pymol-users Mailing List for PyMOL Molecular Graphics System

Yusuf,

alter selection, vdw=3Dradius

eg.

alter elem c, vdw=3D3.2

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
> tan...@st...
> Sent: Thursday, June 30, 2005 8:41 AM
> To: pym...@li...
> Subject: [PyMOL] Radii in Angstrom
>=20
> Hi,
>=20
> if I show up a sphere around an picked atom, and want to=20
> change its radius, I always use the
>   set sphere_scale
> method. But, to which value am I scaling to? Isn't it=20
> possible to change the radius of a sphere with something like=20
> 'set sphere_radius' in Angstroms?
> I could not find any information in the manual and the reference.
> My aim is to project a sphere (or another projection) with a=20
> certain radius like
> 3.2 Angstrom around an atom. After I realized that I could=20
> not do this with the implemented spheres, I checked the
>   set dots_* methods,
> where I did find a
>   set dots_radius.
> But everytime I use this function, the dots stay at their=20
> position and PyMol does not change anything on screen (and=20
> raytracing leeds to a crash).
>=20
> So, am I doing anything wrong or are these methods not=20
> available at the moment?
>=20
> Regards
>=20
> Yusuf Tanrikulu
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration=20
> Strategies from IBM. Find simple to follow Roadmaps,=20
> straightforward articles, informative Webcasts and more! Get=20
> everything you need to get up to speed, fast.=20
> http://ads.osdn.com/?ad_id=3D7477&alloc_id=3D16492&op=3Dclick
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20

Hi,

if I show up a sphere around an picked atom, and want to change its radius, I
always use the
  set sphere_scale
method. But, to which value am I scaling to? Isn't it possible to change the
radius of a sphere with something like 'set sphere_radius' in Angstroms?
I could not find any information in the manual and the reference.
My aim is to project a sphere (or another projection) with a certain radius like
3.2 Angstrom around an atom. After I realized that I could not do this with the
implemented spheres, I checked the
  set dots_* methods,
where I did find a
  set dots_radius.
But everytime I use this function, the dots stay at their position and PyMol
does not change anything on screen (and raytracing leeds to a crash).

So, am I doing anything wrong or are these methods not available at the moment?

Regards

Yusuf Tanrikulu

Hi,
yes it worked. that mistake is so shameful ... :P
thanks

andrea

2005/6/30, li...@ul... <li...@ul...>:
> On Thursday 30 June 2005 13:26, Andrea Spitaleri wrote:
> > from pymol import cmd
> > file=3Dopen("file.nam")
> > for i in file.readlines():
> >     cmd.load(i)
>=20
> You may have to strip the trailing newline ("\n") from each file name by =
using
> "cmd.load(i.strip())".
>=20
> Hope this helps,
> --
> Lieven Buts
> Vrije Universiteit Brussel
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> from IBM. Find simple to follow Roadmaps, straightforward articles,
> informative Webcasts and more! Get everything you need to get up to
> speed, fast. http://ads.osdn.com/?ad_id=3D7477&alloc_id=3D16492&op=3Dclic=
k
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

On Thursday 30 June 2005 13:26, Andrea Spitaleri wrote:
> from pymol import cmd
> file=open("file.nam")
> for i in file.readlines():
>     cmd.load(i)

You may have to strip the trailing newline ("\n") from each file name by using 
"cmd.load(i.strip())".

Hope this helps,
-- 
Lieven Buts
Vrije Universiteit Brussel

On Thursday 30 June 2005 13:26, Andrea Spitaleri wrote:
> from pymol import cmd
> file=open("file.nam")
> for i in file.readlines():
>     cmd.load(i)

You may have to strip the trailing newline ("\n") from each file name by using 
"cmd.load(i.strip())".

