pymol-users Mailing List for PyMOL Molecular Graphics System

> 1) Is the secondary structure assignment function in 0.92 
> more reliable?  Or does the "WARNING: it will make mistakes, 
> so don't publish anything based on this algorithm!" statement 
> still apply?

Good question!  I added that warning message to "util.ss" back when I
believed that there was such as thing as "correct" secondary structure
assignment and because util.ss had a very primitive H-bonding definition
-- distance only.  "dss" is something completely new.

In creating the new "dss", I took some time to go through the 1983 DSSP
paper (Kabsch & Sander) and discovered much to my surprise that the
H-bond criterion used by DSSP has very little to do with what
crystallographers today think about hydrogen bonds.  Did you know that
DSSP H-bonds can be as long as 5.2 Angstroms between heavy atoms (Fig
1)?  Plus, there is no simple analytic form of their criterion provided
which could be implemented by something like PyMOL.   

Furthermor, and more disturbing, I discovered that DSSP doesn't take
backbone torsion geometry into account at all, which finally explained
to me why so many DSSP-assigned PDB structures have obviously
non-helical regions assigned as HELIX.  It's just a naive algorithm, and
as far as I'm concerned, H-bonds just aren't the whole story when it
comes to secondary structure.

Thus, I had to admit that DSSP itself wasn't correct with repect to my
personal interpretation of secondary structure.  In looking at RasMOL's
code it suffers from some of the same problems, and I don't think it
actually implements DSSP -- just an approximation to it.

So I decided to create my own best-attempt at a secondary structure
assignment algorithm based on the spirit of DSSP, but which also takes
into account backbone geometry as well as hydrogen-bonding .  Like DSSP,
PyMOL's hydrogen-bonding criteria is angle-dependent, but the default
range is more contemporary (within 3.2 A at 63 deg, 3.6 A at 0 deg).  

After validating the algorithm manually on ten structures, I sat down
and visually compared PDB (DSSP) assignments to PyMOL's "dss" over
several hundreds proteins.  In general, both programs find the same set
of helices and large sheets.  However, they differ on the exact start
and stop points of these elements.  On small sheets or helices, one
program may miss something that the other finds.  However, divergent
regions seemed to involve borderline cases for the most part.  "dss" and
DSSP seem to do equally well on cut-and-dry idealized systems.  So "dss"
is reasonably validated, in my view, but I am looking for feedback and
specific problem cases when they're found.

But speaking as an artist rather than as a scientist, I think "dss" has
better aesthetics than DSSP when it comes to cartoon diagrams -- there
are simply fewer goofy-looking assignments.  Whether it is more
scientifically correct or not is an open question.  Cartoons themselves
are pretty misleading...one might add.

By the way, there are a some new settings in PyMOL 0.92 which cover
h-bond detection and secondary structure assignment.  Here are the most
important ones:

h_bond_max_angle, 63.0
h_bond_cutoff_center, 3.6
h_bond_cutoff_edge, 3.2

ss_helix_psi_target, -48.0
ss_helix_phi_target, -57.0

ss_strand_psi_target, 124.0
ss_strand_phi_target, -129.0

Basically, if helix or sheet hydrogen bonds are present, and backbone
geometries are close to the target values, PyMOL will assign residues as
helix or sheet.  Otherwise, they're considered loops.   The allowable
Phi/Psi inclusion/exclusion boxes are adjustable with settings too.

For the curious, my algorithm is about 1,000 lines of code and consists
of the SelectorAssignSS function found in layer3/Selector.c around line
500.

> 2) Is there a 0.92 function to calculate and map surface 
> potential?  This would be useful beyond compare.

I wish.  Your choices for this are Grasp, MEAD, Delphi, or Zap.  Only
MEAD is freely available.

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Neiditch, Matthew
> Sent: Friday, October 31, 2003 12:46 PM
> To: 'pym...@li...'
> Subject: [PyMOL] secondary structure assignment and surface 
> potential calc/mapping
> 
> 
> Dear List,
> 
>   
> 
> Regards,
> 
> Matthew Neiditch
> 
> Postdoc
> Hughson Lab
> Princeton University
> nei...@mo... 
> 
> 
> -------------------------------------------------------
> This SF.net email is sponsored by: SF.net Giveback Program. 
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> 

Dear List,

1) Is the secondary structure assignment function in 0.92 more reliable?  Or
does the "WARNING: it will make mistakes, so don't publish anything based on
this algorithm!" statement still apply?

