pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Chandra,

1. Just load the file on the command line or through the interface
("load"). Then to show all structures use 'set all_states,1' or
'split_states' if you want to have them as separate objects.

2. First create an object of the selection.

3. Please read the manual, search the archives and the Wiki, as these
issues have crossed several times already.

Cheers,

Tsjerk

On 7/29/06, Chandra Verma <ch...@bi...> wrote:
> I have two questions:
>
> 1. how does one load in all pdb files from an nmr -type master pdb file
> where the various models are delimited by the keyword MODEL
>
> 2. given two or more chains in a pdb file, how can i draw a surface that
> takes into account only a selection. when i try this after the usual
> selection of say chain A, it draws the surface but if there is an
> interface of chainA and chain B then there is a cut at the interfacial
> region. someone once told me but i accidentally deleted that email
>
> thanks
>
> chandra
>
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
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-- 

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

I have two questions:

1. how does one load in all pdb files from an nmr -type master pdb file 
where the various models are delimited by the keyword MODEL

2. given two or more chains in a pdb file, how can i draw a surface that 
takes into account only a selection. when i try this after the usual 
selection of say chain A, it draws the surface but if there is an 
interface of chainA and chain B then there is a cut at the interfacial 
region. someone once told me but i accidentally deleted that email

thanks

chandra

Folks,

In case there is anyone out there still stuggling to get PyMOL installed on
their new DELL system, below is the latest word on how to work around the
problem (graciously passed along by one of our users):

Cheers,
Warren

"I found the solution, apparently the installer gets screwed up by some
software 
that Dell installs as part of their standard build.   The fix can be found
at: 

http://www.wave.com/support/CSC/CustomerService/Documents/DM-010.htm 

I followed the steps in the above url and PyMol installed without a hitch. 

A detailed discussion on the topic can be found at: 

http://forum.installsite.net/index.php?s=03b224df496bbf806744f85d27c687e9&sh
owtopic=14905&st=0&#entry41109 

Please spread the word."

> Pymol isn't very good at handling many spheres. 

Slanderous! ...but true with default settings.   However:

./pymol -O 1 monster_large_file.pdb 

Will enable PyMOL to display, manipulate, and render at least a million
spheres per GB of RAM.

Also try -O values up through 5 for alternate approaches for handling large
numbers of spheres.  -O 5 uses a shader program on cards which support it in
to create pixel-perfect OpenGL spheres.

(BTW that's a capital O, not a zero).

