pymol-users Mailing List for PyMOL Molecular Graphics System

Hello:
I would like to make one figure consisting of two inhibitors from two
different files. Is there a way that I can move inhibitor from one file
w.r.t. the inhibitor from the second file?
Thanks in advance,
Madhavi

-----Original Message-----
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[mailto:pym...@li...] On Behalf Of
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Sent: Wednesday, November 29, 2006 2:41 PM
To: pym...@li...
Subject: PyMOL-users Digest, Vol 6, Issue 24

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Today's Topics:

   1. Re: morphing between complexes (Nat Echols)
   2. electrostatic potential structure (shivesh kumar)
   3. Re: electrostatic potential structure (Martin H?fling)
   4. Re: APBS and Pymol (Andreas Henschel)


----------------------------------------------------------------------

Message: 1
Date: Tue, 28 Nov 2006 14:04:59 -0800 (PST)
From: Nat Echols <ec...@uc...>
Subject: Re: [PyMOL] morphing between complexes
To: pymol <pym...@li...>
Message-ID: <Pin...@le...>
Content-Type: TEXT/PLAIN; charset=3DUS-ASCII; format=3Dflowed

> unfortunately I've already tried that server and I've seen that also
in
> that case, the ligand is stripped out.I obtain movies with only the
> protein movements. I don't know if i have problems with my pdbs:
> I have 245 residues + 1 ligand (246). it has the ATOM and not the
HETATM
> indication, could be this a problem?

The server itself doesn't deal with heteroatoms, mostly because it makes

dealing with the PDB even more of a nightmare than usual.  The
underlying=20
CNS input file will handle any ligand you want as long as you have the=20
correct topology and parameter files (e.g. from Gerard Kleywegt's HIC-UP

server).

I don't know of any program that will morph between *different* ligands,

though.  You can cheat by using a dummy ligand that has the conserved=20
core, and adding in the rest manually once you have the interpolation.=20
For instance, to show ATP hydrolysis, you use ADP in both PDB files, and

later re-insert the original ATP in place of the ADP in the first=20
frame(s).  PyMOL makes this very easy.

-Nat



------------------------------

Message: 2
Date: Wed, 29 Nov 2006 06:31:25 -0800 (PST)
From: shivesh kumar <shi...@ya...>
Subject: [PyMOL] electrostatic potential structure
To: pym...@li...
Message-ID: <200...@we...>
Content-Type: text/plain; charset=3D"iso-8859-1"

Dear all,
  How can I get the electrostatic potential structure of my protein
molecule.Thanx in advance.
  S


shivesh
=20
---------------------------------
Want to start your own business? Learn how on Yahoo! Small Business.
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Message: 3
Date: Wed, 29 Nov 2006 15:58:09 +0100
From: Martin H?fling <mar...@gm...>
Subject: Re: [PyMOL] electrostatic potential structure
To: pym...@li...
Message-ID: <200...@gm...>
Content-Type: text/plain;  charset=3D"iso-8859-1"

Am Mittwoch, 29. November 2006 15:31 schrieb shivesh kumar:
> Dear all,
>   How can I get the electrostatic potential structure of my protein
> molecule.Thanx in advance. S

what do you mean by "electrostatic potential structure"? The potential
can be=20
calculated with apbs (by hand or via plugin). This produces a map file
which=20
when loaded can be visualized as fieldlines or as equipotential
surfaces. I=20
think coloring of the ses of a protein is also possible.

Cheers
	Martin



------------------------------

Message: 4
Date: Wed, 29 Nov 2006 20:40:31 +0100
From: Andreas Henschel <ah...@bi...>
Subject: Re: [PyMOL] APBS and Pymol
To: Anastassis Perrakis <a.p...@nk...>
Cc: ba...@bi..., pym...@li...
Message-ID: <456...@bi...>
Content-Type: text/plain; charset=3D"iso-8859-1"

Hi Anastassis,

I got the same error with a few pdb files.
The problem is the following. The B-factor in the pymol-generated pdb=20
file is somtimes set to values larger than 100 (119.63 in your case)=20
thus occupying all its columns of the lovely PDB-format and not leaving=20
any space to the preceding occupancy column (1.00 in your case). The=20
script psize.py however parses these lines by splitting on white-spaces=20
and crashes when converting the merged field ...