Hope this helps,
-- 
Lieven Buts
Vrije Universiteit Brussel

Hi
this is my "unsuccessful" first script for pymol.
I have a series of files: prot1.pdb prot4.pdb prot55.pdb and so on I'd
like to open them using a loop (instead to open one by one)
I cat them to a file and then I tried to open all of them in pymol:

from pymol import cmd
file=3Dopen("file.nam")
for i in file.readlines():
    cmd.load(i)

but is says:
ObjectMolecule-ERROR: Unable to open file 'prot1.pdb'
ObjectMolecule-ERROR: Unable to open file 'prot4.pdb'
..........
the file.nam is just a list:
prot1.pdb
prot4.pdb
prot55.pdb
.....

thanks for any help

Regards

andrea

Hello,

thanks for the prompt reply, it works great!

Cheers

Yusuf

Quoting Warren DeLano <wa...@de...>:

> Yusuf,
>
> see
> http://sourceforge.net/mailarchive/forum.php?thread_id=7495694&forum_id=60
>
> Close!  Actually I like you're usage expectation even better than how
> PyMOL currently works -- but at the present time you need to convert
> those indices into selection strings:
>
> from pymol import cmd
> cmd.load("$PYMOL_PATH/test/dat/pept.pdb")
>
> cmd.select('sel01', 'elem c and not (neighbor elem n+o)')
> cmd.color('green', 'sel01')
> cmd.show('spheres', 'sel01')
> atoms = cmd.index('sel01')
> di = 0.0
> for i in atoms:
>    for j in atoms:
>        di += cmd.get_distance("%s`%d"%i,"%s`%d"%j)
> print di
>
> 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
>> tan...@st...
>> Sent: Wednesday, June 29, 2005 7:51 AM
>> To: pym...@li...
>> Cc: g.s...@ch...
>> Subject: [PyMOL] Sum distances in loop via python script
>>
>> Hi everybody,
>>
>> I am new to PyMol and scripting with Python, and I would be
>> very grateful if
>> anybody can help me.
>> After loading serveral superposed molecules, I made a
>> selection of some atoms as
>> follows:
>>
>>  from pymol import cmd
>>  cmd.select('sel01', ('elem c and not (neighbor elem n+o)')
>>  cmd.color ('green', 'sel01')
>>  cmd.show ('spheres', 'sel01)
>>
>> Now, I want to measure the distance from an atom in this
>> selection to all other
>> atoms in sel01 and sum it up. How am I supposed to do this in
>> my Python-Pymol
>> (.py) script?
>>
>> I know that it must be something like:
>>
>>  atoms = cmd.index('sel01')
>>  di = 0
>>  for i in atoms
>> 	 for j in atoms
>> 	 	di += cmd.distance(i,j)
>>  print di
>>
>> But this actually does not work. Any advise?
>>
>> Best regards
>>
>> Yusuf Tanrikulu
>>
>>
>> --
>> Yusuf Tanrikulu
>> Bioinformatics Diploma Student
>> Department of Biosciences
>> Johann Wolfgang Goethe-University
>> Marie-Curie-Str. 11
>> D-60439 Frankfurt, Germany
>> Email: tan...@st...
>>
>>
>> -------------------------------------------------------
>> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
>> from IBM. Find simple to follow Roadmaps, straightforward articles,
>> informative Webcasts and more! Get everything you need to get up to
>> speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>>
>

Hi Joel,

thanks a lot for the tip! excellent stuff using my loved editor!

andr

2005/6/29, Joel Tyndall <joe...@ot...>:
> Hi andrea,
>=20
> I have found an excellent add on tool for emacs which does a lot of
> renumbering stuff (on unix/linux)
>=20
> http://stein.bioch.dundee.ac.uk/~charlie/scripts/pdb-mode.html
>=20
> Cheers
>=20
> Joel
>=20
> Andrea Spitaleri wrote:
>=20
> >Hi all,
> >I couldn't find any command in pymol to renumber the segid of a protein.
> >Is there any way to do it?
> >
> >Regards
> >
> >andrea
> >
> >
> >-------------------------------------------------------
> >SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> >from IBM. Find simple to follow Roadmaps, straightforward articles,
> >informative Webcasts and more! Get everything you need to get up to
> >speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=3Dclick
> >_______________________________________________
> >PyMOL-users mailing list
> >PyM...@li...
> >https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> >
> >
>=20
> --
> Joel Tyndall, PhD
>=20
> Lecturer
> National School of Pharmacy
> University of Otago
> PO Box 913 Dunedin
> New Zealand
>=20
> Pukenga
> Te Kura Taiwhanga Putaiao
> Te Whare Wananga o Otago
> Pouaka Poutapeta 913 Otepoti
> Aotearoa
>=20
> Ph / Waea               +64 3 4797293
> Fax / Waeawhakaahua     +64 3 4797034
>=20
>

