pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] clipping planes

[Nathaniel E. <na...@ma...>]

I don't understand how these work at all.  Is there any straightforward 
way, given a structure's position and dimensions and the desired camera
position, to calculate the ideal position for the plane?   How does
PyMOL decide where to put the planes?  Right now I'm missing by a small
amount and atoms disappear randomly.

thanks,
Nat

RE: [PyMOL] Problem with Seleno-Cysteine

[DeLano, W. <wa...@su...>]

alter eys/,type=3D'ATOM'
sort

The problem is that, by default, PyMOL doesn't create ribbons for =
HETATMs (typically ligands and solvent).  With the above command, you're =
converting selenocysteine residues into regular atoms and sorting them =
into place so that they can be included in the ribbon.

Cheers,
Warren

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606  FAX:(650)-266-3501



> -----Original Message-----
> From: jo...@al... [mailto:jo...@al...]
> Sent: Tuesday, August 06, 2002 7:43 AM
> To: pym...@li...
> Subject: [PyMOL] Problem with Seleno-Cysteine
>=20
>=20
> Hi everybody
>=20
> I have the structure of a Molybdo-CODH (CO-Dehydrogenase),=20
> which contains a
> Seleno-Cysteine as Ligand for the active site cluster (see 1QJ2.pdb)
> The residue b/388 is denoted as EYS in the pdb file.
> In the cartoon representation, pymol does not display this=20
> part of the backbone
> (I get a "hole" in the cartoon structure).
> I can display this residue using "show sticks, resi 388", and=20
> I can pick every
> single atom, even the selenium.
> Any idea how I can display the backbone without break?
>=20
> Thanks
> joerg
>=20
> Internet et mail gratuit AltaVista http://www.altavista.fr
>=20
>=20
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] Problem with Seleno-Cysteine

[<jo...@al...>]

Hi everybody

I have the structure of a Molybdo-CODH (CO-Dehydrogenase), which contains a
Seleno-Cysteine as Ligand for the active site cluster (see 1QJ2.pdb)
The residue b/388 is denoted as EYS in the pdb file.
In the cartoon representation, pymol does not display this part of the backbone
(I get a "hole" in the cartoon structure).
I can display this residue using "show sticks, resi 388", and I can pick every
single atom, even the selenium.
Any idea how I can display the backbone without break?

Thanks
joerg

Internet et mail gratuit AltaVista http://www.altavista.fr

Re: [PyMOL] Polypeptide conformation restriction

[Jason M. <ja...@bi...>]

Hello:

To show the allowed torsion angles, run your protein through procheck
(available at http://www.ccp4.ac.uk/main.html), this will show the allowed
areas.  

I would say that the convergence of an MD simlulation cannot be told by
torsion angles since the protein conformation with the most allowed angles
and/or fastest convergence to allowed regions isn't necessarily the
correct one.  I have seen some protein structures with a diverse array of
torsion angles.  What you may get is one of the conformations of the
"ensemble" of the transition state to folding (read something by David
Baker).

Cheers,
JTM

On Thu, 1 Aug 2002 kk...@ga... wrote:

> Dear pymolers,
> 
> Many of you are interested in SS.
> I think you must be experts on this.
> So, although this is not a pymol problem,
> I hope that you can give me some information.
> 
> I've got some MD simulation results,
> and I calculated the phi-psi angles of each amino acid.
> (Yeah I know that phi-psi calculation is there in pymol.
> I just wrote the program to check if I really understand it correctly.)
> Then, with the data, you can say that I got the variation of
> phi-psi angle 'on the fly'.
> I can look at the change of their values with time in a movie.
> 
> The problem is, I found that many of the amino acids
> have phi-psi angles pairs that fall in the "forbidden area".
> I think that you know what I mean by that.
> Especially, there are a lot of valines in my model protein,
> but often they have phi-psi angles in Glysine area or even
> totally forbidden area.
> Well maybe you will argue that the "forbidden" conformation
> is only meaningful for native structures.
> But what I wish to understand is the correlation between
> the 'forbidden/allow" of phi-psi configuration and the
> convergence of MD simulation, or even better,
> one might point out the pathway of folding by looking at that.
> 
> Anyway, to do further analysis, I wish to be able to obtain
> the 'contour' of the chain conformation restriction map.
> You know, when you go to the protein data bank and view the
> Ramachandran diagram, in the background they show those area.
> But where can I obtain information like that?
> 
> Thank you in advance if you can provide me suggestions.
> 
> Regards,
> K.K.Liang
> 
> 
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