The remedy is to modify psize.py like this:

around line 108, replace
words =3D string.split(subline)
with
words =3D line[30:38], line[38:46], line[46:54], line[54:60], =
line[60:66],

line[72:76], line[76:78]  ## PDB-format is fixed-space!

Hope that works for you, in any case attached is my debugged psize.py
file.

Another error occurs when calculating the electrostatics of pdb 1F88, a=20
transmembrane protein. The same thing happens
on the pdb2pqr Server (http://nbcr.net/pdb2pqr): 'NoneType' object has=20
no attribute 'getCoords'

looks a bit like strange atom name problem, I get the script working by=20
inserting:
if not nextatom: return 0
in line 608, however I am not 100% sure whether its still sound...

Cheers,
Andreas


Peter Adrian Meyer wrote:

>Hi,
>
> =20
>
>>parseInput
>>     self.parseLines(file.readlines())
>>   File "/usr/local/apbs-0.4.0/tools/manip/psize.py", line 116, in
>>parseLines
>>     self.q =3D self.q + float(words[3])
>>ValueError: invalid literal for float(): 1.00119.63
>>
>>
>>Any clues ?
>>   =20
>>
>
>It looks like it's reading from a pdb file when it's expecting a pqr
file,
>and that the split statement didn't produce the expected input due to
the
>B factor in the pdb file being too large.
>Possibly you have to generate a pqr file before setting the grid (I'm
not
>farmilar enough with the apbs-pymol plugin to remember offhand).
>
>Good luck,
>
>Pete
>
>
>Pete Meyer
>Fu Lab
>BMCB grad student
>Cornell University
>
>
>
>
>
>-----------------------------------------------------------------------
--
>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
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DEVD
EV
>_______________________________________________
>PyMOL-users mailing list
>PyM...@li...
>https://lists.sourceforge.net/lists/listinfo/pymol-users
> =20
>

--=20
Andreas Henschel
Bioinformatics Group
TU Dresden
Tatzberg 47-51
01307 Dresden, Germany

Phone: +49 351 463 40063
EMail: ah...@bi...


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End of PyMOL-users Digest, Vol 6, Issue 24
******************************************

Dear Warren & pymol-users,

If you remember about my freeGLUT problem, I have partially solved it,=20
but still not 100%.
Yes, PyMOL works OK with freeGLUT 2.4.x. My problem was that if I launch=20
the program from command line, in a terminal window, the error appears:

freeglut (/home/hteran/tmp/programs/pymol/pymol.exe): Unable to create=20
direct context       rendering for window 'PyMOL Viewer'
This may hurt performance.

BUT if I launch the program from the KDE menu, it simply works great! I=20
can enable the option "run in terminal window" and even though no=20
freeGLUT error appears in the term, and PyMOL is as fast as it should be!

So, the question is can adv linux user can point me how to solve the=20
problem when I want to run pymol from command line? It seems a problem=20
with the path, but I can not go further ...