Hi andrea,

I have found an excellent add on tool for emacs which does a lot of=20
renumbering stuff (on unix/linux)

http://stein.bioch.dundee.ac.uk/~charlie/scripts/pdb-mode.html

Cheers

Joel

Andrea Spitaleri wrote:

>Hi all,
>I couldn't find any command in pymol to renumber the segid of a protein.=

>Is there any way to do it?
>
>Regards
>
>andrea
>
>
>-------------------------------------------------------
>SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
>from IBM. Find simple to follow Roadmaps, straightforward articles,
>informative Webcasts and more! Get everything you need to get up to
>speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=3Dclick
>_______________________________________________
>PyMOL-users mailing list
>PyM...@li...
>https://lists.sourceforge.net/lists/listinfo/pymol-users
>
> =20
>

--=20
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand                    =20

Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea               +64 3 4797293=20
Fax / Waeawhakaahua     +64 3 4797034

We are interested in having Pymol installed and run on one of our
computers in the lab.  However, our lab IT says she needs more
information on how the license works, and what the "subscription"
entails.

Douglas McKinney
Biological Sciences Dept.
Northern Illinois University.


		
____________________________________________________ 
Yahoo! Sports 
Rekindle the Rivalries. Sign up for Fantasy Football 
http://football.fantasysports.yahoo.com

Andrea,

alter selection, segi=3D'SEGI'
sort

for example

alter 10-150/, segi=3D'PRT1'
alter 510-650/, segi=3D'PRT2'
sort

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
> Andrea Spitaleri
> Sent: Wednesday, June 29, 2005 12:44 AM
> To: pym...@li...
> Subject: [PyMOL] Renumber protein segid
>=20
> Hi all,
> I couldn't find any command in pymol to renumber the segid of=20
> a protein.
> Is there any way to do it?
>=20
> Regards
>=20
> andrea
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration=20
> Strategies from IBM. Find simple to follow Roadmaps,=20
> straightforward articles, informative Webcasts and more! Get=20
> everything you need to get up to speed, fast.=20
> http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=3Dick
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20

Hi everybody,

I am new to PyMol and scripting with Python, and I would be very grateful if
anybody can help me.
After loading serveral superposed molecules, I made a selection of some atoms as
follows:

 from pymol import cmd
 cmd.select('sel01', ('elem c and not (neighbor elem n+o)')
 cmd.color ('green', 'sel01')
 cmd.show ('spheres', 'sel01)

Now, I want to measure the distance from an atom in this selection to all other
atoms in sel01 and sum it up. How am I supposed to do this in my Python-Pymol
(.py) script?

I know that it must be something like:

 atoms = cmd.index('sel01')
 di = 0
 for i in atoms
	 for j in atoms
	 	di += cmd.distance(i,j)
 print di

But this actually does not work. Any advise?

Best regards

Yusuf Tanrikulu


--
Yusuf Tanrikulu
Bioinformatics Diploma Student
Department of Biosciences
Johann Wolfgang Goethe-University
Marie-Curie-Str. 11
D-60439 Frankfurt, Germany
Email: tan...@st...

Hi all,
I couldn't find any command in pymol to renumber the segid of a protein.
Is there any way to do it?

Regards

andrea

PyMOL Users,

I am taking a short vacation July 8th-15th and will be out of email
contact, so you will need to rely exclusively on the mailing list for
help with urgent PyMOL usage issues during that week.  Joni will however
be able to process any business matters that arise during that time
period.