2) Is there a 0.92 function to calculate and map surface potential?  This
would be useful beyond compare.
  

Regards,

Matthew Neiditch

Postdoc
Hughson Lab
Princeton University
nei...@mo... 

Hello all.
    I am relatively new to pymol, so please excuse me if these questions 
are too simple for the list as a whole.  I am running 0.90 on a Linux 
system by way of introduction.

1)  What is the easiest way to select one molecule out of several on the 
screen and translate it independently from everything else?  I try 
selecting it. but moving the mouse while holding the mov button still 
translates everything.

2)  Is there an easy way to superimpose many molecules independently?  I 
know that I can do individual pairwise alignments, but that seems like a 
good way to let more errors creep into the process.

3)  Is there an automated way to take HET groups in a structure read from a 
PDB file and make independent molecules out of them?

Thanks,
	Andy

Andrew Fant
and...@tu...

Alan,

	Unfortunately, secondary structure is currently defined as an
atom rather than a coordinate property.  Thus, in order to "animate"
secondary structure, you'll need to run dss automatically for each
state.  For example:

mset 1 -5
mdo 1, dss state=3D1
mdo 2, dss state=3D2
mdo 3, dss state=3D3
mdo 4, dss state=3D4
mdo 5, dss state=3D5

Of course, Python can automate this:

from pymol import cmd
cmd.mset("1 -%d"%cmd.count_states())
for a in range(1,cmd.count_states()+1): \
   cmd.mdo(a,"dss state=3D%d"%a)

After which...
  =20
PyMOL>mdump
 Movie: General Purpose Commands:
    1: dss state=3D1
    2: dss state=3D2
    3: dss state=3D3

etc.

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Alan Wilter Sousa da Silva
> Sent: Friday, October 31, 2003 3:48 AM
> To: pym...@li...
> Subject: [PyMOL] secondary structure and movie
>=20
>=20
> Hi List!
>=20
> I did a polyalanine in helix ss.
> I tested:
> 1: dss (ok)
> 2: run stride_ss.py, stride2pymol (ok)
> 3: dssp (from rtools) (???)
>=20
> Case (1) differs a little bit from (2) in N term.
>=20
> Case (3) seems not to work. Or, maybe, I do not know how to=20
> use it. Tried via menu and via command dssp.  Got the same=20
> thing: two new objects=20
> (helix and sheet) that show nothing!
>=20
> In a crystallographic protein (HIV protease), (1) gave-me a=20
> better (and
> faster) result than (2).  (3) still gave-me nothing (except=20
> the ref to=20
> Dssp, which is properly installed in my box).
> I really want to see dssp working.
>=20
> Anyway, all that said, what I want to do is loading a=20
> multi-pdb file and see dss calculating different ss for each=20
> frame.  How could I do it?
>=20
> Cheers,
> -=20
> --------------------------
> Alan Wilter Sousa da Silva
> --------------------------
> B.Sc. - Dep. F=EDsica - UFPA
> M.Sc. - Dep. F=EDsica - PUC/RJ
> D.Sc. - IBCCF/UFRJ
> Bolsista Pesquisador LAC-INPE
> S=E3o Jos=E9 dos Campos (SP), Brasil
> www.lac.inpe.br/~alan
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: SF.net Giveback Program.=20
> Does SourceForge.net help you be more productive?  Does it
> help you create better code?   SHARE THE LOVE, and help us help
> YOU!  Click Here: http://sourceforge.net/donate/=20
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> PyMOL-users mailing list
> PyM...@li...=20
> " rel="nofollow">https://lists.sourceforge.net/lists/listinfo/p> ymol-users
>=20

Hi List!

I did a polyalanine in helix ss.
I tested:
1: dss (ok)
2: run stride_ss.py, stride2pymol (ok)
3: dssp (from rtools) (???)

Case (1) differs a little bit from (2) in N term.

Case (3) seems not to work. Or, maybe, I do not know how to use it.
Tried via menu and via command dssp.  Got the same thing: two new objects=
=20
(helix and sheet) that show nothing!