Hugo


DeLano Scientific wrote:
> Hugo,
>
> I believe Donnie is mistaken:  PyMOL runs just fine with FreeGLUT 2.4.0
> (don't know about all 2.4.x though).  Lack of an ability to create a di=
rect
> rendering context is most likely a problem with your graphics driver, X=
11
> configuration, pixel depth, or with the interaction between FreeGLUT an=
d
> your graphics driver. =20
>
> Cheers,
>
> DeLano Scientific LLC
> Email Support Services=20
>
>  =20
>> -----Original Message-----
>> From: pym...@li...=20
>> [mailto:pym...@li...] On Behalf=20
>> Of Hugo Guti=E9rrez de Teran
>> Sent: Friday, November 03, 2006 1:30 AM
>> To: Donnie Berkholz
>> Cc: pym...@li...
>> Subject: Re: [PyMOL] freeglut problem
>>
>> Same problem with freeglut2.2.0
>> Isn't it strange that pymol + freeglut2.4 is NOT compatible,=20
>> when it is specifically said in pymol distribution that 
>> of the dependences is freeglut2.4????
>>
>> Thanks,
>> Hugo
>>
>> Donnie Berkholz wrote:=20
>>
>> 	Hugo Guti=E9rrez de Teran wrote:
>> 	 =20
>>
>> 		freeglut=20
>> (/home/hteran/tmp/programs/pymol/pymol.exe): Unable to create=20
>> 		direct context rendering for window 'PyMOL=20
>> Viewer' This may hurt=20
>> 		performance.
>> 	=09
>> 		But my system says I have freeglut installed:
>> 	=09
>> 		# yum search glut
>> 		freeglut.i386                           =20
>> 2.4.0-4                installed
>> 		freeglut.x86_64                         =20
>> 2.4.0-4                installed
>> 		   =20
>>
>> =09
>> 	freeglut-2.4 + pymol =3D broken. Try glut instead, or=20
>> perhaps freeglut-2.2
>> 	or freeglut CVS.
>> =09
>> 	Thanks,
>> 	Donnie
>> =09
>> 	 =20
>>
>>
>>
>> --
>> Hugo G. de Teran, PhD.
>> Departmento de Farmacolog=EDa / Instituto de Farmacia=20
>> Industrial Universidade Santiago de Compostela
>>
>> Facultad de Farmacia           Phone: +34 981 563 100 ext 13040
>> Campus Sur, s/n E-15782        Fax: +34 981 594595           =20
>> Santiago de Compostela (SPAIN) e-mail:hu...@us...  =20
>>
>>
>>
>>    =20
>
>
>  =20


--=20
Hugo G. de Teran, PhD.
Departmento de Farmacolog=EDa / Instituto de Farmacia Industrial
Universidade Santiago de Compostela

Facultad de Farmacia           Phone: +34 981 563 100 ext 13040
Campus Sur, s/n E-15782        Fax: +34 981 594595           =20
Santiago de Compostela (SPAIN) e-mail:hu...@us...  =20

Hi Anastassis,

I got the same error with a few pdb files.
The problem is the following. The B-factor in the pymol-generated pdb 
file is somtimes set to values larger than 100 (119.63 in your case) 
thus occupying all its columns of the lovely PDB-format and not leaving 
any space to the preceding occupancy column (1.00 in your case). The 
script psize.py however parses these lines by splitting on white-spaces 
and crashes when converting the merged field ...

The remedy is to modify psize.py like this:

around line 108, replace
words = string.split(subline)
with
words = line[30:38], line[38:46], line[46:54], line[54:60], line[60:66], 
line[72:76], line[76:78]  ## PDB-format is fixed-space!

Hope that works for you, in any case attached is my debugged psize.py file.

Another error occurs when calculating the electrostatics of pdb 1F88, a 
transmembrane protein. The same thing happens
on the pdb2pqr Server (http://nbcr.net/pdb2pqr): 'NoneType' object has 
no attribute 'getCoords'

looks a bit like strange atom name problem, I get the script working by 
inserting:
if not nextatom: return 0
in line 608, however I am not 100% sure whether its still sound...

Cheers,
Andreas


Peter Adrian Meyer wrote:

>Hi,
>
>  
>
>>parseInput
>>     self.parseLines(file.readlines())
>>   File "/usr/local/apbs-0.4.0/tools/manip/psize.py", line 116, in
>>parseLines
>>     self.q = self.q + float(words[3])
>>ValueError: invalid literal for float(): 1.00119.63
>>
>>
>>Any clues ?
>>    
>>
>
>It looks like it's reading from a pdb file when it's expecting a pqr file,
>and that the split statement didn't produce the expected input due to the
>B factor in the pdb file being too large.
>Possibly you have to generate a pqr file before setting the grid (I'm not
>farmilar enough with the apbs-pymol plugin to remember offhand).
>
>Good luck,
>
>Pete
>
>
>Pete Meyer
>Fu Lab
>BMCB grad student
>Cornell University
>
>
>
>
>
>-------------------------------------------------------------------------
>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
>  
>

-- 
Andreas Henschel
Bioinformatics Group
TU Dresden
Tatzberg 47-51
01307 Dresden, Germany

Phone: +49 351 463 40063
EMail: ah...@bi...

Am Mittwoch, 29. November 2006 15:31 schrieb shivesh kumar:
> Dear all,
>   How can I get the electrostatic potential structure of my protein
> molecule.Thanx in advance. S

what do you mean by "electrostatic potential structure"? The potential can be 
calculated with apbs (by hand or via plugin). This produces a map file which 
when loaded can be visualized as fieldlines or as equipotential surfaces. I 
think coloring of the ses of a protein is also possible.