Also note that we have been having some trouble with our Email ISP over
the past week or two.  If your email to us has bounced with an "invalid
email address" message, then please try resending. =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

Hello everyone!

 

I have a problem. I load the pdb file and than use the command "create" to
divide the molecule into smaller parts. The objects are created, however
some small parts are missing, giving an effect of holes in the structure, or
that pieces of molecule are separated from the main part. I need to create
the objects in order to split the molecule in half in a movie. I tried to
use "hide" and "show" and then "translate" to obtain the same splitting
effect, but there's also a problem by that, because I cannot put the
molecule back together for playing the movie continuously, even if I perform
the same steps I did for splitting it. What can I do to avoid losing parts
of the molecule by "create" command? I use Python to make the movie by the
way.

Could anyone help me?

 

Thanks,

 

          Aga

On Sun, 12 Jun 2005, Dyda wrote:

> I'd like to know what charges Pymol uses when
> generates a pqr file from a pdb.
>
> The follow-up would be is whether there was
> a way to change this, say if one wanted to
> use charmm charges rather than amber.

PyMOL uses amber99 charges and radii.  This is taken care of in 
pymol/modules/chempy/champ/amber99.py.  It would be possible to add a 
different forcefield by using that as a template and changing a few things 
in pymol/modules/chempy/champ/assign.py, but it would take more free time 
than I have right now.

> It seems that APBS hates chain IDs. Is that
> really so, or just my imagination?

This is true, but has been fixed in the current version of the PyMOL/APBS 
Plugin.  Warren has added a couple of other nice features to the current 
version.  Here's a copy of a message that I just sent to the APBS list:

Hi all,

This is fixed in the current PyMOL source tree, and it'll be fixed in the 
next released version of PyMOL.  In the meantime, you can
download the current version here:

http://www-personal.umich.edu/~mlerner/PyMOL/apbs_tools.py

There are installation instructions at the top of

http://www-personal.umich.edu/~mlerner/PyMOL/

but it boils down to "replace your 
$PYMOL_PATH/modules/pmg_tk/startup/apbs_tools.py with the current one."

There are a few other new features, including:

  - More reasonable starting dielectric constants
  - The ability to set a maximum number of grid points
  - The ability to display solvent accessible surfaces as well as molecular
    surfaces
  - Better warnings when PyMOL is unable to generate appropriate parameters
    in the PQR file.

Sometime soon, I'll probably also change the .in file to say things like 
"bcfl sdh" instead of "bcfl 1" etc.

Given that the PyMOL/APBS Plugin is getting updated a bit, please let me 
know if there are any features/changes you'd like.

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

hello All:

  i want to creat a pymol script to creat publication quality image such 
as using "actions preset publication" menu.

  i have tried using "color" command to determine the cartoon second 
structure color. it seems using this command the color of "lines resdiues" 
will also be changed. but if i use "actions preset publication" then 
using "show lines" command the color of "lines residues" will not be 
changed.

 So what is the correct steps that can changing the cartoon color only?

 regards
                                                 caoch
-- 
ca...@ch...

Joel,

> align 1kjg & i. 1-99 & n. ca, 1kjh & i. 1-99 & n. ca

pair_fit 1kjg///1-99/ca, 1kjh///1-99/ca

pair_fit will use all atoms, whereas align will only use atoms that are
matched with respect to a dynamic-programming sequence alignment.