In a crystallographic protein (HIV protease), (1) gave-me a better (and
faster) result than (2).  (3) still gave-me nothing (except the ref to=20
Dssp, which is properly installed in my box).
I really want to see dssp working.

Anyway, all that said, what I want to do is loading a multi-pdb file and
see dss calculating different ss for each frame.  How could I do it?

Cheers,
-=20
--------------------------
Alan Wilter Sousa da Silva
--------------------------
B.Sc. - Dep. F=EDsica - UFPA
M.Sc. - Dep. F=EDsica - PUC/RJ
D.Sc. - IBCCF/UFRJ
Bolsista Pesquisador LAC-INPE
S=E3o Jos=E9 dos Campos (SP), Brasil
www.lac.inpe.br/~alan

Warning.  

Several bugs have emerged in the 0.92 release which will cause me to
issue a rapid 0.93 update in the next day or so.  Thus, if you haven't
upgraded yet, you might want to wait a few days for 0.93.  

The bugs are:

1) problems reading O maps (high frequency)
2) problems saving PNG files (frequecy unknown).
3) problems with version 0.86 session files containing CGO's (rare).

Bugs 1 and 3 have been fixed, but bug 2 is still outstanding, and I have
been utterly unable to reproduce this problem on any of my test
machines.  Thus, I would like to get a handle on how widespread the
problem is.  

If you get this email on October 30th (today), and if you have
downloaded 0.92, can you take a minute to your ability to save "PNG"
files, and let me know what the result is?  Please respond only to me
mailto:wa...@de... in order to avoid flooding the
mailing list.  

Note on the Mac, if you are saving PNG files, you will need to direct
them to a suitable location.  For example:

cd ~
png example.png

or

png ~/example.png

will save the PNG file in your home directory.  Otherwise, the files may
end up in PyMOL.app/Contents/Resources, which may be practically
invisible to you.

By the way, if you notice any other serious bugs with the new version,
please report them ASAP -- I'd like to fix them in 0.93 if possible.

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> I would like to make a movie from a trajectory of 50 frames 
> with varying sec structure. Following Warren's advice in a 
> previous thread (see below) I load every pdb file into a 
> different object *and* state using
>   file_list1 = glob("*_first.pdb")
>   for file in file_list1:
>      cmd.load(file,file,file[:1])
> 
> { files are named 1_first.pdb, 2_first.pdb ...}
> However, the object loaded to the first frame also appears in 
> the following ones. 

Honest -- that's a feature, not a bug : )

set static_singletons, 0

to get the behavior you want...

> dssp calculation with rtools just gives 
> the sec structure of the object in the first frame. As a 
> workaround I tried to start loading into the 2nd frame and 
> not to load anything into the first one. But then the command 
> "dssp (2_first.pdb)" gives an error "no atoms selected" 
> instead of any calculation.

This is an rtool's specific issue.  If you're running version 0.92, you
might try

dss state=2

The results won't be identical to DSSP, but they are usually no worse...

Cheers,
Warren

Huiying,

	PyMOL will recognize the following extensions for O maps:

.o
.omap
.brix

The following will render the entire brick at 1 sigma:

load map.o
isomesh m1, map, 1

Or if you have a pdb

load model.pdb
isomesh m1, map, 1, 100/, 8

will give you an 8 A brick around residue 100, etc.

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Huiying Li
> Sent: Wednesday, October 29, 2003 3:52 PM
> To: pym...@li...
> Subject: [PyMOL] How to load O/BRIX map
> 
> 
> 
> I am wondering how to load the O/BRIX maps into Pymol using 
> version 0.92. Is there a default file extension, say *.dsn6, 
> for O map, or need to define the map format with a keyword?
> 
> Thanks for any help.
> 
> --------------------------------------------------
> Huiying Li, Ph. D
> Department of Molecular Biology and Biochemistry
> Natural Sciences I, Rm 2443
> University of California at Irvine
> Irvine, CA 92697, USA
> Tel: 949-824-4322(or -1953);  Fax: 949-824-3280
> email: hl...@br...
> --------------------------------------------------
> 
> 
> 
> 
> -------------------------------------------------------
> This SF.net email is sponsored by: SF.net Giveback Program. 
> Does SourceForge.net help you be more productive?  Does it
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> 

Einat,

	with version 0.92:

set dash_gap,0
set dash_length,1

	seems to do the trick for me, raytraced or not.