Cheers
	Martin

Dear all,
  How can I get the electrostatic potential structure of my protein molecule.Thanx in advance.
  S


shivesh
 
---------------------------------
Want to start your own business? Learn how on Yahoo! Small Business.

> unfortunately I've already tried that server and I've seen that also in
> that case, the ligand is stripped out.I obtain movies with only the
> protein movements. I don't know if i have problems with my pdbs:
> I have 245 residues + 1 ligand (246). it has the ATOM and not the HETATM
> indication, could be this a problem?

The server itself doesn't deal with heteroatoms, mostly because it makes 
dealing with the PDB even more of a nightmare than usual.  The underlying 
CNS input file will handle any ligand you want as long as you have the 
correct topology and parameter files (e.g. from Gerard Kleywegt's HIC-UP 
server).

I don't know of any program that will morph between *different* ligands, 
though.  You can cheat by using a dummy ligand that has the conserved 
core, and adding in the rest manually once you have the interpolation. 
For instance, to show ATP hydrolysis, you use ADP in both PDB files, and 
later re-insert the original ATP in place of the ADP in the first 
frame(s).  PyMOL makes this very easy.

-Nat

Il giorno mar, 28/11/2006 alle 11.22 -0500, Mat...@im...
ha scritto:

> 
> Dear Andrea -
> 
> You should try using the Gerstein Morph Server:
> http://www.molmovdb.org/molmovdb/morph/
> 
> The core algorithm uses CNS, so if your structure is parsed properly by
> CNS, it should emerge from the server looking OK.  You'll get a small movie
> back from the server, and you can also ask it to send you the PDB files
> used for each frame, so you can make your own movies in Pymol.
> 
Thanks a lot for your reply,
unfortunately I've already tried that server and I've seen that also in
that case, the ligand is stripped out.I obtain movies with only the
protein movements. I don't know if i have problems with my pdbs:
I have 245 residues + 1 ligand (246). it has the ATOM and not the HETATM
indication, could be this a problem?
> For making movies in complicated situations like this, I've usually used
> script files to explicitly define each frame of the movie:
> 
> load file1.pdb
> (rendering commands)
> ray 2400,2400
> png frame1.png
> delete file1
> load file2.pdb
> etc...
> 
> You get a long script file, but you can use a text editor to copy & paste
> the text blocks.
I think that the resolution or quality could be a useful setting to add
in the program to overcome this "manual" procedure.
> 
> Hope that helps,
> 
Thanks,
it helped me
Andrea

pym...@li... wrote on 11/28/2006 05:25:15 AM:

> Hi all,
> I'm new to this list and I'm a newbie of Pymol.
> I'm trying to do some morphing movies between different complexes (same
> protein but different ligands). I'm having troubles cause the morphed
> structures (pdbs generated by lsqman (procedure taken by this page
> http://ginsberg.med.virginia.edu/~dcoop/Help/morph.html )) partially
> lost the informations about the ligands (only the core of the similar
> portion of each ligand is mantained, but the substituent are lost). Do
> you know if there is a way to solve/overcome this problem?
> Another related question is if was possible to set a ray resolution
> (let's say ray 2400, 2400) for the creation of all the frames of the
> movie (multiple png). I've been able to do that for one frame at time,
> manually...is there the possibility to set a different resolution
> recursively for all the image creation processes?
> Many thanks in advance and sorry for the long message
> Andrea
>
>

Dear Andrea -

You should try using the Gerstein Morph Server:
http://www.molmovdb.org/molmovdb/morph/

The core algorithm uses CNS, so if your structure is parsed properly by
CNS, it should emerge from the server looking OK.  You'll get a small movie
back from the server, and you can also ask it to send you the PDB files
used for each frame, so you can make your own movies in Pymol.

For making movies in complicated situations like this, I've usually used
script files to explicitly define each frame of the movie:

load file1.pdb
(rendering commands)
ray 2400,2400
png frame1.png
delete file1
load file2.pdb
etc...

You get a long script file, but you can use a text editor to copy & paste
the text blocks.

