parsePBE:  Warning -- parsed deprecated "calcforce 0" statement.
> parsePBE:  Please use "calcforce no" instead.
> PBEparm_check: SDENS not set!
> NOsh:  MG parameters not set correctly!
> Error while parsing input file.
>
>
>
>
> --__--__--
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

--
Stephen Graham
Crystallography Group
School of Molecular and Microbial Biosciences
University of Sydney

Re: [PyMOL] Has anyone got apbs 0.4 to work with the pymol apbs plugin?

[Michael G. L. <ml...@um...>]

There's a new version on my website 
(http://www.umich.edu/~mlerner/PyMOL/).  Please feel free to try it out 
and let me know if it works.  I've tested it on a few systems that I work 
with, and it seems fine.  One person has reported some difficulties, but 
these may not be related to my plugin.

Thanks,

-michael

--
www.umich.edu/~mlerner |                        _  |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) |   Michigan
it's a cheer-ocracy.   |  - against HTML email  X  |  Biophysics
-Torrence,  Bring It On|                       / \ | mlerner@umich

On Tue, 20 Dec 2005, William Scott wrote:

> I'm not getting very far...
>
> parsePBE:  Warning -- parsed deprecated "calcforce 0" statement.
> parsePBE:  Please use "calcforce no" instead.
> PBEparm_check: SDENS not set!
> NOsh:  MG parameters not set correctly!
> Error while parsing input file.
> 
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
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> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>

[PyMOL] Has anyone got apbs 0.4 to work with the pymol apbs plugin?

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

I'm not getting very far...

parsePBE:  Warning -- parsed deprecated "calcforce 0" statement.
parsePBE:  Please use "calcforce no" instead.
PBEparm_check: SDENS not set!
NOsh:  MG parameters not set correctly!
Error while parsing input file.
  

RE: [PyMOL] Where can I find the definition of class Atom and Bond ?

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

modules/chempy/__init__.py

--
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
> Xiao Jianfeng
> Sent: Thursday, December 15, 2005 8:21 PM
> To: pym...@li...
> Subject: [PyMOL] Where can I find the definition of class=20
> Atom and Bond ?
>=20
> Hello,
>=20
> I saw "from chempy import Storage, Atom, Bond" in pymol source files.
>=20
> I can import chempy Atom successfully, but where can I find=20
> the defeintion of class Atom and bond ? I tried to print=20
> chempy.Atom.__file__, but it didn't work.
>=20
> Thanks.
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
> search engine that makes searching your log files as easy as=20
> surfing the  web.  DOWNLOAD SPLUNK!
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> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

Re: [PyMOL] Re: PyMOL-users digest, Vol 1 #1085 - 5 msgs

[Michael G. L. <ml...@um...>]

It's broken at the moment.  I'm working on a new version.  It should be 
out asap.

--
www.umich.edu/~mlerner |                        _  |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) |   Michigan
it's a cheer-ocracy.   |  - against HTML email  X  |  Biophysics
-Torrence,  Bring It On|                       / \ | mlerner@umich

On Mon, 19 Dec 2005, aar...@gs... wrote:

> Hello,
>
> Has anyone gotten the new apbs-0.4.0 to work with the apbs_tools.py plugin
> script?  It doesn't seem to be working for me.  My guess is that there are
> new parameters needed in the input file for 0.4.0 that are not created
> correctly by the plugin script.  I have used the older version (0.3.2)
> with success but the newer version gives me an error:
>
> PBEparm_check:  SDENS not set!
> NOsh:  MG parameters not set correctly!
> Error while parsing input file.
>
> Thanks
>
> Aaron
>
>
> Aaron B. Miller
> Computational Chemist
> GlaxoSmithKline R & D
> Five Moore Drive, North M1407
> RTP, NC 27709-3398
> (919) 483-6069  Fax (919) 315-0430
> Aar...@gs...
>

[PyMOL] Re: PyMOL-users digest, Vol 1 #1085 - 5 msgs

[<aar...@gs...>]

Hello,

Has anyone gotten the new apbs-0.4.0 to work with the apbs_tools.py plugin 
script?  It doesn't seem to be working for me.  My guess is that there are 
new parameters needed in the input file for 0.4.0 that are not created 
correctly by the plugin script.  I have used the older version (0.3.2) 
with success but the newer version gives me an error:

PBEparm_check:  SDENS not set!
NOsh:  MG parameters not set correctly!
Error while parsing input file.