Cheers,
Warren

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Tsjerk Wassenaar
> Sent: Friday, July 28, 2006 1:14 AM
> To: Phi...@ou...
> Cc: pym...@li...
> Subject: Re: [PyMOL] problem: choking on big files
> 
> Hi Philippe,
> 
> Pymol isn't very good at handling many spheres. However, 
> Povray is extremely efficient with raytracing scenes 
> consisting of spheres and if you know the perspective you 
> want to have the image from, you can convert your atom set to 
> spheres (with desired radii) and apply the view from Pymol. 
> If you would like, I can send you the script (Povray
> macro) to export the Pymol view to Povray.
> 
> Best regards,
> 
> Tsjerk
> 
> On 7/25/06, Phi...@ou... 
> <Phi...@ou...> wrote:
> > Hi again, list.
> >
> > I need help on how to render an unconventional 
> (non-protein) pdb file with a big number of atoms in it. Even 
> with no display (console mode), pymol still crashes due to 
> insufficient memory.
> > A different hardware is out of the question and a smaller 
> file would defeat my purpose, so I would like to simplify the 
> representation. What i do is to 'show sphere', then 'set 
> sphere_scale,0.01'. However, it seems it takes the same 
> amount of memory for pymol to display small or large spheres 
> (i thought that by using very small sphere_scale, pymol would 
> tend to treat each atom more and more as a single pixel). The 
> dots representation is also very complex to display I 
> believe. In my case the line display can not be used either.
> >
> > Are there some settings to increase the memory allocated to pymol ?
> > Are there settings of the dots representation so that only 
> one dot is represented for each atom ?
> > Any additional ideas are of course welcome !
> >
> > Thanks in advance !
> >
> > Garteiser Philippe
> > OMRF, Cardiovascular Biology dpt.
> > Doctoral candidate, OU Bioengineering
> > Advisors: Dr. Tim Mather, Dr M. Uli Nollert 12600 N Macarthur Crown 
> > Pointe apt. #1423 Oklahoma City, OK 73142
> > home: (405) 603 7091
> > work:   (405) 271 4924
> >
> > "It does not pay to leave a live
> > dragon out of your calculations"
> >  - Tolkien
> >
> >
> >
> >
> > 
> ----------------------------------------------------------------------
> > --- Take Surveys. Earn Cash. Influence the Future of IT Join 
> > SourceForge.net's Techsay panel and you'll get the chance to share 
> > your opinions on IT & business topics through brief surveys -- and 
> > earn cash 
> > 
> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEV
> > DEV _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> 
> 
> -- 
> 
> Tsjerk A. Wassenaar, M.Sc.
> Groningen Biomolecular Sciences and Biotechnology Institute 
> (GBB) Dept. of Biophysical Chemistry University of Groningen 
> Nijenborgh 4 9747AG Groningen, The Netherlands
> +31 50 363 4336
> 
> --------------------------------------------------------------
> -----------
> Take Surveys. Earn Cash. Influence the Future of IT Join 
> SourceForge.net's Techsay panel and you'll get the chance to 
> share your opinions on IT & business topics through brief 
> surveys -- and earn cash 
> http://www.techsay.com/default.php?page=join.php&p=sourceforge
> &CID=DEVDEV
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

Hi Elo,

Unless I've misunderstood you, all you have to do is find the maximum 
value (perhaps 2.33, based on your email) and divide all the numbers (in 
  all PDB files) by this number. You can write a simple Perl/Python 
program to do this or, if you're careful to get everything imported and 
exported correctly, use a spreadsheet program.

This should scale everything so that your largest overall value is 1.0 
and all other values are less than this.

Michelle

> 
> Message: 1
> Date: Mon, 24 Jul 2006 22:24:22 +0200
> From: "Caspar Elo Christensen" <el...@ad...>
> Subject: [PyMOL] Putty
> To: <PyM...@li...>
> Message-ID: <002001c6af5f$267c1da0$6500a8c0@elolaptop>
> Content-Type: text/plain; charset="us-ascii"
> 
> Hi,
>  
> I'm using cartoon putty to display rmsd between an enzyme with and without
> ligand. I've got two enzymes (that is four structures all in all) and have
> prepared two figures. The problem is that the extreme rmsd values vary; in
> one figure it goes from 0.1 to 1.66 while in the other it goes from 0.1 to
> 2.33. It seems that the rmsd values are normalized by putty, so that the
> figures only allow me to compare the distribution of rmsd values in each set
> of structures, not the actual values.How do I put the two figures on the
> same scale, so that I can compare them quantitatively? 
>  
> I've tried to play around with the scale range parameters with little luck.
>  
> Any help will be much appreciated,
>  
> Elo

Hi Philippe,

Pymol isn't very good at handling many spheres. However, Povray is
extremely efficient with raytracing scenes consisting of spheres and
if you know the perspective you want to have the image from, you can
convert your atom set to spheres (with desired radii) and apply the
view from Pymol. If you would like, I can send you the script (Povray
macro) to export the Pymol view to Povray.