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
> Joel Tyndall
> Sent: Sunday, June 26, 2005 4:08 PM
> To: pym...@li...
> Subject: [PyMOL] align/fit
>=20
> Hi folks,
>=20
> Been sitting here getting a little confused with the=20
> seemingly endless possibilities of the fit and align=20
> commands. What I want to do is a pairwise alignment of  the=20
> ca atoms of protein portion of some HIV complexes ie 2 chains=20
> of 99 residues).
>=20
> When I use the command
>=20
> align 1kjg & i. 1-99 & n. ca, 1kjh & i. 1-99 & n. ca
>=20
> pinched from robert campbells website (ta) I get the=20
> following results:
>=20
>  Match: read scoring matrix.
>  Match: assigning 208 x 209 pairwise scores.
>  MatchAlign: aligning residues (208 vs 209)...
>  ExecutiveAlign: 195 atoms aligned.
>  ExecutiveRMS: 5 atoms rejected during cycle 1 (RMS=3D2.49).
>  ExecutiveRMS: 6 atoms rejected during cycle 2 (RMS=3D0.67).
>  Executive: RMS =3D    0.475 (184 to 184 atoms)
>=20
> I know how to turn off the refinement so thats and that=20
> aligns 195 atoms without refinement. (This can be also=20
> complicated when the 2 chains are A and B or 1-99 and=20
> 101-199). So what I am after is the protein alignment which=20
> will align 198 atoms (2 x chain of 99 residues) to give me a=20
> pairwise alignment to compare _multiple _structures.
>=20
> Could someone point me in the right direction please.
>=20
> Many thanks
>=20
> Joel
>=20
> --
> Joel Tyndall, PhD
>=20
> Lecturer
> National School of Pharmacy
> University of Otago
> PO Box 913 Dunedin
> New Zealand                    =20
>=20
> Pukenga
> Te Kura Taiwhanga Putaiao
> Te Whare Wananga o Otago
> Pouaka Poutapeta 913 Otepoti
> Aotearoa
>=20
> Ph / Waea               +64 3 4797293=20
> Fax / Waeawhakaahua     +64 3 4797034
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration=20
> Strategies from IBM. Find simple to follow Roadmaps,=20
> straightforward articles, informative Webcasts and more! Get=20
> everything you need to get up to speed, fast.=20
> http://ads.osdn.com/?ad_id=3D7477&alloc_id=3D16492&op=3Dclick
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20

you can set the number of cycles of refinement on the command line.
change this:

> align 1kjg & i. 1-99 & n. ca, 1kjh & i. 1-99 & n. ca

to this:

> align 1kjg & i. 1-99 & n. ca, 1kjh & i. 1-99 & n. ca, 0, 0

I forget what the first 0 means; the second means "don't refine."  It'll
use all matching atoms this way.

So whilst I'm picking your collective brains, how would I set up a 
superimposition using say 4 different residues usingthe backbones or ca 
atoms? ie two from each separate chain of the homodimer?

Thanks again

J

-- 
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
Pouaka Poutapeta 913 Otepoti
Aotearoa

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

Hi folks,

Been sitting here getting a little confused with the seemingly endless 
possibilities of the fit and align commands. What I want to do is a 
pairwise alignment of  the ca atoms of protein portion of some HIV 
complexes ie 2 chains of 99 residues).

When I use the command

align 1kjg & i. 1-99 & n. ca, 1kjh & i. 1-99 & n. ca

pinched from robert campbells website (ta) I get the following results:

 Match: read scoring matrix.
 Match: assigning 208 x 209 pairwise scores.
 MatchAlign: aligning residues (208 vs 209)...
 ExecutiveAlign: 195 atoms aligned.
 ExecutiveRMS: 5 atoms rejected during cycle 1 (RMS=2.49).
 ExecutiveRMS: 6 atoms rejected during cycle 2 (RMS=0.67).
 Executive: RMS =    0.475 (184 to 184 atoms)

I know how to turn off the refinement so thats and that aligns 195 atoms 
without refinement. (This can be also complicated when the 2 chains are 
A and B or 1-99 and 101-199). So what I am after is the protein 
alignment which will align 198 atoms (2 x chain of 99 residues) to give 
me a pairwise alignment to compare _multiple _structures.

Could someone point me in the right direction please.

Many thanks

Joel

-- 
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
Pouaka Poutapeta 913 Otepoti
Aotearoa

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

I have MacPyMOL, which I downloaded as macpymol-0_98rc2, running on a 
G5 with the Jaguar OS X (10.3.9).  I used to be able to cut and paste 
from text files and into the PyMOL GUI, for example to access a view 
that I stored in a log file using get_view and set_view.  Now I can no 
longer paste successfully into the GUI (either the Native GUI or the 
Viewer window).

