[PyMOL] Secondary structure and surface

[Alex W. Smith]

Greetings PyMolers:

I have a couple of questions.  I am working on some figures and have 
found, at least for my particular protein,  the DSS in PyMol does a 
better job with secondary structure assignments than DSSP.  I have 
checked the assignments against the map and model in O.  Is there any 
way to output the assignments from PyMol?


Also I want to display surfaces and was wondering if anyone has an 
opinion on the reliability of PyMol vs. MSMS (or any other surface 
calculation programs).  Any input would be greatly appreciated.


Best regards,

Alex

Re: [PyMOL] running APBS plugin on macG5

[Alex W. Smith]

Michael:

I followed the directions for installing from source and used Bill 
Scott's tweak (both links below).  Everything seems to be running fine. 
 I am a bit short of memory using my Al G4PB, but everything configured 
and complied with no problems.  I have only used APBS with the Pymol 
plugin but it seems to run fine.  Slow but fine.


http://agave.wustl.edu/apbs/doc/html/user-guide/x122.html
http://chips.csb.ki.se/pymol/msg02192.html


I created the directory /usr/local/APBS.  Then made all the directories 
the instructions called for within the APBS directory I created.  The 
psize.py script ended up in 
/usr/local/APBS/src/apbs-0.3.1/tools/manip/psize.py


Alex






On Sep 2, 2004, at 8:36 AM, Michael George Lerner wrote:



Hi,

I don't have a Mac, so I can't really help you here .. I know there are
quite a few people on the PyMOL list who've gotten APBS to work on 
Macs,
though, so maybe one of them will chime in.  If you don't get help 
here,
you can probably get some more advice on the APBS mailing list.  In 
case

you didn't sign up when you downloaded APBS, the webpage is
http://cholla.wustl.edu/mailman/listinfo/apbs-users

Once you get APBS installed, the APBS+PyMOL plugin should just work (it
doesn't really need APBS's psize.py).

But .. can anyone who has installed APBS on this platform tell me where
APBS puts psize.py?  I'd like to list that on my webpage.

Thanks,

-michael

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

On Wed, 1 Sep 2004, Ann Mullin wrote:


Hi,
All I want to do is be able to create an electrostatic surface
representation of a simple molecule.

I am seriously overwhelmed by the information for compiling and 
setting

APBS on their website.  I was happy to fine a link to download a
package with an installer, but when I run it it fails at the very end
and tells me to try installing again.  Also, is there any place that I
should be installing this?  I tried in the Applications folder and in
the folder I made to surround PyMOL and it's user manual.

I also notice that there is a binary ready to use for G5 on the
website, but where do I put this to work, and where is the psize.py
file.  I rarely work on a UNIX platform and I have a very hard time
switching from macOS to UNIX and back, since macOS is almost all point
and click.

Thanks for any help.  Ann


Ann Mullin
Research Scientist
Cell and Molecular Biology Dept.
Tulane University
New Orleans, LA 70118-5698
504-865-6742 (Ph)
504-865-6785 (FAX)
amul...@tulane.edu




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[PyMOL] non_bonded size

[Alex W. Smith]

Is there a way to set the size of non-bonded spheres to two different 
sizes within the same residue?  For example, I have a metal ion with a 
bound water and have both in the same residue but I want the metal ion 
to be bigger than the water.


I have check the list archives and googled "PyMol non-bonded sphere 
size" and have had no luck.


Suggestions?

Best regards,

Alex

Re: [PyMOL] non_bonded size

[Alex W. Smith]

Thanks Scott.  I keep trying to mess with the non-bonded size instead 
of the regular sphere size.


Alex


On Sep 8, 2004, at 2:38 PM, Scott Classen wrote:


Alex,
You need to create two separate objects one for your metal and another 
for your water


create MG, (chain M)
create WAT, (chain W)

then you can change the properties of each object individually

set sphere_scale, 1.2, MG
set sphere_scale, 0.8, WAT

good luck,
Scott


On Sep 8, 2004, at 2:19 PM, Alex W. Smith wrote:

Is there a way to set the size of non-bonded spheres to two different 
sizes within the same residue?  For example, I have a metal ion with 
a bound water and have both in the same residue but I want the metal 
ion to be bigger than the water.


I have check the list archives and googled "PyMol non-bonded sphere 
size" and have had no luck.


Suggestions?

Best regards,

Alex


  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




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