Best regards,

Tsjerk

On 7/25/06, Phi...@ou... <Phi...@ou...> wrote:
> Hi again, list.
>
> I need help on how to render an unconventional (non-protein) pdb file with a big number of atoms in it. Even with no display (console mode), pymol still crashes due to insufficient memory.
> A different hardware is out of the question and a smaller file would defeat my purpose, so I would like to simplify the representation. What i do is to 'show sphere', then 'set sphere_scale,0.01'. However, it seems it takes the same amount of memory for pymol to display small or large spheres (i thought that by using very small sphere_scale, pymol would tend to treat each atom more and more as a single pixel). The dots representation is also very complex to display I believe. In my case the line display can not be used either.
>
> Are there some settings to increase the memory allocated to pymol ?
> Are there settings of the dots representation so that only one dot is represented for each atom ?
> Any additional ideas are of course welcome !
>
> Thanks in advance !
>
> Garteiser Philippe
> OMRF, Cardiovascular Biology dpt.
> Doctoral candidate, OU Bioengineering
> Advisors: Dr. Tim Mather, Dr M. Uli Nollert
> 12600 N Macarthur
> Crown Pointe apt. #1423
> Oklahoma City, OK 73142
> home: (405) 603 7091
> work:   (405) 271 4924
>
> "It does not pay to leave a live
> dragon out of your calculations"
>  - Tolkien
>
>
>
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
> opinions on IT & business topics through brief surveys -- and earn cash
> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


-- 

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

Hi Elo
=20
=20
The formula for cmputing the putty radius is found in layer1/ Extrude.c
in the source:
=20
        switch(source_field) {
        default: /* b*/
          scale =3D (range+(at->b - mean)/stdev)/range;
          if(scale<0.0F)
            scale =3D 0.0F;
          scale=3D(float)pow(scale,power);
          if(scale<min_scale)
            scale=3Dmin_scale;
          if(scale>max_scale)
            scale=3Dmax_scale;
          *sf =3D scale;
          break;

>From this I can see:
=20
* The "cartoon_putty_scale_max" and "cartoon_putty_scale_min" settings
are not scaling factors, but rather cut-off values to avoid extremely
thin or thick tubes.
* "cartoon_putty_scale_power" is a kind of "gamma correction" which
allows to enhanche areas with extreme b-factors. Set it to 1 if you want
linear scaling to b-factor.
* "cartoon_putty_range" is the only user-adjustable parameter that
affects the actual scaling. =20
* The mean value and standard deviation of the b-factors is used for the
scaling. This seems very strange to me - is this a bug or a feature? :-)
=20
It is quite hard to make a workaround (without changing the source).
The best I could find was to combine all the (aligned) structures into
one object, but with different chainid, eg
=20
alter obj01, chain=3D'A'
alter obj02, chain=3D'B'
create comb, obj01+obj02
=20
Then make the putty cartoon
=20
show cartoon, comb    # Notice that the complete object must be
selected, the putty scaling works only on the displayed atoms!
cartoon putty, comb
=20
But then your putty cartoons of the different structures are - at least
partly - covering each other. Then translate the different chains to
create the view you want, eg:
=20
translate [20, 0 0 ], comb and chain A
=20
You can use this view directly, or just translate the "unwanted" chains
far enough to be off the screen
=20
Hope this helps :-) =20
=20
But I I would really like an option to do manual scaling on the putty
cartoon, eg by changing the source line to.
=20
scale =3D at->b * cartoon_putty_myscaling;=20
=20
Where cartoon_putty_myscaling is a new setting.
=20
=20
Cheers,
=20
Esben
=20
=20
 ----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Caspar
Elo Christensen
Sent: 24. juli 2006 22:24
To: PyM...@li...
Subject: [PyMOL] Putty



	Hi,
	=20
	I'm using cartoon putty to display rmsd between an enzyme with
and without ligand. I've got two enzymes (that is four structures all in
all) and have prepared two figures. The problem is that the extreme rmsd
values vary; in one figure it goes from 0.1 to 1.66 while in the other
it goes from 0.1 to 2.33. It seems that the rmsd values are normalized
by putty, so that the figures only allow me to compare the distribution
of rmsd values in each set of structures, not the actual values.How do I
put the two figures on the same scale, so that I can compare them
quantitatively?=20
	=20
	I've tried to play around with the scale range parameters with
little luck.
	=20
	Any help will be much appreciated,
	=20
	Elo

Hi again, list.