Has this happened to anyone else?  Any suggestions for fixing?

Many Thanks,

Sarina Bromberg
1 (888) 291-5196 | Toll Free Long Distance
(650) 879-1492 | Local
PO Box 12, Pescadero, CA 94060
sa...@ac... 

Hi list,

I'm very new to PyMOL, so please be gentle. I use macPyMOL 0.98

I ran into a problem when trying to run what may seem like a very  
simple script in order to create a movie that zooms into a ligand  
binding site of a protein:

     set ray_trace_frames, 1
     set cache_frames, 0
     set hash_max, 400
     cmd.mset("1 x5")
     for a in range (1, 5):
         cmd.mdo(a, "move z, 10")
     cmd.mpng("/frames/frame")

When I run this script, I do get 5 rendered png files, but they're  
all the same. The move command does not get executed. The log reveals  
the following:

PyMOL>set ray_trace_frames, 1
  Setting: ray_trace_frames set to on.
PyMOL>set cache_frames, 0
  Setting: cache_frames set to off.
PyMOL>set hash_max, 400
  Setting: hash_max set to 400.
PyMOL>cmd.mset("1 x5")
PyMOL>for a in range (1, 5):
Traceback (most recent call last):
   File "/users/warren/pymol/products/MacPyMOL.app/pymol/modules/ 
pymol/parser.py", line 194, in parse
     exec(com2[nest]+"\n",pymol_names,pymol_names)
   File "<string>", line 1
      for a in range (1, 5):
                            ^
  SyntaxError: unexpected EOF while parsing
PyMOL>cmd.mdo(a, "move z, 20")
Traceback (most recent call last):
   File "/users/warren/pymol/products/MacPyMOL.app/pymol/modules/ 
pymol/parser.py", line 356, in parse
     exec(com2[nest]+"\n",pymol_names,pymol_names)
   File "<string>", line 1, in ?
NameError: name 'a' is not defined
PyMOL>cmd.mpng("/frames/frame")
  Ray: total time: 8.47 sec. = 425.2 frames/hour. (8.47 sec. accum.)
  Ray: total time: 8.55 sec. = 421.0 frames/hour. (17.02 sec. accum.)
  Ray: total time: 8.51 sec. = 423.2 frames/hour. (25.52 sec. accum.)
  Ray: total time: 8.49 sec. = 424.1 frames/hour. (34.01 sec. accum.)
  Ray: total time: 8.49 sec. = 424.1 frames/hour. (42.50 sec. accum.)

The file path in the Traceback obviously does not exist on my Mac.  
Does anyone know what's going on here?

TIA for any advice. I really would like to get this zoom thing  
accomplished.

-Reinhold

Hi Anders,

With cmd.get_povray() (i.e. cmd.get_povray()[1]) you'll=20
get all vertex-coordinates describing the surface, but I=20
wouldn't know how you could use it to map something on=20
there neatly.