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Einat Sitbon
> Sent: Thursday, October 30, 2003 4:29 AM
> To: PyM...@li...
> Subject: [PyMOL] Ray tracing dashed lines
> 
> 
> 
> Hello Pymolers,
> 
> I'm using pymol 0.92. I changes some of the dash parameters - 
> I want the 
> distance lines to look continuous. This works fine, until I 
> ray trace the 
> protein. Then the dash returns to it's default settings...
> Any suggestions?
> thanks, Einat.
> 
> Einat Sitbon
> Department of Molecular Genetics
> Weizmann Institute of Science
> 
> _________________________________________________________________
> The new MSN 8: smart spam protection and 2 months FREE*  
> http://join.msn.com/?page=features/junkmail
> 
> 
> 
> -------------------------------------------------------
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> help you create better code?   SHARE THE LOVE, and help us help
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> _______________________________________________
> PyMOL-users mailing list
> PyM...@li... 
> " rel="nofollow">https://lists.sourceforge.net/lists/listinfo/p> ymol-users
> 

Hello Pymolers,

I'm using pymol 0.92. I changes some of the dash parameters - I want the 
distance lines to look continuous. This works fine, until I ray trace the 
protein. Then the dash returns to it's default settings...
Any suggestions?
thanks, Einat.

Einat Sitbon
Department of Molecular Genetics
Weizmann Institute of Science

_________________________________________________________________
The new MSN 8: smart spam protection and 2 months FREE*  
http://join.msn.com/?page=features/junkmail

Hi all,

I would like to make a movie from a trajectory of 50 frames with varying
sec structure. Following Warren's advice in a previous thread (see below)
I load every pdb file into a different object *and* state using
  file_list1 = glob("*_first.pdb")
  for file in file_list1:
     cmd.load(file,file,file[:1])

{ files are named 1_first.pdb, 2_first.pdb ...}
However, the object loaded to the first frame also appears in the
following ones. dssp calculation with rtools just gives the sec structure
of the object in the first frame.
As a workaround I tried to start loading into the 2nd frame and not to
load anything into the first one. But then the command "dssp
(2_first.pdb)" gives an error "no atoms selected" instead of any calculation.

Any suggestions?
Frauke


--------
RE: [PyMOL] secondary structure

    * From: "DeLano, Warren" <wa...@RE...>
    * Date: Wed, 13 Feb 2002 13:43:10 -0800
    * List-archive:
<" rel="nofollow">http://www.geocrawler.com/redir-sf.php3?list=pymol-users>
    * List-id: PyMOL Users Group <pymol-users.lists.sourceforge.net>
    * List-post: <mailto:pym...@li...>
    * Thread-index: AcG0WofecTamzeK5QwiLfKAn/1zEHgAe2fOQ
    * Thread-topic: [PyMOL] secondary structure

> How does this affect movies involving conformation changes?  Secondary
> structure info from the first frame appears to carry over
> into the others-
> whereas in reality some helixes or sheets change to varying
> degrees.  This
> leads to warping in something like calmodulin.  Would I need to render
> frames separately and run 'alter'?

Secondary structure in PyMOL is currently an atomic not a coordinate
property.  This is probably a design flaw, which will need to be fixed
later on.  Same goes for occupancy and B-factors (anything else?).

Anyway, if you want it to change secondary structure during a
trajectory, the easiest thing to do is split the trajectory over two
objects with non-overlapping states (ie. use the 'state' option to
load), and then assign the secondary structure independently...

state    1 2 3 4 5 6 7 8
object1  X X X X
object2          X X X X

Dear All,

I want to look at my structure in PyMOL and, having centered on something
defined by my selection script, pick atoms nearby and see what residues they
belong to. That is, I want to pick select an atom with the mouse and have its
name, residue name and residue number appear on screen, like it does in O.

I figured out that [Ctrl] + Left-Mouse-Button selects the atom as "lb", and that
the command 'label (lb),"%s %s %s" % (name,resn,resi)' gives me the label I
want. Now how could I get something like that to appear as a menu function in
the GUI so I don't have type it in all the time? Can it be a command executed as
part of my startup script?