*************************
Jason Thomas Maynes
MD/PhD Program
Faculty of Medicine
University of Alberta
ja...@bi...
*************************

[PyMOL] =?ISO-8859-1?B?UmU6IFLpZi46IFtQeU1PTF0gSGVscCEgQ29sb3IgYnkgYXRvbS9ILWJvbmQgZGlzcGxheS9tb3VzZSBvbiBPU1ggIA==?=

[Joerg J. <jo...@al...>]

Le Wed, 31 July 2002, Luca Jovine a =E9crit

<snip>
> BTW, do people on the PyMol bulletin=20
> boar normally post (or are at least expected to post) summaries of the=20
> answers they received to a particular problem?
</snip>

Depends. On a low-traffic list like this one, everybody can easily check al=
l the
answers in a thread, so summaries are not relly necessary.
Just if you get input from off the list (a flash of genius or so...) it wou=
ld be
nice to get this information, too. It will be stored on the sourceforge
mail-archives and everybody can check it later.

I hope the others see it the same way as I do.

joerg
=0D
Internet et mail gratuit AltaVista http://www.altavista.fr

RE: [PyMOL] Polypeptide conformation restriction

[Frank V. <Fra...@sy...>]

Hi Liang:

The most up-to-date contour on the Ramachandran plot you can find at the
molprobity website:  http://kinemage.biochem.duke.edu/molprobity/

It's a bit indirect, you have to submit a structure and then it will
give back a Ramachandran plot - but this plot agrees pretty well with
what we tend to see in Xray structures.  Better than the procheck (etc.)
plots. 

Good luck
phx.


> -----Original Message-----
> From: kk...@ga... [mailto:kk...@ga...]
> Sent: Thursday, August 01, 2002 12:06 AM
> To: pym...@li...
> Subject: [PyMOL] Polypeptide conformation restriction
> 
> 
> Dear pymolers,
> 
> Many of you are interested in SS.
> I think you must be experts on this.
> So, although this is not a pymol problem,
> I hope that you can give me some information.
> 
> I've got some MD simulation results,
> and I calculated the phi-psi angles of each amino acid.
> (Yeah I know that phi-psi calculation is there in pymol.
> I just wrote the program to check if I really understand it 
> correctly.)
> Then, with the data, you can say that I got the variation of
> phi-psi angle 'on the fly'.
> I can look at the change of their values with time in a movie.
> 
> The problem is, I found that many of the amino acids
> have phi-psi angles pairs that fall in the "forbidden area".
> I think that you know what I mean by that.
> Especially, there are a lot of valines in my model protein,
> but often they have phi-psi angles in Glysine area or even
> totally forbidden area.
> Well maybe you will argue that the "forbidden" conformation
> is only meaningful for native structures.
> But what I wish to understand is the correlation between
> the 'forbidden/allow" of phi-psi configuration and the
> convergence of MD simulation, or even better,
> one might point out the pathway of folding by looking at that.
> 
> Anyway, to do further analysis, I wish to be able to obtain
> the 'contour' of the chain conformation restriction map.
> You know, when you go to the protein data bank and view the
> Ramachandran diagram, in the background they show those area.
> But where can I obtain information like that?
> 
> Thank you in advance if you can provide me suggestions.
> 
> Regards,
> K.K.Liang
> 
> 
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


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[PyMOL] Polypeptide conformation restriction

[<kk...@ga...>]

Dear pymolers,

Many of you are interested in SS.
I think you must be experts on this.
So, although this is not a pymol problem,
I hope that you can give me some information.

I've got some MD simulation results,
and I calculated the phi-psi angles of each amino acid.
(Yeah I know that phi-psi calculation is there in pymol.
I just wrote the program to check if I really understand it correctly.)
Then, with the data, you can say that I got the variation of
phi-psi angle 'on the fly'.
I can look at the change of their values with time in a movie.

The problem is, I found that many of the amino acids
have phi-psi angles pairs that fall in the "forbidden area".
I think that you know what I mean by that.
Especially, there are a lot of valines in my model protein,
but often they have phi-psi angles in Glysine area or even
totally forbidden area.
Well maybe you will argue that the "forbidden" conformation
is only meaningful for native structures.
But what I wish to understand is the correlation between
the 'forbidden/allow" of phi-psi configuration and the
convergence of MD simulation, or even better,
one might point out the pathway of folding by looking at that.