I need help on how to render an unconventional (non-protein) pdb file with a big number of atoms in it. Even with no display (console mode), pymol still crashes due to insufficient memory.
A different hardware is out of the question and a smaller file would defeat my purpose, so I would like to simplify the representation. What i do is to 'show sphere', then 'set sphere_scale,0.01'. However, it seems it takes the same amount of memory for pymol to display small or large spheres (i thought that by using very small sphere_scale, pymol would tend to treat each atom more and more as a single pixel). The dots representation is also very complex to display I believe. In my case the line display can not be used either. 

Are there some settings to increase the memory allocated to pymol ?
Are there settings of the dots representation so that only one dot is represented for each atom ?
Any additional ideas are of course welcome !

Thanks in advance !

Garteiser Philippe 
OMRF, Cardiovascular Biology dpt. 
Doctoral candidate, OU Bioengineering 
Advisors: Dr. Tim Mather, Dr M. Uli Nollert 
12600 N Macarthur 
Crown Pointe apt. #1423 
Oklahoma City, OK 73142 
home: (405) 603 7091 
work:   (405) 271 4924 

"It does not pay to leave a live
dragon out of your calculations"
 - Tolkien 

Hi Hasan,

Have a look at "label"... (and read the manual :))

Cheers,

Tsjerk

On 7/27/06, Demirci, Hasan <Has...@br...> wrote:
> I have a cross-eye stereo image generated by PYMOL. Is there an easy way of custom labeling the residues by using PYMOL ?
> Or should I use a photo editor program to label everything manually?
>
> Thanks.
>
> Hasan Demirci
> Department of Molecular Biology, Cellular Biology & Biochemistry
> Brown University
> 69 Brown Street
> Providence, RI    02912
>
> (401) 863-3652 lab
> (401) 226-7852 cell
>
> Has...@Br...
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
> opinions on IT & business topics through brief surveys -- and earn cash
> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


-- 

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

I have a cross-eye stereo image generated by PYMOL. Is there an easy way =
of custom labeling the residues by using PYMOL ?
Or should I use a photo editor program to label everything manually?
=20
Thanks.
=20
Hasan Demirci
Department of Molecular Biology, Cellular Biology & Biochemistry
Brown University
69 Brown Street
Providence, RI    02912

(401) 863-3652 lab
(401) 226-7852 cell

Has...@Br...

Hi Elo
=20
=20
The formula for cmputing the putty radius is found in layer1/ Extrude.c
in the source:
=20
        switch(source_field) {
        default: /* b*/
          scale =3D (range+(at->b - mean)/stdev)/range;
          if(scale<0.0F)
            scale =3D 0.0F;
          scale=3D(float)pow(scale,power);
          if(scale<min_scale)
            scale=3Dmin_scale;
          if(scale>max_scale)
            scale=3Dmax_scale;
          *sf =3D scale;
          break;