Thanks

Aaron


Aaron B. Miller
Computational Chemist
GlaxoSmithKline R & D
Five Moore Drive, North M1407
RTP, NC 27709-3398
(919) 483-6069  Fax (919) 315-0430
Aar...@gs...

[PyMOL] points under surface

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

Dear pymol users.

Is there an easy way to determine whether a point (represented by its
x,y,z-coordinates) lies under the surface or not?

Any help would be appreciated.

Regards,
Martin

---
Martin Weisel
Diploma Student
Department of Bioinformatics
Frankfurt University

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

[PyMOL] representing regions in an ed map

[afyfe <af...@so...>]

I'd like to represent the surface of a connected region of an ed map, 
not an iso-value surface, and would be grateful for any clues on how to 
do this.
thanks,
Alastair

[PyMOL] plugin error

[Randy H. <he...@in...>]

There seems to be a bug in the code that allows for a plugin
installation -- at least on the Linux .98rc3 version:

In ...pymol/modules/pmg_tk/skins/normal/__init__.py , after first fixing
the typo 'install_plugin()' -> 'install_plugins()' (as has already been
reported), there still seems to be a bug in checking for write
permission on the plugin dir which always leads to:

Error: Unable to write to plugin directory (insufficient privileges?)

This reflects my situation:
>>> os.path.split(__file__)
('/home/heiland/pymol/modules/pmg_tk/skins/normal', '__init__.py')
>>> os.path.split(__file__)[:-2]
()


--Randy

[PyMOL] Where can I find the definition of class Atom and Bond ?

[Xiao J. <fdu...@gm...>]

Hello,

I saw "from chempy import Storage, Atom, Bond" in pymol source files.

I can import chempy Atom successfully, but where can I find the
defeintion of class Atom and bond ? I tried to print
chempy.Atom.__file__, but it didn't work.

Thanks.

RE: [PyMOL] double-click

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

Nat,

Have you tried using right-click for menus?

You can disable single_click to select in viewing mode with:

button single_left, none, none=20

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
> Nat Echols
> Sent: Wednesday, December 14, 2005 9:11 PM
> To: pym...@li...
> Subject: [PyMOL] double-click
>=20
>=20
> This is a new pet peeve of mine: it's too easy to select a=20
> residue instead of bringing up the menu of actions.  I still=20
> haven't figured out what the difference is, but I keep=20
> selecting by mistake.  Is there any way to either control the=20
> sensitivity of the clicking, or turn off mouse selections=20
> altogether?  (I tried changing mouse_selection_mode but this=20
> didn't help, and now it's stuck selecting everything with a=20
> single click.)
>=20
> thanks,
> Nat
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
> search engine that makes searching your log files as easy as=20
> surfing the  web.  DOWNLOAD SPLUNK!
> http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

RE: [PyMOL] Iterative Magic Fit - Why not?

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

Shiven,=20
=20
"align" does indeed work just fine for 3hck and 2src...
=20
3hck is an NMR structure ensemble, and PyMOL superimposes ensembles =
based on their average ensemble coordinates, not based on just one =
arbitrary structure (as is perhaps the case with DeepView?). =20
=20
The problem here is that members of the 3hck NMR ensemble are =
distributed randomly in space instead of being superimposed about a mean =
structure. =20
=20
To see this:
=20
set all_states, on
=20
To fix this:
=20
intra_fit 3hck
=20
Then, and only then, can you reasonably superimpose the 3hck ensemble =
onto the 2src crystal structure:
=20
align 3hck////ca, align 2src////ca
=20
Note that the align algorithm has been revised since 0.98.  For best =
results, use one of the latest beta versions:
=20
http://delsci.com/beta
=20
which have an "align" entry in the object and selection "action" menu.
=20
Another approach would be to specify that only state one source_state be =
used for the alignment:
=20
align 3hck////ca, align 2src////ca, source_state=3D1
=20
Regarding your comments, I would be surprised if DeepView magic fit =
owned PyMOL "align" in the general case -- but if it does, then by all =
means, please use the better product.  No one has ever forced a Troll to =
use "pathetic" software when there are such "fantastic" and =
"intelligent" alternatives available...but for some reason, they just =
do.  Pretty strange, eh?
=20
Cheers,
Warren
=20
________________________________

From: pym...@li... on behalf of Shivender =
Shandilya
Sent: Thu 12/15/2005 10:58 AM
To: pym...@li...
Subject: [PyMOL] Iterative Magic Fit - Why not?