Anyway, to do further analysis, I wish to be able to obtain
the 'contour' of the chain conformation restriction map.
You know, when you go to the protein data bank and view the
Ramachandran diagram, in the background they show those area.
But where can I obtain information like that?

Thank you in advance if you can provide me suggestions.

Regards,
K.K.Liang

[PyMOL] three button mouse

[Bronwyn C. <br...@bi...>]

Hi, Dumb question, but I can't find the answer anywhere.  I'm trying out 
a 3 button mouse on my OS X G4, and have set mouse 
three_button_editing - how do I turn it off? (apart from quitting and 
starting again)

Bronwyn Carlisle
Biochemistry Department
University of Otago
Dunedin
New Zealand

Tel 64 3 479 7704

Re: [PyMOL] Help! Color by atom/H-bond display/mouse on OSX

[Florian N. <fl...@na...>]

> Luca Jovine wrote:
>> 3) And finally, how do people who use PyMol on Mac OSX cope with the mouse
>> issue? Is any of you using a 3-button mouse, and, if so, which one?

Hi Luca,

A simple logitech wheel optical mouse works wonderfully with PyMol on MacOS
X.
MacOS X has basic built-in drivers for multi-button mice.
It supports the 3 buttons + the wheel. I'm still wondering why Apple is not
selling multi-button mice with their computers...

Bye


-- 
Florian NACHON, phD    CRSSA Grenoble, France - UNMC Omaha, USA

"Every man has two nations, and one of them is France"

 Benjamin Franklin & Thomas Jefferson             ICQ# 43686170

[PyMOL] =?ISO-8859-1?B?UulmLjogW1B5TU9MXSBIZWxwISBDb2xvciBieSBhdG9tL0gtYm9uZCBkaXNwbGF5L21vdXNlIG9uIE9TWCA=?=

[<jo...@al...>]

Le Tue, 30 July 2002, Luca Jovine a =E9crit

>=20
> Hello again PyMol users,
>=20
> I've now been playing with PyMol on OSX for 10 days or so and still love=
=20
> it. I also developed three more questions though ;)
>=20
> 1) Is there any typed command one can use to color a selection by atom=20
> type (rather than manually doing so by using the internal GUI pop-up menu=
s)
> ?

Hi Luca,
I can just answer question 1.)
color black, (*/CA)
will paint all C\alpha atoms black (looks good on black background... ;) )
See the manual (page 13 in the pdf version, IIRC) for the other atom names,=
=20
and the hierarchical selection method.

hth
joerg
=0D
Internet et mail gratuit AltaVista http://www.altavista.fr

Re: [PyMOL] Help! Color by atom/H-bond display/mouse on OSX

[Lieven B. <li...@ul...>]

Luca Jovine wrote:
> 1) Is there any typed command one can use to color a selection by atom
> type (rather than manually doing so by using the internal GUI pop-up menus)?

The "util" module contains a number of functions that color the atoms
according to type, with different colors for the C atoms. For instance,

  util.cbay three

in a .pml script will color object "three" by atom type, with the carbon
atoms in yellow ("color by atom yellow").

Other functions from ../modules/pymol/util.py are cbag, cbac, cbas,
cbap, cbak, cbaw and cbab (grey (carbon), cyan, salmon, purple, pink, 
white (hydrogen) and slate).
 

-- 
Lieven Buts
Brussels Free University

[PyMOL] Help! Color by atom/H-bond display/mouse on OSX

[Luca J. <luc...@ma...>]

Hello again PyMol users,

I've now been playing with PyMol on OSX for 10 days or so and still love 
it. I also developed three more questions though ;)

1) Is there any typed command one can use to color a selection by atom 
type (rather than manually doing so by using the internal GUI pop-up menus)
?

2) Is there any way to detect and display hydrogen bonds (say with nice 
dashed lines!)?

3) And finally, how do people who use PyMol on Mac OSX cope with the mouse 
issue? Is any of you using a 3-button mouse, and, if so, which one?

Thanks a lot and ciao

Luca

--------------------------------------------------------
Luca Jovine, Ph.D.
Department of Molecular, Cell & Developmental Biology
Mount Sinai School of Medicine
Annenberg Building, Room 25-18
One Gustave L. Levy Place, New York, NY 10029-6574, USA
Voice: +1.212.241-8620  FAX: +1.509.356-2832
E-Mail: luc...@ma...
W3: http://www.mssm.edu/students/jovinl02
--------------------------------------------------------

RE: [PyMOL] Suppress some output

[DeLano, W. <wa...@su...>]

Even better: try the "feedback" command:

feedback disable,all,actions
feedback disable,all,results

Will suppress most of PyMOL's normal chatter.