Maybe some function like this already exists, otherwise I think it is a very
useful thing.

regards,

Richard Baxter

I am wondering how to load the O/BRIX maps into Pymol using version
0.92. Is there a default file extension, say *.dsn6, for O map, or need to
define the map format with a keyword?

Thanks for any help.

--------------------------------------------------
Huiying Li, Ph. D
Department of Molecular Biology and Biochemistry
Natural Sciences I, Rm 2443
University of California at Irvine
Irvine, CA 92697, USA
Tel: 949-824-4322(or -1953);  Fax: 949-824-3280
email: hl...@br...
--------------------------------------------------

Hi,

I'm having some trouble with PyMOL on my SGI's.  When we upgraded from (I
think) 6.5.11 to 6.5.20m, things stopped working for me.  Here's what we
have right now:

<oregano> mlerner: uname -aR
IRIX64 oregano 6.5 6.5.20m 04091957 IP30

We also upgraded the compilers, and we're now using this:

<oregano> mlerner: cc -version
MIPSpro Compilers: Version 7.3.1.3m

<oregano> mlerner: /usr/freeware/bin/gcc -v
Reading specs from /usr/freeware/lib/gcc-lib/mips-sgi-irix6.5/3.3/specs
Configured with: ../configure --prefix=/usr/freeware
--enable-version-specific-runtime-libs
--disable-shared --enable-threads --enable-haifa --enable-libgcj
--disable-c-mbchar
Thread model: single
gcc version 3.3

In case this is relevant, here's the hardware setup:

<oregano> mlerner: hinv
2 360 MHZ IP30 Processors
CPU: MIPS R12000 Processor Chip Revision: 3.5
FPU: MIPS R12010 Floating Point Chip Revision: 0.0
Main memory size: 512 Mbytes
Xbow ASIC: Revision 1.4
Instruction cache size: 32 Kbytes
Data cache size: 32 Kbytes
Secondary unified instruction/data cache size: 2 Mbytes
Integral SCSI controller 0: Version QL1040B (rev. 2), single ended
  Disk drive: unit 1 on SCSI controller 0
Integral SCSI controller 1: Version QL1040B (rev. 2), single ended
IOC3/IOC4 serial port: tty1
IOC3/IOC4 serial port: tty2
IOC3 parallel port: plp1
Graphics board: V6
Integral Fast Ethernet: ef0, version 1, pci 2
Iris Audio Processor: version RAD revision 12.0, number 1


I downloaded pymol-0_92-bin-irix65-r10k.tar today, and when I run
pymol.com, both windows (the Viewer window and the Tk window) show up and
look good.  The Tk window seems to work (I can use the menus to load a pdb
file, etc.), but the Viewer window is completely unresponsive.  The
display never updates, and it doesn't seem to notice any key presses or
mouse clicks.

If I recall correctly, this breakage happened when we upgraded.  We were
using PyMOL 0.86 at the time, and it just stopped working.  I downloaded
0.90 and it didn't work either.  I tried compiling 0.90 from source and
had the same result (i.e. I was able to compile everything, but the Viewer
window was unresponsive).

Clearly, I should have asked about this earlier, but I was pretty busy,
and I hoped that things would magically fix themselves with the next
release :).

Anyway, does anyone have any idea what could be wrong?  I'll be glad to
recompile things and try out various fixes, but I don't quite know where
to start.  It's possible that I used an older gcc (2.8.1) when I tried to
compile PyMOL before, so maybe I should just try recompiling, but I'm not
sure that's the problem.

Thanks,

-michael

--
Michael Lerner

> Hi Warren,
> 	When will PyMol 0.92 be available via fink?
> Thanks,
> Scott

I wrote an email to Matt Stephenson who is the package maintainer.
Hope he will reply soon.
If you want to write him yourself, his email is 
ca...@us...