>From this I can see:
=20
* The "cartoon_putty_scale_max" and "cartoon_putty_scale_min" settings
are not scaling factors, but rather cut-off values to avoid extremely
thin or thick tubes.
* "cartoon_putty_scale_power" is a kind of "gamma correction" which
allows to enhanche areas with extreme b-factors. Set it to 1 if you want
linear scaling to b-factor.
* "cartoon_putty_range" is the only user-adjustable parameter that
affects the actual scaling. =20
* The mean value and standard deviation of the b-factors is used for the
scaling. This seems very strange to me - is this a bug or a feature? :-)
=20
It is quite hard to make a workaround (without changing the source).
The best I could find was to combine all the (aligned) structures into
one object, but with different chainid, eg
=20
alter obj01, chain=3D'A'
alter obj02, chain=3D'B'
create comb, obj01+obj02
=20
Then make the putty cartoon
=20
show cartoon, comb    # Notice that the complete object must be
selected, the putty scaling works only on the displayed atoms!
cartoon putty, comb
=20
But then your putty cartoons of the different structures are - at least
partly - covering each other. Then translate the different chains to
create the view you want, eg:
=20
translate [20, 0 0 ], comb and chain A
=20
You can use this view directly, or just translate the "unwanted" chains
far enough to be off the screen
=20
Hope this helps :-) =20
=20
But I I would really like an option to do manual scaling on the putty
cartoon, eg by changing the source line to.
=20
scale =3D at->b * cartoon_putty_myscaling;=20
=20
Where cartoon_putty_myscaling is a new setting.
=20
=20
Cheers,
=20
Esben
=20
=20
 ----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Caspar
Elo Christensen
Sent: 24. juli 2006 22:24
To: PyM...@li...
Subject: [PyMOL] Putty



	Hi,
	=20
	I'm using cartoon putty to display rmsd between an enzyme with
and without ligand. I've got two enzymes (that is four structures all in
all) and have prepared two figures. The problem is that the extreme rmsd
values vary; in one figure it goes from 0.1 to 1.66 while in the other
it goes from 0.1 to 2.33. It seems that the rmsd values are normalized
by putty, so that the figures only allow me to compare the distribution
of rmsd values in each set of structures, not the actual values.How do I
put the two figures on the same scale, so that I can compare them
quantitatively?=20
	=20
	I've tried to play around with the scale range parameters with
little luck.
	=20
	Any help will be much appreciated,
	=20
	Elo

PyMOL Users,

We have received a number of emails recently about LCD-based stereo 3D
options, so this may interest you:  One of our hardware collaborators will
be showing off a 19" autostereoscopic LCD display running PyMOL at Siggraph
in Boston next week.  Please let me know what you think if you get a chance
to see it!  

Details below.

Cheers, 
Warren

--

Siggraph 2006 Boston, August 1st., 2nd, and 3rd. 

Visit the 3D consortium booth #120 to see the DTI 19" 2D/3D LCD display
featuring PyMol.  For additional information about the DTI 19" 2D/3D LCD
display and Siggraph 2006 click on these links.

http://dti3d.com/   http://www.siggraph.org/s2006/  
 

Oh, if it helps, the residues are all named things like ACYS and BCYS
for the different conformations.

On 7/25/06, Michael Lerner <mgl...@gm...> wrote:
> I have a crystal structure that contains two conformations for a
> flexible loop.  They're both in the crystal structure, but have
> occupancies less than one.   When I look at the structure in PyMOL, I
> see only one conformation.  Is there a command similar to split_states
> that will allow me to view both conformations at once?
>
> Thanks,
>
> -michael
>

I have a crystal structure that contains two conformations for a
flexible loop.  They're both in the crystal structure, but have
occupancies less than one.   When I look at the structure in PyMOL, I
see only one conformation.  Is there a command similar to split_states
that will allow me to view both conformations at once?

Thanks,

-michael

Hi frnds
Can any one please tell me the commands for
calculating the atom by atom RMSD of two pdb
structures in Pymol? Both the structure has same no.
of residues.
chiradip



		
___________________________________________________________ 
To help you stay safe and secure online, we've developed the all new Yahoo! Security Centre. http://uk.security.yahoo.com

Hi,
 
I'm using cartoon putty to display rmsd between an enzyme with and without
ligand. I've got two enzymes (that is four structures all in all) and have
prepared two figures. The problem is that the extreme rmsd values vary; in
one figure it goes from 0.1 to 1.66 while in the other it goes from 0.1 to
2.33. It seems that the rmsd values are normalized by putty, so that the
figures only allow me to compare the distribution of rmsd values in each set
of structures, not the actual values.How do I put the two figures on the
same scale, so that I can compare them quantitatively? 
 