Hope that helps,

Matt

--
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems
180 Varick Street, 6th floor
New York, NY 10014
phone:(917)606-4116   fax:(212)645-2054



Confidentiality Note:  This e-mail, and any attachment to it, contains
privileged and confidential information intended only for the use of the
individual(s) or entity named on the e-mail.  If the reader of this e-mail
is not the intended recipient, or the employee or agent responsible for
delivering it to the intended recipient, you are hereby notified that
reading it is strictly prohibited.  If you have received this e-mail in
error, please immediately return it to the sender and delete it from your
system.  Thank you.

Hi all,
I'm new to this list and I'm a newbie of Pymol.
I'm trying to do some morphing movies between different complexes (same
protein but different ligands). I'm having troubles cause the morphed
structures (pdbs generated by lsqman (procedure taken by this page
http://ginsberg.med.virginia.edu/~dcoop/Help/morph.html )) partially
lost the informations about the ligands (only the core of the similar
portion of each ligand is mantained, but the substituent are lost). Do
you know if there is a way to solve/overcome this problem?
Another related question is if was possible to set a ray resolution
(let's say ray 2400, 2400) for the creation of all the frames of the
movie (multiple png). I've been able to do that for one frame at time,
manually...is there the possibility to set a different resolution
recursively for all the image creation processes? 
Many thanks in advance and sorry for the long message
Andrea

Hi,

> parseInput
>      self.parseLines(file.readlines())
>    File "/usr/local/apbs-0.4.0/tools/manip/psize.py", line 116, in
> parseLines
>      self.q = self.q + float(words[3])
> ValueError: invalid literal for float(): 1.00119.63
>
>
> Any clues ?

It looks like it's reading from a pdb file when it's expecting a pqr file,
and that the split statement didn't produce the expected input due to the
B factor in the pdb file being too large.
Possibly you have to generate a pqr file before setting the grid (I'm not
farmilar enough with the apbs-pymol plugin to remember offhand).

Good luck,

Pete


Pete Meyer
Fu Lab
BMCB grad student
Cornell University

Hi Florian

I have also been unable to use pdb2pqr within the
plugin (I had similar problems althought I was only
using standard residues), but what I did is to use
pqr2pdb as stand-alone
program and then feed the plugin with the previously
generated pqr files.

Hope it helps

Raul

 
> Message: 2
> Date: Wed, 22 Nov 2006 09:27:50 +0100
> From: Florian Schmitzberger
> <Flo...@ki...>
> Subject: [PyMOL] apbs plugin in pymol
> To: pym...@li...
> Message-ID:
> <E29...@ki...>
> Content-Type: text/plain; charset="us-ascii"
> 
> Dear All,
> 
> I am having a small problem using the apbs plugin in
> pymol on my pdb  
> (I am using fink installed pymol and apbs versions
> on Mac OSX 10.4.8).
> 
> When I try to run apbs I received the following
> message:
> 
> "Unable to assign parameters for 100 atoms in the
> selection  
> unassigned. Please either remove these unassigned
> atoms and re- 
> start ..."
> 
> In principle, I think I understand the problem is
> that pdb2pqr cannot  
> assign charges to certain atoms, in my case
> posttranslationally  
> modified cysteine residues.
> 
> My question would be what the best way to fare with
> those atoms is.  
> Since the modification introduces an acidic patch,
> if possible I  
> would like to leave the atoms in (rather than remove
> them) when  
> calculating surface charge representation, as this
> could be informative.


__________________________________________________
Correo Yahoo!
Espacio para todos tus mensajes, antivirus y antispam ¡gratis! 
Regístrate ya - http://correo.espanol.yahoo.com/ 

Hi Shivesh,

I like the interactive Wizard/Measurement from the top bar in the tcl/tk
GUI.
Works for angles and dihedrals too.

Cheers,
Jurgen

2006/11/24, shivesh kumar <shi...@ya...>:
>
> Dear all,
> Is there anyway to calculate the bond distances in pymol and to show the
> bond distances also...
>
>
-- 
Jurgen F. Doreleijers, Ph.D.
BMRB, Univ. of Wisconsin-Madison, WI, USA
mailto:jur...@gm...

Hi -

I installed apbs and tools (0.4.0) in a Linux box.