From Python:

cmd.feedback("disable","all","actions")
cmd.feedback("disable","all","results")

Warren

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606  FAX:(650)-266-3501


> -----Original Message-----
> From: kk...@ga... [mailto:kk...@ga...]
> Sent: Monday, July 29, 2002 10:23 PM
> To: pym...@li...
> Subject: [PyMOL] Suppress some output
>=20
>=20
> Dear Pymolers,
>=20
> Well I asked about the possibility of supressing some output
> from pymol earlier.
> I'm so happy that I found something important.
>=20
> In my case, what bothered me is that I have to do a lot of
> selections and analyze the selected residues.
> There are roughly 10,000 selection for each pdb file that I analyze.
> That is crazily slow if there is always a
> "Selection: xxxx" output for each selection I make.
>=20
> But today I decided to dig in the code and found that
> there are two undocumented arguments to "selection"...
>=20
> def select(name,selection=3D"",quiet=3D0,show=3D0):
>=20
> I tried the combinations of the use of them and found that
> the selection operation will be quiet if we just set quiet=3D1.
> However, the value of show has no effect in my tests.
>=20
> I will try to dig out more cases like this if I run into
> other routines which also output to console too often.
> But you who have your own problem may try to find out
> if there is such option in the routine you want to use.
>=20
> Cheers,
> K.K.Liang=20

[PyMOL] Suppress some output

[<kk...@ga...>]

Dear Pymolers,

Well I asked about the possibility of supressing some output
from pymol earlier.
I'm so happy that I found something important.

In my case, what bothered me is that I have to do a lot of
selections and analyze the selected residues.
There are roughly 10,000 selection for each pdb file that I analyze.
That is crazily slow if there is always a
"Selection: xxxx" output for each selection I make.

But today I decided to dig in the code and found that
there are two undocumented arguments to "selection"...

def select(name,selection="",quiet=0,show=0):

I tried the combinations of the use of them and found that
the selection operation will be quiet if we just set quiet=1.
However, the value of show has no effect in my tests.

I will try to dig out more cases like this if I run into
other routines which also output to console too often.
But you who have your own problem may try to find out
if there is such option in the routine you want to use.

Cheers,
K.K.Liang

Re: [PyMOL] Secondary structure assignments

[Kristian R. <kri...@be...>]

OK, heres what we've got:

The DSSP program is available for Linux and Windows from
http://www.cmbi.kun.nl/swift/dssp/ .

I have written a Python script that parses the output of DSSP and alters 
the annotation in PyMOL. You just start the script, then You have a

dssp <object>

command available.

The script can be found on my homepage,

http://www.rubor.de/bioinf/pymol_extensions.html

along with some useful stuff

http://www.rubor.de/bioinf/index.html

However, the script works for sure only on Unix. For Windows, i still 
need to figure out how to
- redirect the output of Dssp on Windows
- assign platform-independent Paths correctly.

If someone could test the script, that would be great.


Kristian

Re: [PyMOL] Secondary structure assignments

[Nathaniel E. <na...@ma...>]

> Ideally util.ss could become a shell that would know (from the environment?) 
> if dssp or similar was installed, then either run dssp and parse the output 
> to assign the ss, or else run the ss asignment code in the current util.ss if 
> no other options were available.

I've basically done this, though right now it uses STRIDE because the
output is easier to parse- it just uses popen2() to read the output from
the STRIDE executable (Does anyone actually know what the difference is
between these two programs?). But since I already wrote a dssp parser in
Perl, it shouldn't take long to modify.  My feeling is that it would be
better to have a robust secondary structure algorithm built in, since I've
already hit limitations in the method I'm using.  Though to be honest,
I've been getting away with using util.ss for some time now.

> The ability to write a pdb with the newly generated ss information would be 
> useful as well (or perhaps pymol already can do this if it knows the 
> protein's ss?).

I've done this too, though I think it breaks with more than one chain
right now.  If I get around to cleaning this up I'd be more than happy to
pass it on.

-Nat

Re: [PyMOL] Secondary structure assignments

[Russell P. <rp...@fa...>]

Nat,

You read my mind.  Having just converted the output of DSSP manually to PDB 
records last week I was eyeing the source to util.ss wondering how to turn it 
into a dssp parser.  