Cheers,

Tsjerk

On Wed, 22 Jun 2005 08:55:05 +0200
  madsen <ma...@cc...> wrote:
> Dear Robert, Tsjerk, Jean-Philippe and Tim
> thanks for your replies.
>=20
> The colouring of atoms according to B-factors
> or some other property is nice, but I really need
> sub-atomic resolution of the properties that I would
> like to map on the surface.
>=20
> So, as Jean-Philippe and Tim are discussing, I would=20
>like
> to access the defining coordinates of the surface, or by=20
>some
> other means be able to hack the colouring of the=20
>surface.
>=20
> There is apparantly no standard trick for doing just=20
>that.
>=20
> I will have a look at povscript+.
> Thanks for the hint!
>=20
> regards
> 		Anders
>=20
> On Tue, Jun 21, 2005 at 02:23:24PM -0400, Robert=20
>Campbell wrote:
>> Anders,
>>=20
>> * Anders Madsen <ma...@cc...> [2005-06-21 16:33]=20
>>wrote:
>> > Dear PyMol users,
>> > I would like to colour the beautiful
>> > PyMol molecular surfaces according to
>> > properties of the atoms involved.
>> > Has anyone experimented with this?
>> >=20
>> > E.g. by accessing the coordinates that define
>> > the surface and assign a colour to each triangle
>> > involved in the surface mesh?
>>=20
>> If you only need to colour it at the resolution of the=20
>>atoms (as opposed
>> to individual surface vertices), then you can do so by=20
>>altering the
>> B-factor or occupancy values and colouring the structure=20
>>on those. I
>> have a script for reading a file of data and applying it=20
>>to the B-factor
>> or occupancy. Then you just need to colour using the=20
>>built-in spectrum
>> method or using my color_b.py script. See the=20
>>data2bfactor.py script in:
>>=20
>>   http://adelie.biochem.queensu.ca/~rlc/work/pymol
>>=20
>> Within that script, four functions are defined:
>>   data2b_atom
>>   data2b_res
>>   data2q_atom
>>   data2q_res
>>=20
>> The "2b" functions alter the B-factor and the "2q"=20
>>functions alter the
>> occupancy.  The "_atom" functions are used to apply a=20
>>value to
>> individual atoms, while the "_res" functions are used to=20
>>apply a single
>> value to the whole residue.
>>=20
>> You just need to create a data file that looks like:
>>=20
>> A 1 ALA N  data
>> A 1 ALA CA  data
>> A 1 ALA C  data
>> A 1 ALA O  data
>> A 1 ALA CB  data
>>=20
>> etc.  (or omit the chain if not defined in your=20
>>structure)
>>=20
>> or=20
>>=20
>> A 1 ALA data
>> A 2 SER data
>> A 3 PRO data
>>=20
>> etc. (again omit the chain if not defined).
>>=20
>>=20
>> Cheers,
>> Rob
>> --=20
>> Robert L. Campbell, Ph.D.=20
>>                        <rl...@po...>
>> Senior Research Associate=20
>>                           phone: 613-533-6821
>> Dept. of Biochemistry, Queen's University,=20
>>            fax: 613-533-2497
>> Kingston, ON K7L 3N6  Canada=20
>>      http://adelie.biochem.queensu.ca/~rlc
>>     PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238=20
>>A8F5 F635 C0E2
>>=20
>>=20
>> -------------------------------------------------------
>> SF.Net email is sponsored by: Discover Easy Linux=20
>>Migration Strategies
>> from IBM. Find simple to follow Roadmaps,=20
>>straightforward articles,
>> informative Webcasts and more! Get everything you need=20
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>=20
> --=20
> Anders =D8stergaard Madsen                         =20
> Centre for Crystallographic Studies                =20
> Department of Chemistry, University of Copenhagen  =20
> Universitetsparken 5 DK-2100 KBH Denmark           =20
> home: R=F8de Mellemvej 18, 1. DK-2300 Kbh. S         =20
> email: ma...@cc... =20
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux=20
>Migration Strategies
> from IBM. Find simple to follow Roadmaps,=20
>straightforward articles,
> informative Webcasts and more! Get everything you need=20
>to get up to
> speed, fast.=20
>http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=FFick
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Dear All,

Is there a way in which you can rotate the camera (say turn y, 90) whilst
leaving the clipping planes (and objects) where they are? I want to an
oblique slab a slice through an electron density map (which I can do fine),
and then rotate around y by 90deg to see the "side view" of that cut map
(which can't think how to do at all!). Maybe there's a fiendishly clever
way..?

Cheers

Neil.

 

 

 

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

Neil Ranson PhD

University Research Fellow,

Astbury Centre for Structural Molecular Biology,

School of Biochemistry & Microbiology,

University of Leeds,

Leeds, LS2 9JT. UK.

 

Tel: +44 (0) 113 343 7065

Fax: +44 (0) 113 343 3167

n.a...@le...

 

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