Florian

Hi Warren,
	When will PyMol 0.92 be available via fink?
Thanks,
Scott

On Oct 26, 2003, at 11:06 PM, Warren L. DeLano wrote:

> PyMOL version 0.92 can be obtained from http://pymol.sf.net at your
> convenience.
>
> Though this is mostly an "under the hood" improvements release, there
> are some developments worth noting:
>
>   Significant changes
>
>    - New "dss" command assigns secondary structure quickly.
>    - PyMOL can now read O/BRIX maps and some Biosym GRiDs maps.
>    - Improved ray tracing quality and speed.
>    - Long lists of residues in selections are now allowed.
>
>   Other changes
>
>    - New "import pymol" support for RPM & Win32 builds that use system
> Python.
>        [Don't forget to call pymol.finish_launching() afterwards
> though!]
>    - Improved alpha-channel support for transparent surfaces and
> backgrounds.
>    - API's "cmd.do" can now take multi-line strings and lists.
>    - New "split_states" command for separating NMR ensembles.
>    - New "cartoon_transparency" setting.
>    - Can display bond valences while in stick mode.
>    - New "stick_ball", "stick_ball_ratio" settings for ball & stick
> models.
>    - Gaussian map generation from model coordinates.
>    - Can preserve original PDB atom IDs (pdb_retain_ids) & order
> (retain_order).
>    - Much much faster loading of multi-model PDB files and 
> trajectories.
>    - Deuterium and Calcium handling improved.
>    - New "set_symmetry" & "get_symmetry" commands.
>    - Mutagenesis wizard preserves cartoons.
>    - New "get_pdbstr" API function.
>    - New "movie_loop" setting can disable looping.
>    - Sculpting engine now aware of simple sp3-sp3 torsions.
>    - Finer Z-scaling/movement control.
>    - Upgrade facility for secure enterprises running Windows.
>
> PyMOL 0.92 also includes various bugs fixes with cartoons, rendering,
> CGOs, sessions, endianness, multithreading, raytracing, OS X, and
> isosurfaces.
>
> As always, upgrade with caution.  Don't update right before an 
> important
> presentation, and be sure to test your existing session files. Please
> report any trouble.
>
> Probably the most problematic aspect of the new version will be the
> increased WYSIWYG behavior of the ray-tracer with respect to line
> widths.  If the bonds in your figure just got thinner, that's the
> culprit.  You can manually adjust the various *_width or *_radius
> settings to achieve the desired results.
>
> Cheers,
> Warren
>
>
> --
> mailto:wa...@de...
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154
> Fax   (650)-593-4020
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: The SF.net Donation Program.
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   Scott Classen, Ph.D.
   ACS Postdoctoral Fellow
   Department of Molecular & Cell Biology
   University of California, Berkeley
   237 Hildebrand Hall #3206
   Berkeley, CA 94720-3206
   LAB 510.643.9491
   FAX 510.643.9290
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

> Currently, i=20
> work on a complexe proteinic which includes two proteins.
> I calculate distances (in a cut-off of 10 Angstr=F6m in order=20
> to obtain atoms=20
> which are within the interface of both molecules) between=20
> these proteins. Now, i would like to know what atoms belong=20
> to my selection and write them=20
> in a file. Could you help me please ?

iterate selection, python-code

For example:

load $PYMOL_DATA/demo/pept.pdb
output=3D open("output.txt",'w')
iterate (name ca), output.write("%s %s %s %s\n"%(resn,chain,resi,name))
output.close()

Would create "output.txt" containing:

ASP E 1 CA
CYS E 2 CA
ALA E 3 CA
TRP E 4 CA
HIS E 5 CA
LEU E 6 CA
GLY E 7 CA
GLU E 8 CA
LEU E 9 CA
VAL E 10 CA
TRP E 11 CA
CYS E 12 CA
THR E 13 CA

Notice how you can freely intersperse Python and PyMOL commands in PyMOL
command scripts in order to accomplish tasks such as this.

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax   (650)-593-4020

PyMOL version 0.92 can be obtained from http://pymol.sf.net at your
convenience.

Though this is mostly an "under the hood" improvements release, there
are some developments worth noting:

  Significant changes

   - New "dss" command assigns secondary structure quickly.
   - PyMOL can now read O/BRIX maps and some Biosym GRiDs maps.
   - Improved ray tracing quality and speed.
   - Long lists of residues in selections are now allowed.