Ideally util.ss could become a shell that would know (from the environment?) 
if dssp or similar was installed, then either run dssp and parse the output 
to assign the ss, or else run the ss asignment code in the current util.ss if 
no other options were available.

The ability to write a pdb with the newly generated ss information would be 
useful as well (or perhaps pymol already can do this if it knows the 
protein's ss?).

Thanks

Russell Poyner


I've been fiddling with this for my own work; I wrote a parser in Perl to
embed structural annotation in a PDB file based on output from DSSP,
STRIDE, or RasMol.  Unfortunately it doesn't handle multiple chains yet,
but I'm working on making it more general.  I suppose since I only use
this for loading files into PyMOL, I could just write it in Python as a
PyMOL module. . . would that be useful to anyone else?

[PyMOL] moving objects independently?

[Richard K. <rk...@Tr...>]

Dear Pymolers,

I am trying to manually superimpose a couple of structures that are =
simultaneously opened in Pymol.  I can't figure out how to move one =
structure independent of the other.  Is there a way to select just one =
object, move it with the mouse, deselect it, select the other object, =
move it, etc?  Help would be much appreciated.  Thank you!


richard
Triad Therapeutics, Inc.
9381 Judicial Dr., Suite 200
San Diego, CA 92121
rk...@tr...
858-964-1575
858-457-7893 fax

Re: [PyMOL] Secondary structure assignments

[Nathaniel E. <na...@ma...>]

> Yes, please. There are some structures that have to be generated by using
> symmetry operations defined in the "REMARK 350" lines in the pdb file (example:
> 1jjy.pdb). The only way (I know of, if you know a better one, please tell me) to
> do this is going to http://pqs.ebi.ac.uk where the complete structure is
> generated for you. However, the caveat is: This service removes the secondary
> structure information, and up to now I have manually copy-pasted it into the new
> pdb file (Annoying work, really).

Unfortunately, the script I came up with won't deal with that; it
basically uses a third-party program to rescan the input file and uses the
alter command to correctly set the structure (or combines this with file
loading as a single command). If anyone would like this, I'm happy to
email it to them, but it's not really a good general solution.

How hard would it be to incorporate the DSSP algorithm?  I was looking at
the source for RasMol, which has a complete implementation.  My feeling is
that this could be ported without too much misery.  However, RasMol's
license terms are different, and I suspect even a complete translation
into Python with the ChemPy API  would still be considered a "derivative
work", meaning it wouldn't be able to be part of the main distribution,
and meaning someone would still have to code DSSP from scratch.  (I have
utterly no idea how it works, but RasMol's code seems clear enough despite
lack of comments)

-Nat

Re: [PyMOL] Secondary structure assignments

[<jo...@al...>]

Le Sun, 28 July 2002, Nathaniel Echols a =E9crit

<snip>
> but I'm working on making it more general.  I suppose since I only use
> this for loading files into PyMOL, I could just write it in Python as a
> PyMOL module. . . would that be useful to anyone else?

Yes, please. There are some structures that have to be generated by using
symmetry operations defined in the "REMARK 350" lines in the pdb file (exam=
ple:
1jjy.pdb). The only way (I know of, if you know a better one, please tell m=
e) to
do this is going to http://pqs.ebi.ac.uk where the complete structure is
generated for you. However, the caveat is: This service removes the seconda=
ry
structure information, and up to now I have manually copy-pasted it into th=
e new
pdb file (Annoying work, really).

> However, PyMOL's built-in commands end up being much easier to use... I
> wish I'd realized that before I wrote my parser.

Hehe, will have to learn them,...
joerg
=0D
Internet et mail gratuit AltaVista http://www.altavista.fr

Re: [PyMOL] Secondary structure assignments

[<jo...@al...>]

Le Sun, 28 July 2002, Nathaniel Echols a =E9crit

<snip>
> but I'm working on making it more general.  I suppose since I only use
> this for loading files into PyMOL, I could just write it in Python as a
> PyMOL module. . . would that be useful to anyone else?

Yes, please. There are some structures that have to be generated by using
symmetry operations defined in the "REMARK 350" lines in the pdb file (exam=
ple:
ijjy.pdb). The only way (I know of, if you know a better one, please tell m=
e) to
do this is going to http://pqs.ebi.ac.uk where the complete structure is
generated for you. However, the caveat is: This service removes the seconda=
ry
structure information, and up to now I have manually copy-pasted it into th=
e new
pdb file (Annoying work, really).

> However, PyMOL's built-in commands end up being much easier to use... I
> wish I'd realized that before I wrote my parser.