I then specified the location of psize.py and apbs executable.

when i load a protein and click on 'set grid' according to  
instructions I get on a new window a rather cryptic response:

Error: 6
ValueError Exception in Tk callback
   Function: <function <lambda> at 0x414cfbc4> (type: <type 'function'>)
   Args: ()
Traceback (innermost last):
   File "/Xsoftware/pymol/ext/lib/python2.3/Pmw/Pmw_1_2/lib/ 
PmwBase.py", line 1747, in __call__
     return apply(self.func, args)
   File "/Xsoftware/pymol/ext/lib/python2.3/Pmw/Pmw_1_2/lib/ 
PmwDialog.py", line 153, in <lambda>
     command=lambda self=self, name=name: self._doCommand(name))
   File "/Xsoftware/pymol/ext/lib/python2.3/Pmw/Pmw_1_2/lib/ 
PmwDialog.py", line 132, in _doCommand
     return command(name)
   File "/Xsoftware/pymol/modules/pmg_tk/startup/apbs_tools.py", line  
1055, in execute
     self.runPsize()
   File "/Xsoftware/pymol/modules/pmg_tk/startup/apbs_tools.py", line  
1096, in runPsize
     size.runPsize(pdb_filename)
   File "/usr/local/apbs-0.4.0/tools/manip/psize.py", line 267, in  
runPsize
     self.parseInput(filename)
   File "/usr/local/apbs-0.4.0/tools/manip/psize.py", line 102, in  
parseInput
     self.parseLines(file.readlines())
   File "/usr/local/apbs-0.4.0/tools/manip/psize.py", line 116, in  
parseLines
     self.q = self.q + float(words[3])
ValueError: invalid literal for float(): 1.00119.63


Any clues ?

	A.

On Mon, Nov 20, 2006 at 10:27:48AM -0800, DeLano Scientific wrote:
> My preference would be for a fast, clean, back-end cheminformatics library
> with a simple C API that could be exposed to and interporate with Python,
> Java, C, C++, SQL, and .NET.  Several proprietary examples of this design
> exist, and they are all quite successful.  
> 
> We need an open-source equivalent!

Well, openbabel tries to do that but could need more help from the
community maybe.  (It is C++ rather than C, though, but has binding for
python and other languages).


Michael

Shivesh,

Well, what would you think of the command 'dist'?
You could have read the manual...

Tsjerk

On 11/24/06, shivesh kumar <shi...@ya...> wrote:
> Dear all,
> Is there anyway to calculate the bond distances in pymol and to show the
> bond distances also...
> thanx in advance
> S
>
> shivesh
>
>  ________________________________
> Access over 1 million songs - Yahoo! Music Unlimited.
> -------------------------------------------------------------------------
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Dear all,
  Is there anyway to calculate the bond distances in pymol and to show the bond distances also...
  thanx in advance
  S


shivesh
 
---------------------------------
Access over 1 million songs - Yahoo! Music Unlimited.

Hi,
at this purpose, what kind of range (positive - negative) should be
used in order to visualize correctly the potential surface on a
protein? Normally I used -10 to +10 but I am wondering how you behaves
with this issue too.