  Other changes

   - New "import pymol" support for RPM & Win32 builds that use system
Python.
       [Don't forget to call pymol.finish_launching() afterwards
though!]
   - Improved alpha-channel support for transparent surfaces and
backgrounds.
   - API's "cmd.do" can now take multi-line strings and lists.
   - New "split_states" command for separating NMR ensembles.
   - New "cartoon_transparency" setting.
   - Can display bond valences while in stick mode.
   - New "stick_ball", "stick_ball_ratio" settings for ball & stick
models.
   - Gaussian map generation from model coordinates.
   - Can preserve original PDB atom IDs (pdb_retain_ids) & order
(retain_order).
   - Much much faster loading of multi-model PDB files and trajectories.
   - Deuterium and Calcium handling improved.
   - New "set_symmetry" & "get_symmetry" commands.
   - Mutagenesis wizard preserves cartoons.
   - New "get_pdbstr" API function.
   - New "movie_loop" setting can disable looping.
   - Sculpting engine now aware of simple sp3-sp3 torsions.
   - Finer Z-scaling/movement control.
   - Upgrade facility for secure enterprises running Windows.

PyMOL 0.92 also includes various bugs fixes with cartoons, rendering,
CGOs, sessions, endianness, multithreading, raytracing, OS X, and
isosurfaces.

As always, upgrade with caution.  Don't update right before an important
presentation, and be sure to test your existing session files. Please
report any trouble.

Probably the most problematic aspect of the new version will be the
increased WYSIWYG behavior of the ray-tracer with respect to line
widths.  If the bonds in your figure just got thinner, that's the
culprit.  You can manually adjust the various *_width or *_radius
settings to achieve the desired results.

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

Marcelo,

PyMOL doesn't currently do a very good job with a solid solvent
accessible surfaced because they aren't smooth like the Connolly
surface. But here's what you can do:

show spheres
set sphere_solvent,1

   or

hide spheres
show mesh
set solvent_mesh,1

   now add in

show surface

   for a nice combination of the solvent and molecular surfaces.

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Marcelo Castilho
> Sent: Sunday, October 26, 2003 4:04 AM
> To: pym...@li...
> Subject: [PyMOL] solvent accesible surface
>=20
>=20
> Dear all,
>=20
> I am new to pymol and appologyze if his is an "easy=20
> question", anyway here it goes;
>=20
> Is it possible to change the surface radius in pymol so that=20
> I can represent the solvente accesible surface ?
>=20
> By the way, I am running pymol 0.90 under windows XP
>=20
> Thanks,
>=20
> Marcelo Castilho
>=20
> =3D=3D=3D=3D=3D
> Marcelo Santos Castilho
> tel 016 273 98 68
> R; Am=E9rico J. Canhoto 223 Apto 23 Bl 2
> S=E3o Carlos CEP 13564-350
> e-mail alternativo: cas...@if...
>=20
> __________________________________
> Do you Yahoo!?
> Exclusive Video Premiere - Britney Spears=20
> http://launch.yahoo.com/promos/britneyspears/
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: The SF.net Donation=20
> Program. Do you like what SourceForge.net is doing for the=20
> Open Source Community?  Make a contribution, and help us add=20
> new features and functionality. Click here:=20
> http://sourceforge.net/donate/=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...=20
> " rel="nofollow">https://lists.sourceforge.net/lists/listinfo/p> ymol-users
>=20

Douglas,

	Simply:

save filename.pse

ie

save today.pse

Cheers,
Warren



--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Douglas Freymann
> Sent: Sunday, October 26, 2003 2:26 PM
> To: pym...@li...
> Subject: [PyMOL] Save session on Mac OSX latest version?
> 
> 
> I'm having a hard time finding how to save my session running on a G4 
> Powerbook, using PyMOL v0.91.  The command, File::Save, is grayed 
> out, and there's no command File::Save Session as described in the 
> Users Manual.  Is there a trick, or a command line statement? 
> By the way, is there a way to set a default working directory when 
> PyMOL starts?
> Sorry if these are FAQ's but I didn't find the answers 
> anywhere. Thanks, Doug
> 
> -- 
> 
> Douglas M. Freymann          fre...@no...
> 
> Molecular Pharmacology & Biological Chemistry
> Ward 7-247,  Northwestern University
> 303 E. Chicago Ave., Chicago, IL  60611
> 
> (312) 503-1877                    fax: (312) 503-5349
> 
> 
> -------------------------------------------------------
> This SF.net email is sponsored by: The SF.net Donation 
> Program. Do you like what SourceForge.net is doing for the 
> Open Source Community?  Make a contribution, and help us add 
> new features and functionality. Click here: 
> http://sourceforge.net/donate/ 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li... 
> " rel="nofollow">https://lists.sourceforge.net/lists/listinfo/p> ymol-users
> 