Hehe, will have to learn them,...
joerg
=0D
Internet et mail gratuit AltaVista http://www.altavista.fr

Re: [PyMOL] Secondary structure assignments

[Nathaniel E. <na...@ma...>]

> programs.  So I am in search of a solution.  Can one manually create a
> secondary structure assignment matrix to insert into the PDB file?  I must
> admit that as a novice I do not understand the formatting of the secondary
> structure matrices that I have seen embedded  in some PDB files.  Is there a
> resource somewhere that explains the formatting of such a matrix?

I've been fiddling with this for my own work; I wrote a parser in Perl to
embed structural annotation in a PDB file based on output from DSSP,
STRIDE, or RasMol.  Unfortunately it doesn't handle multiple chains yet,
but I'm working on making it more general.  I suppose since I only use
this for loading files into PyMOL, I could just write it in Python as a
PyMOL module. . . would that be useful to anyone else?

The complete PDB specification for SS annotation is here:
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_42.html
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_44.html
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_45.html

However, PyMOL's built-in commands end up being much easier to use... I
wish I'd realized that before I wrote my parser.

> Alternatively, is there a manual series of Pymol commands to directly assign
> secondary structure for a protein for insertion into the .pml script file?

alter atom_selection, ss='L' (or 'H' or 'S', I think)

> Even better, is there a separate program that can assign secondary structure
> and then allow you to save the revised PDB file with the secondary structure
> assignments inserted into the PDB output.  I would be willing to accept any

If there is, I'd like to know too!

-Nat Echols
Gerstein Lab
Yale University

[PyMOL] Secondary structure assignments

[Kelley M. <mo...@ar...>]

Dear Pymol users,

I am very pleased with Pymol as a visualization tool for the generation of
publication quality images, but I am having a problem with one aspect of the
problem.  I am working with several PDB files that do not have embedded
secondary structure assignments.  I have been trying to render these
structures as cartoon diagrams, and as you might expect, the secondary
structures are not revealed unless you tell the program where they exist.
One option is the command: util.ss.  As is mentioned in the manual this is
not a reliable assignment algorithm.  I have confirmed this problem with
several of my PDB files. The assignments do not match those found by other
programs.  So I am in search of a solution.  Can one manually create a
secondary structure assignment matrix to insert into the PDB file?  I must
admit that as a novice I do not understand the formatting of the secondary
structure matrices that I have seen embedded  in some PDB files.  Is there a
resource somewhere that explains the formatting of such a matrix?
Alternatively, is there a manual series of Pymol commands to directly assign
secondary structure for a protein for insertion into the .pml script file?
Even better, is there a separate program that can assign secondary structure
and then allow you to save the revised PDB file with the secondary structure
assignments inserted into the PDB output.  I would be willing to accept any
of the above!!  One further consideration:  I have limited accessibility to
unix-based programs.  I am presently running Pymol on a Mac under X-windows
(it works great by the way, although rather slow).  Replies for workarounds
should please take into account that alternative programs should be
available to a windows or preferably a Mac environment.

Thanks, and I hope that there is a solution.

-Kelley      


Dr. Kelley Moremen 
Associate Professor
Complex Carbohydrate Research Center
Department of Biochemistry and Molecular Biology
University of Georgia, Athens, GA 30602-7229
Office (706) 542-1705    Fax: (706) 542-1759
Email: mo...@ar...
(send email with large attachments to: mo...@bm...)
Website: http://bmbiris.bmb.uga.edu/moremen/lab/

[PyMOL] Pymol and Raster3D

[<jo...@al...>]

Hello

I know I can use the Raster3d output from molscript to view and render it in
pymol. But is there a way to output a pymol-generated structure in r3d-format for
rendering with Raster3d's "render" program? (It's because render is a lot faster
than pymol's built-in raytracer...)

thanks
joerg

Internet et mail gratuit AltaVista http://www.altavista.fr

[PyMOL] Cartoon representation of 310 helices, pi helicies, and H-bonded turns?

[Russell P. <rp...@fa...>]

I am working on making some cartoon-ribbon figures and I wonder if there is 
any consensus on how to represent secondary structures other than 
alpha-helices and beta-sheets.  My particular protein has a couple of helices 
that DSSP assigns as 310-Helices.  Do I just stick HELIX records in the pdb 
for these and call it good?  

Does anyone do anything special for H-bonded turns?

Or perhaps protein cartoons are just a matter of personal taste?

Thanks

Russell Poyner