I've tried to play around with the scale range parameters with little luck.
 
Any help will be much appreciated,
 
Elo

Brownwyn,
 
It is adaptive and based on the range of values in the PDB structure.
 
label all, "%0.2f"%b
 
to see the actual values.
 
Cheers,
Warren
 
 



  _____  

From: pym...@li...
[mailto:pym...@li...] On Behalf Of Bronwyn
Carlisle
Sent: Sunday, July 23, 2006 8:15 PM
To: pym...@li...
Subject: [PyMOL] B-factor colours


Can someone please tell me either a) what the scale is for B-factor
colouring as it comes with Pymol, or b) how to find out?




Bronwyn Carlisle
Room 231
Biochemistry Department
University of Otago
PO Box 56
710 Cumberland St
Dunedin

email: bro...@st...
tel: +64 (0)3 4797704
fax: +64 (0)3 4797866

Esben,

The two algorithms are different.  For efficiency & performance reasons,
PyMOL by default uses an anisotropic marching tetrahedrons algorithm, which
ends up generating fewer triangles along (+X,+Y,+Z).  Note that

map_double map-name

can increase sampling, but the result still suffers from anisotropy.

Hmm...now that the "marching cubes" patent has finally expired, we really
should implement that in PyMOL as well :)!

Cheers,
Warren

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Esben Jannik Bjerrum
> Sent: Monday, July 24, 2006 8:31 AM
> To: pym...@li...
> Subject: [PyMOL] Difference in isosurface and isomesh 
> representations withindexed brick object.
> 
> Hi
>   Im using Pymol as a 3d plotter of some "volume density data".
> However, theres a difference in surface or mesh 
> representations near zero.
> The following script illustrate(doesnt work without recompile 
> of NumPy support into pymol on linux, but works on both mac 
> and windows
> directly)
> 
> from chempy.brick import Brick
> brik2=Brick()
> brik2.setup_from_min_max(
>   	[0,0,0],
>    	[2,2,2],
>    	[1,1,1])
> brik2.lvl[1,1,1]=1
> cmd.load_brick(brik2,"brick")
> for a in range(2):
> 	lvl = a/2.
> 	cmd.do("isomesh lvlmesh%1.1f,brick,%1.1f" %(lvl,lvl))
> 	cmd.do("isosurface lvlsurf%1.1f,brick,%1.1f" %(lvl,lvl))
> 
> it seems like the isosurface do not get interpolated to 
> certain diagonal points, but not to other, while the mesh 
> only gets interpolated to neighbor points. Its probably not a 
> problem for "normal" data, but as I have sparse and indexed 
> data it do look a bit strange. Is there a way to make 
> isosurface behave like isomesh in that regard or add the 
> missing interpolation to diagonal points?
> 
> Esben
> 
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection 
> around http://mail.yahoo.com 
> 
> --------------------------------------------------------------
> -----------
> Take Surveys. Earn Cash. Influence the Future of IT Join 
> SourceForge.net's Techsay panel and you'll get the chance to 
> share your opinions on IT & business topics through brief 
> surveys -- and earn cash 
> http://www.techsay.com/default.php?page=join.php&p=sourceforge
&CID=DEVDEV
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