Thanks in advance

andrea

2006/11/23, D. Eric Dollins <d.e...@gm...>:
> Florian,
> I had the same problem and I couldnt get everything to work internally
> in pymol. I never got pymol to write the *.pqr files. I couldn't
> figure it out. However, you can give your pdb to the PDB2PQR server:
> http://agave.wustl.edu/pdb2pqr/server.html
> Strip the waters/ligands and load in your pdb. Choose that you want to
> create an APBS input file. You get 2 files: *.pqr and *.in.  Rename
> without .txt extension (if the output has them. My mac put them on).
> You can load input pdb (the one with waters/ligands stripped).  Change
> the temp file locations (temp.pqr, *.pdb, and APBS input file). Don't
> change the "pymol generated dx".  Under main, choose "use another
> pqr".  Choose "externally generated" pqr and browse for your x.pqr.
> Click "set grid". Click "run APBS".  That will spit out a
> "pymol-generated.dx". In pymol type load_dx [file].dx. In APBS window,
> go to the visualization tab and choose "show mol. surface".  Change
> levels and update.
> Perhaps not the best way to get this to work, but it will give you a
> surface to look at. Good luck,
> Eric
>
>
>
> On 11/22/06, Florian Schmitzberger <Flo...@ki...> wrote:
> > Dear All,
> >
> > I am having a small problem using the apbs plugin in pymol on my pdb (I=
 am
> > using fink installed pymol and apbs versions on Mac OSX 10.4.8).
> >
> > When I try to run apbs I received the following message:
> >
> > "Unable to assign parameters for 100 atoms in the selection unassigned.
> > Please either remove these unassigned atoms and re-start ..."
> >
> > In principle, I think I understand the problem is that pdb2pqr cannot a=
ssign
> > charges to certain atoms, in my case posttranslationally modified cyste=
ine
> > residues.
> >
> > My question would be what the best way to fare with those atoms is. Sin=
ce
> > the modification introduces an acidic patch, if possible I would like t=
o
> > leave the atoms in (rather than remove them) when calculating surface c=
harge
> > representation, as this could be informative.
> >
> > So perhaps my question boils down to what the optimal way to manually a=
ssign
> > reasonable charges (in the pqr-file) for this oxidised cysteine (sulfin=
ic
> > acid; O-S=3DO) is.
> >
> > I also noticed that I get the same error message with residues where
> > side-chain atoms have been removed (such as surface lysines), while lea=
ving
> > the original residue name. But then I suppose there is no way around th=
is.
> >
> > Thank you very much in advance for any comments!
> >
> > Best regards,
> >
> > Florian
> >
> > --------------------------------------------
> > Florian Schmitzberger
> > Medical Biochemistry and Biophysics
> > Karolinska Institute
> > Scheeles vaeg 2
> > SE-171 77 Stockholm, Sweden
> > Tel: +46-8-524-86875
> >
> >
> >
> >
> > -----------------------------------------------------------------------=
--
> > 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=3Djoin.php&p=3Dsourceforge&CID=
=3DDEVDEV
> >
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> >
> >
>
>
> --
> D. Eric Dollins
> C266 LSRC, Box 3813
> Duke University Medical Center
> Durham, NC 27710
> (919)681-1668
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share y=
our
> opinions on IT & business topics through brief surveys - and earn cash
> http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D=
DEVDEV
> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


--=20
The last one to die please turn out the light=85(children of men)

Florian,
I had the same problem and I couldnt get everything to work internally
in pymol. I never got pymol to write the *.pqr files. I couldn't
figure it out. However, you can give your pdb to the PDB2PQR server:
http://agave.wustl.edu/pdb2pqr/server.html
Strip the waters/ligands and load in your pdb. Choose that you want to
create an APBS input file. You get 2 files: *.pqr and *.in.  Rename
without .txt extension (if the output has them. My mac put them on).
You can load input pdb (the one with waters/ligands stripped).  Change
the temp file locations (temp.pqr, *.pdb, and APBS input file). Don't
change the "pymol generated dx".  Under main, choose "use another
pqr".  Choose "externally generated" pqr and browse for your x.pqr.
Click "set grid". Click "run APBS".  That will spit out a
"pymol-generated.dx". In pymol type load_dx [file].dx. In APBS window,
go to the visualization tab and choose "show mol. surface".  Change
levels and update.
Perhaps not the best way to get this to work, but it will give you a
surface to look at. Good luck,
Eric



On 11/22/06, Florian Schmitzberger <Flo...@ki...> wrote:
> Dear All,
>
> I am having a small problem using the apbs plugin in pymol on my pdb (I am
> using fink installed pymol and apbs versions on Mac OSX 10.4.8).
>
> When I try to run apbs I received the following message:
>
> "Unable to assign parameters for 100 atoms in the selection unassigned.
> Please either remove these unassigned atoms and re-start ..."
>
> In principle, I think I understand the problem is that pdb2pqr cannot assign
> charges to certain atoms, in my case posttranslationally modified cysteine
> residues.
>
> My question would be what the best way to fare with those atoms is. Since
> the modification introduces an acidic patch, if possible I would like to
> leave the atoms in (rather than remove them) when calculating surface charge
> representation, as this could be informative.
>
> So perhaps my question boils down to what the optimal way to manually assign
> reasonable charges (in the pqr-file) for this oxidised cysteine (sulfinic
> acid; O-S=O) is.
>
> I also noticed that I get the same error message with residues where
> side-chain atoms have been removed (such as surface lysines), while leaving
> the original residue name. But then I suppose there is no way around this.
>
> Thank you very much in advance for any comments!
>
> Best regards,
>
> Florian
>
> --------------------------------------------
> Florian Schmitzberger
> Medical Biochemistry and Biophysics
> Karolinska Institute
> Scheeles vaeg 2
> SE-171 77 Stockholm, Sweden
> Tel: +46-8-524-86875
>
>
>
>
> -------------------------------------------------------------------------
> 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
>
>
>