Hi All,

Is there any possibility that Pymol may have the ability to =
"intelligently" superimpose two(or more) structures, without requiring =
the user to fiddle with selecting exactly the same number of =
atoms/residues. The "align" command fails pathetically in many =
instances, case in point, try aligning (or fitting) 3HCK and 2SRC.

In this scenario, DeepView (Swiss PDB Viewer) excels fantastically. Just =
select "Magic Fit" or "Iterative Magic Fit" from the "Fit" menu, then =
select the structures and alignment level from a simple drop down menu =
and viola! I wonder how they do it. (And lament that DeepView is no =
longer being developed).

Apologies for sounding so trollish!

Best,
Shiven


--
___________________________________________________
Play 100s of games for FREE! http://games.mail.com/



-------------------------------------------------------
This SF.net email is sponsored by: Splunk Inc. Do you grep through log =
files
for problems?  Stop!  Download the new AJAX search engine that makes
searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
http://ads.osdn.com/?ad_idv37&alloc_id=16865&op=3Dick
_______________________________________________
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PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users

[PyMOL] Video adapter recommendations?

[Vsevolod (S. I. <si...@cs...>]

Hi,

What recent video cards do you recommend for running Pymol on Windows?
We can spend around $500 on a card, but we'd like to make sure that it's 
worth buying.

Thanks,
Simon
-- 

Simon (Vsevolod ILyushchenko)   si...@cs...
				http://www.simonf.com

"Think like a man of action, act like a man of thought."

		         Henri Bergson

[PyMOL] Iterative Magic Fit - Why not?

[Shivender S. <sh...@ma...>]

Hi All,

Is there any possibility that Pymol may have the ability to "intelligently"=
 superimpose two(or more) structures, without requiring the user to fiddle =
with selecting exactly the same number of atoms/residues. The "align" comma=
nd fails pathetically in many instances, case in point, try aligning (or fi=
tting) 3HCK and 2SRC.

In this scenario, DeepView (Swiss PDB Viewer) excels fantastically. Just se=
lect "Magic Fit" or "Iterative Magic Fit" from the "Fit" menu, then select =
the structures and alignment level from a simple drop down menu and viola! =
I wonder how they do it. (And lament that DeepView is no longer being devel=
oped).

Apologies for sounding so trollish!

Best,
Shiven


--=20
___________________________________________________
Play 100s of games for FREE! http://games.mail.com/

[PyMOL] double-click

[Nat E. <ec...@uc...>]

This is a new pet peeve of mine: it's too easy to select a residue instead 
of bringing up the menu of actions.  I still haven't figured out what the 
difference is, but I keep selecting by mistake.  Is there any way to 
either control the sensitivity of the clicking, or turn off mouse 
selections altogether?  (I tried changing mouse_selection_mode but this 
didn't help, and now it's stuck selecting everything with a single click.)

thanks,
Nat

RE: [PyMOL] Coloring "ladder" differently from "ribbon" in nucleic acid representation

[Alex L. <tap...@ya...>]

Hi,

  If I am understanding your answer, you are saying to use
the cartoon_ladder_color to set the color for all sticks in
the object and then dictate the color of the one stick I
want to change using the atom. That's what I was trying to
do. The problem is that it doesn't work in
"nucleic_acid_mode, 1" b/c the C3* atom dictates the color
of both the ribbon as well as the stick. And if I change
the color of the N1 atom, I get a gradient from the C3*
color to the N1 atom. I want the entire stick to be one
color (and different from the ribbon).

  Nevertheless, and since my message I figured out a
convulated way to do it by duplicating the object:

# To color a stick with a different color from its ribbon
in 
# nucleic_acid_mode, 1
# obj01's sticks and ribbons are red
# I want resi 150 "stick" (but not ribbon) changed to blue
copy obj02, obj01
show cartoon, /obj02///150/N1
set cartoon_ladder_color,blue,obj02

  Obviously, not a very elegant solution especially 
given that pymol has the inherent ability to do the same 
thing without the duplication of objects. But nice to see 
that there is a way after all! So, in the end let's just 
leave it as a feature suggestion  - "A command to change
the
color of a specific ladder stick directly (and without
changing ribbon color)"

  -Alex

--- Warren DeLano <wa...@de...> wrote:

> Alex,
> 
> Hmm...not exactly.  you could set a uniform cartoon color
> for an object
> and then color the residue on a per-atom basis, or vice
> versa by setting
> the cartoon_ladder_color and relying on the atomic color
> for the
> cartoon, but there isn't a specific per-residue ladder or
> cartoon color
> (yet).
> 
> 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...      
>  
> 
> > -----Original Message-----
> > From: pym...@li... 
> > [mailto:pym...@li...] On
> Behalf Of 
> > Alex Luso
> > Sent: Wednesday, December 14, 2005 7:01 AM
> > To: pym...@li...
> > Subject: [PyMOL] Coloring "ladder" differently from
> "ribbon" 
> > in nucleic acid representation
> > 
> >   Hi,
> > 
> >   The new nucleic acid representation options are very
> welcome.
> > 
> >   One question regarding the coloring of the ladder
> > "sticks":
> > 
> > If I am in:
> > cartoon_nucleic_acid_mode, 1
> > cartoon_ladder_mode, 1
> > cartoon_ring_mode, 0
> > 
> > Is there a way to color the stick of a specified
> nucleotide 
> > differently from its ribbon? 
> > I can get a gradient color for the stick by doing
> "color 
> > green, /object///res/N1"
> > but if I try to change the color of the other atom
> involved 
> > in the ladder "stick" (i.e. "color green, 
> > /object///res/C3*"), then the color of the ribbon
> changes too 
> > (because we are in cartoon_nucleic_acid_mode,1). It's
> clearly 
> > possible to do b/c I can change the color of all sticks
> by 
> > doing "set cartoon_ladder_color, green" but this
> command acts 
> > globally.
> > I guess a related point is that perhaps it would be
> better to 
> > control the color of cartoon components directly, and 
> > selectively, rather than through the indirect method of
> color 
> > of atom -> maps to color of stick.
> > 
> >   Anyway, great job of integrating cartoon ribbons and
> the 
> > various ladder and ring options for nucleic acids. They
> look 
> > great. I am sure other options are on the way (as well
> as 
> > actual documentation!!).
> > 
> >   -Alex
> > 
> > BTW: the wiki is wrong in
> >
>
http://www.pymolwiki.org/index.php/Examples_of_cartoon_ring_an
> > d_cartoon_ladder_settings
> > where it says that cartoon_nucleic_acid_mode,1 #
> follows 
> > phosphates. That should read # follows C3*, as far as I
> can tell.
> > 
> > __________________________________________________
> > Do You Yahoo!?
> > Tired of spam?  Yahoo! Mail has the best spam
> protection 
> > around http://mail.yahoo.com 
> > 
> > 
> > -------------------------------------------------------
> > This SF.net email is sponsored by: Splunk Inc. Do you
> grep 
> > through log files
> > for problems?  Stop!  Download the new AJAX search
> engine that makes
> > searching your log files as easy as surfing the  web.  
> > DOWNLOAD SPLUNK!
> > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> >
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> > 
> > 
> > 
> > 
> 



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RE: [PyMOL] translating and rotating protein in space

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

Vanessa,

You're missing commas, and you need to issue the command in the model
frame of reference (camera frame of reference is the default):

translate [-14.911, -23.457, -1.534], camera=3D0

\
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
> Vanessa Oklejas
> Sent: Wednesday, December 14, 2005 4:36 PM
> To: pym...@li...
> Subject: [PyMOL] translating and rotating protein in space
>=20
> Hi all,
>=20
> I would like to translate and rotate a protein in pymol such=20
> that the pdb coordinates place the center at a specific atom=20
> in the pdb structure.  For example,  if the atom of interest=20
> has the coordinates
> [14.911 23.457 1.534], then I would the pdb coordinates to be [0 0 0].
>=20
> I've tried to use the "translate" keyword from the command line:
>=20
>  >> translate [-14.911 -23.457 -1.534]
>=20
> However I get the following error message:
> Traceback (most recent call last):
>    File "C:\Program Files\DeLano
> Scientific\PyMOL/modules\pymol\parser.py", line 188, in parse
>      result=3Dapply(kw[nest][0],args[nest],kw_args[nest])
>    File "C:\Program Files\DeLano
> Scientific\PyMOL/modules\pymol\editing.py", line 1126, in translate
>      vector =3D [float(vector[0]),float(vector[1]),float(vector[2])]
>=20
>=20
>=20
>=20
> Any help out there?
>=20
> Muchos Gracias,
> Vanessa
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
> search engine that makes searching your log files as easy as=20
> surfing the  web.  DOWNLOAD SPLUNK!
> http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

[PyMOL] translating and rotating protein in space

[Vanessa O. <vok...@st...>]

Hi all,

I would like to translate and rotate a protein in pymol such that the 
pdb coordinates place the center at a specific atom in the pdb 
structure.  For example,  if the atom of interest has the coordinates 
[14.911 23.457 1.534], then I would the pdb coordinates to be [0 0 0].