My guess is that the path may contain "wide" characters (e.g. asian =
language
characters).  For some reason, those characters do not work on Windows, =
but
they work fine on Mac and Linux...
=20
> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf=20
> Of Tsjerk Wassenaar
> Sent: Friday, June 30, 2006 1:33 AM
> To: LIU Changdong
> Cc: pym...@li...
> Subject: Re: [PyMOL] error in loading pdb file
>=20
> Hi Dong,
>=20
> My guess is (but ofcourse Warren knows best) that pymol=20
> chokes in the full pathname, including the spaces. Note that=20
> under windows the actual pathname would be=20
> D:\DOCUME~1\1LTL.pdb The long pathname is an alias.
>=20
> Cheers,
>=20
> Tsjerk
>=20
> On 6/29/06, LIU Changdong <cd...@us...> wrote:
> > Dear all:
> >  After I install pymol successfully,I load a pdb file,but=20
> the progroam=20
> > give me a error message below.Can you give me any suggestions?My=20
> > operate system is windows xp sp2.
> >
> > excecutiveprocessPDBfile-error:unableto open file'D:/Documents and=20
> > settings/1LTL.pdb Function:<bound method Normal.file_open of <=20
> > pmg_tk.skins.normal.Normal instance at 0x09477F30>>(type: < type=20
> > `instancemethod~>)
> >
> > Arg:
> > ()Traceback=A3=A8inner most last):
> >
> > File"D\Program files\Delano
> > scientific\PyMOL/modules\pmw_1_2\lib\PmwBase.py", line=20
> 1747,in _call_=20
> > return apply (self.func,args) File"D\Program files\Delano=20
> > scientific\PyMOL/modules\pmw_1_2\lib\PmwBase.py", line438, in=20
> > file_open
> > self.cmd.load=A3=A8ofile,quiet=3D0)
> > File"D\Program files\Delano
> > scientific\PyMOL/modules\pmw_1_2\lib\PmwBase.py", line585,in load=20
> > if_raising(r):raise pymol.cmdexpception=20
> > cmdexception:<pymol.cmdexception instance at 0x0961e620
> >
> >
> >
> >
> > Many thanks!
> > Best
> >  Dong
> >
> >
> >
> > Using Tomcat but need to do more? Need to support web=20
> services, security?
> > Get stuff done quickly with pre-integrated technology to=20
> make your job=20
> > easier Download IBM WebSphere Application Server v.1.0.1 based on=20
> > Apache Geronimo
> >=20
> =
http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D=
1216
> > 42 _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
>=20
>=20
> --=20
>=20
> Tsjerk A. Wassenaar, M.Sc.
> Groningen Biomolecular Sciences and Biotechnology Institute=20
> (GBB) Dept. of Biophysical Chemistry University of Groningen=20
> Nijenborgh 4 9747AG Groningen, The Netherlands
> +31 50 363 4336
>=20
> Using Tomcat but need to do more? Need to support web=20
> services, security?
> Get stuff done quickly with pre-integrated technology to make=20
> your job easier Download IBM WebSphere Application Server=20
> v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&
dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

Hi
  Im using Pymol as a 3d plotter of some "volume density data".
However, theres a difference in surface or mesh representations near
zero.
The following script illustrate(doesnt work without recompile of NumPy
support into pymol on linux, but works on both mac and windows
directly)

from chempy.brick import Brick
brik2=Brick()
brik2.setup_from_min_max(
  	[0,0,0],
   	[2,2,2],
   	[1,1,1])
brik2.lvl[1,1,1]=1
cmd.load_brick(brik2,"brick")
for a in range(2):
	lvl = a/2.
	cmd.do("isomesh lvlmesh%1.1f,brick,%1.1f" %(lvl,lvl))
	cmd.do("isosurface lvlsurf%1.1f,brick,%1.1f" %(lvl,lvl))

it seems like the isosurface do not get interpolated to certain
diagonal points, but not to other, while the mesh only gets
interpolated to neighbor points. Its probably not a problem for
"normal" data, but as I have sparse and indexed data it do look a bit
strange. Is there a way to make isosurface behave like isomesh in that
regard or add the missing interpolation to diagonal points?