I'm having a hard time finding how to save my session running on a G4 
Powerbook, using PyMOL v0.91.  The command, File::Save, is grayed 
out, and there's no command File::Save Session as described in the 
Users Manual.  Is there a trick, or a command line statement?
By the way, is there a way to set a default working directory when 
PyMOL starts?
Sorry if these are FAQ's but I didn't find the answers anywhere.
Thanks,
Doug

-- 

Douglas M. Freymann          fre...@no...

Molecular Pharmacology & Biological Chemistry
Ward 7-247,  Northwestern University
303 E. Chicago Ave., Chicago, IL  60611

(312) 503-1877                    fax: (312) 503-5349

Dear all,

I am new to pymol and appologyze if his is an "easy question", anyway here it
goes;

Is it possible to change the surface radius in pymol so that I can represent
the solvente accesible surface ?

By the way, I am running pymol 0.90 under windows XP

Thanks,

Marcelo Castilho

=====
Marcelo Santos Castilho
tel 016 273 98 68
R; Américo J. Canhoto 223 Apto 23 Bl 2
São Carlos CEP 13564-350
e-mail alternativo: cas...@if...

__________________________________
Do you Yahoo!?
Exclusive Video Premiere - Britney Spears
http://launch.yahoo.com/promos/britneyspears/

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

| Message: 4
| From: "Warren L. DeLano" <wa...@de...>
| To: <pym...@li...>
| Date: Sat, 25 Oct 2003 13:12:51 -0700
| Subject: [PyMOL] Release in progress...
|
| (in a whisper)
|
| I'm still in the process of building binaries, but pioneers are welcome
| to start downloading 0.92, if your platform is represented.  It has been
| a long time since our last release, so proceed with caution!
|
| http://sourceforge.net/project/showfiles.php?group_id=4546
|
| Please bring any problems to my attention ASAP, before the Monday
| deluge.

Looks nice, I found one little glitch (or is it a feature) which might
have been there before:

A raw traceback if you type a command which does not exist:

For example:

PyMOL>k
Traceback (most recent call last):
~  File "//tuxprog/pymol/pymol_0.92/modules/pymol/parser.py", line 255,
in parse
~    exec(com2[nest]+"\n",pymol_names,pymol_names)
~  File "<string>", line 1, in ?
NameError: name 'k' is not defined

which makes perfect sense, but might look a bit strange to the end-user
(something like "command "k" not found" might be more usefull).

Also probably not good without another security-measure:

Typing "q" <Return> (will immediately quit Pymol).

- --
Bye,
Marc Saric  http://www.marcsaric.de
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Version: GnuPG v1.0.7 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iD8DBQE/m7VYvKxJUF29wRIRArhbAJ928s/6nrRnCqg4mfEEAPO4WarTMQCgx08I
wyMNr7nlUUmDsIJh4tvv1pk=
=rsZP
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What's been added?  I didn't see a changelog. . .

(the 'dss' command, by the way, looks unbelievably awesome.)

On Sat, 25 Oct 2003, Warren L. DeLano wrote:

> (in a whisper)
>
> I'm still in the process of building binaries, but pioneers are welcome
> to start downloading 0.92, if your platform is represented.  It has been
> a long time since our last release, so proceed with caution!
>
> http://sourceforge.net/project/showfiles.php?group_id=4546
>
> Please bring any problems to my attention ASAP, before the Monday
> deluge.
>
> Warren
>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: The SF.net Donation Program.
> Do you like what SourceForge.net is doing for the Open
> Source Community?  Make a contribution, and help us add new
> features and functionality. Click here: http://sourceforge.net/donate/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

(in a whisper) 

I'm still in the process of building binaries, but pioneers are welcome
to start downloading 0.92, if your platform is represented.  It has been
a long time since our last release, so proceed with caution!

http://sourceforge.net/project/showfiles.php?group_id=4546

Please bring any problems to my attention ASAP, before the Monday
deluge.

Warren