I've tried to use the "translate" keyword from the command line:

 >> translate [-14.911 -23.457 -1.534]

However I get the following error message:
Traceback (most recent call last):
   File "C:\Program Files\DeLano 
Scientific\PyMOL/modules\pymol\parser.py", line 188, in parse
     result=apply(kw[nest][0],args[nest],kw_args[nest])
   File "C:\Program Files\DeLano 
Scientific\PyMOL/modules\pymol\editing.py", line 1126, in translate
     vector = [float(vector[0]),float(vector[1]),float(vector[2])]




Any help out there?

Muchos Gracias,
Vanessa

RE: [PyMOL] Coloring "ladder" differently from "ribbon" in nucleic acid representation

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

Alex,

Hmm...not exactly.  you could set a uniform cartoon color for an object
and then color the residue on a per-atom basis, or vice versa by setting
the cartoon_ladder_color and relying on the atomic color for the
cartoon, but there isn't a specific per-residue ladder or cartoon color
(yet).

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
> Alex Luso
> Sent: Wednesday, December 14, 2005 7:01 AM
> To: pym...@li...
> Subject: [PyMOL] Coloring "ladder" differently from "ribbon"=20
> in nucleic acid representation
>=20
>   Hi,
>=20
>   The new nucleic acid representation options are very welcome.
>=20
>   One question regarding the coloring of the ladder
> "sticks":
>=20
> If I am in:
> cartoon_nucleic_acid_mode, 1
> cartoon_ladder_mode, 1
> cartoon_ring_mode, 0
>=20
> Is there a way to color the stick of a specified nucleotide=20
> differently from its ribbon?=20
> I can get a gradient color for the stick by doing "color=20
> green, /object///res/N1"
> but if I try to change the color of the other atom involved=20
> in the ladder "stick" (i.e. "color green,=20
> /object///res/C3*"), then the color of the ribbon changes too=20
> (because we are in cartoon_nucleic_acid_mode,1). It's clearly=20
> possible to do b/c I can change the color of all sticks by=20
> doing "set cartoon_ladder_color, green" but this command acts=20
> globally.
> I guess a related point is that perhaps it would be better to=20
> control the color of cartoon components directly, and=20
> selectively, rather than through the indirect method of color=20
> of atom -> maps to color of stick.
>=20
>   Anyway, great job of integrating cartoon ribbons and the=20
> various ladder and ring options for nucleic acids. They look=20
> great. I am sure other options are on the way (as well as=20
> actual documentation!!).
>=20
>   -Alex
>=20
> BTW: the wiki is wrong in
> http://www.pymolwiki.org/index.php/Examples_of_cartoon_ring_an
> d_cartoon_ladder_settings
> where it says that cartoon_nucleic_acid_mode,1 # follows=20
> phosphates. That should read # follows C3*, as far as I can tell.
>=20
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection=20
> around http://mail.yahoo.com=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web. =20
> DOWNLOAD SPLUNK!
> http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

[PyMOL] Coloring "ladder" differently from "ribbon" in nucleic acid representation

[Alex L. <tap...@ya...>]

  Hi,

  The new nucleic acid representation options are very
welcome.

  One question regarding the coloring of the ladder
"sticks":

If I am in:
cartoon_nucleic_acid_mode, 1
cartoon_ladder_mode, 1
cartoon_ring_mode, 0

Is there a way to color the stick of a specified nucleotide
differently from its ribbon? 
I can get a gradient color for the stick by doing
"color green, /object///res/N1"
but if I try to change the color of the other atom involved
in the ladder "stick" (i.e. "color green,
/object///res/C3*"), then the color of the ribbon changes
too (because we are in cartoon_nucleic_acid_mode,1). It's
clearly possible to do b/c I can change the color of all
sticks by doing "set cartoon_ladder_color, green" but this
command acts globally.
I guess a related point is that perhaps it would be better
to control the color of cartoon components directly, and
selectively, rather than through the indirect method of
color of atom -> maps to color of stick.

  Anyway, great job of integrating cartoon ribbons and the
various ladder and ring options for nucleic acids. They
look great. I am sure other options are on the way (as well
as actual documentation!!).

  -Alex

BTW: the wiki is wrong in
http://www.pymolwiki.org/index.php/Examples_of_cartoon_ring_and_cartoon_ladder_settings
where it says that cartoon_nucleic_acid_mode,1 # follows
phosphates. That should read # follows C3*, as far as I can tell.

__________________________________________________
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