Esben

__________________________________________________
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Hi,
the command intra_fit was the one! However, if I'd like to visualize
the first, let's say, 20 structures of my bundle?

thanks again

andrea

2006/7/19, Robert Campbell <rl...@po...>:
> Hi,
>
> * Joel Tyndall <joe...@ot...> [2006-07-15 14:29] wrote:
> > Hi andrea,
> >
> > you can easily do this by
> >
> > split_states my_struct
> > dele my_struct
> >
> >
> > for the NMR ensemble, then I would use the action menu, align function
> > and align them  to state_1. This is in effect aligning the separate
> > states as objects, unless I misunderstood you
> >
> > J
> >
> > Andrea Spitaleri wrote:
> > > Hi all,
> > > in pymol is it possible to align states rather than object. I mean, I
> > > have loaded a pdb file with n-structures and I'd like to align each of
> > > them on the first one of the bundle.
>
> If in fact the n-structures contain all the same atoms, then you can use
> the intra_fit command instead:
>
>   PyMOL> help intra_fit
>
>   intra_fit
>
>   DESCRIPTION
>
>      "intra_fit" fits all states of an object to an atom selection
>      in the specified state.  It returns the rms values to python
>      as an array.
>
>   USAGE
>
>      intra_fit (selection),state
>
>   PYMOL API
>
>      cmd.intra_fit( string selection, int state )
>
>   EXAMPLES
>
>      intra_fit ( name ca )
>
>   PYTHON EXAMPLE
>
>      from pymol import cmd
>      rms = cmd.intra_fit("(name ca)",1)
>
>   SEE ALSO
>
>      fit, rms, rms_cur, intra_rms, intra_rms_cur, pair_fit
>
>
> Cheers,
> Rob
> --
> Robert L. Campbell, Ph.D.
> Senior Research Associate/Adjunct Assistant Professor
> Department of Biochemistry, Queen's University
> Kingston, ON K7L 3N6  Canada
>   <rl...@po...>         http://adelie.biochem.queensu.ca/~rlc
>   phone: 613-533-6821            fax: 613-533-2497
>   PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2
>
> -------------------------------------------------------------------------
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>


-- 
Why stand on a silent platform?
Fight the war, fuck the norm
(RATM)

On Friday 21 July 2006 22:19, Phi...@ou... wrote:
> I need to work with a very large pdb file that stalls my pymol. Hence, I
> have tried to launch pymol with the -c switch, to no success. Under
> WindowsXP, pymol starts as usual, but disappears as soon as it is loaded. I
> tried also on a linux distribution (mepis). The console prints the regular
> welcome text you usually see under the display (with the esc toggle), but
> then I get: Command mode. No graphics front end.

What has worked for me is to start PyMOL with the "-c" option and a .pml 
command script on the command line:

pymol -c generate.pml

PyMOL then executes the instructions in the script, which should include 
a "ray" command if you want to save an image (since there is no OpenGL 
display to take bitmpa data from), and then terminate.

Alternatively, start PyMOL with "pymol -cp", and it will respond to commands 
from standard input, which can be your terminal.

Hope this helps,

-- 
Lieven Buts
Ultrastructure Laboratory
Vrije Universiteit Brussel

Can someone please tell me either a) what the scale is for B-factor  
colouring as it comes with Pymol, or b) how to find out?


Bronwyn Carlisle
Room 231
Biochemistry Department
University of Otago
PO Box 56
710 Cumberland St
Dunedin

email: bro...@st...
tel: +64 (0)3 4797704
fax: +64 (0)3 4797866

You can use the builder functionality to add a carbonyl and then  a 
methyl to your lysine amine terminus. Unfortuantely you cannot optimize 
in Pymol. You could use Prodrug or CNS if you have some experience.

Cheers

Joel

LIU Changdong wrote:
> Hi,evreyone:
>  I've got a pdb file of short peptide (11aa),I want to add an acetyl group
> on Lys residue and optimize the structure.Is there anyone who can tell me
> how to do it?
>
> Best
> Dong
>
>
> -------------------------------------------------------------------------
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> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>   

-- 
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin 9054
New Zealand                     

Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti 9054
Aotearoa

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

Hi,evreyone:
 I've got a pdb file of short peptide (11aa),I want to add an acetyl group
on Lys residue and optimize the structure.Is there anyone who can tell me
how to do it?

Best
Dong