-- 
D. Eric Dollins
C266 LSRC, Box 3813
Duke University Medical Center
Durham, NC 27710
(919)681-1668

Hi Nian,

I believe that happens becouse you are creating a new object with only th=
e loop
that you need to show and PyMol smothes it in a different fashion. Try cr=
eating
a new object containing the same selection you used originally, but 
that one loop, for exemple:

>load protein.pdb, prot
>hide everything, prot
>show cartoon, (prot and resi 120-140)

That should keep all residues in equivalent position.

All the best,

Mario Sanches

Citando Nian Huang <hua...@gm...>:

> Hi, all,
> I am trying to change the radius of one loop by making it as a new
> object. But every time I do that, because the smooth-loop setting is
> on, that loop just won't match its orignal position, i.e. connecting
> to other part of the cartoon. I certainly can set  the smooth-loop
> off, but it will make the figure ugly. Is there a better way to do
> that?
>
> Thanks.
>
> Nian
>
> -----------------------------------------------------------------------=
--
> 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=3Djoin.php&p=3Dsourceforge&CID=3D=
DEVDEV
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

Dear All,

I am having a small problem using the apbs plugin in pymol on my pdb  
(I am using fink installed pymol and apbs versions on Mac OSX 10.4.8).

When I try to run apbs I received the following message:

"Unable to assign parameters for 100 atoms in the selection  
unassigned. Please either remove these unassigned atoms and re- 
start ..."

In principle, I think I understand the problem is that pdb2pqr cannot  
assign charges to certain atoms, in my case posttranslationally  
modified cysteine residues.

My question would be what the best way to fare with those atoms is.  
Since the modification introduces an acidic patch, if possible I  
would like to leave the atoms in (rather than remove them) when  
calculating surface charge representation, as this could be informative.

So perhaps my question boils down to what the optimal way to manually  
assign reasonable charges (in the pqr-file) for this oxidised  
cysteine (sulfinic acid; O-S=O) is.

I also noticed that I get the same error message with residues where  
side-chain atoms have been removed (such as surface lysines), while  
leaving the original residue name. But then I suppose there is no way  
around this.

Thank you very much in advance for any comments!

Best regards,

Florian
--------------------------------------------
Florian Schmitzberger
Medical Biochemistry and Biophysics
Karolinska Institute
Scheeles vaeg 2
SE-171 77 Stockholm, Sweden
Tel: +46-8-524-86875

Hi, all,
I am trying to change the radius of one loop by making it as a new
object. But every time I do that, because the smooth-loop setting is
on, that loop just won't match its orignal position, i.e. connecting
to other part of the cartoon. I certainly can set  the smooth-loop
off, but it will make the figure ugly. Is there a better way to do
that?

Thanks.

Nian

Am Dienstag, 21. November 2006 15:58 schrieb Christian Seifert:
> $PYTHONPATH is not set on my machine.
>
>
>
> You wrote:
>
>       Re: segmentation fault after switching mainwindow between
> visualisation and commandline
>       From: Martin <martin.hoefling@gm...> - 2006-11-13 05:15
>
>        ... i had a similar Problem this morning. What is your PYTHONPATH?
> For me,
>        unsetting it solved the problems.

Pythonpath is still set. Found "the solution" just right now: Killing the 
x-server and restarting it solved the issue for me. No idea why it did.

Cheers.
	Martin

$PYTHONPATH is not set on my machine.



You wrote:

      Re: segmentation fault after switching mainwindow between visualisation 
and commandline
      From: Martin <martin.hoefling@gm...> - 2006-11-13 05:15

       ... i had a similar Problem this morning. What is your PYTHONPATH? For 
me, 
       unsetting it solved the problems.
       
       Cheers	
       	Martin
       


segmentation fault after switching mainwindow between visualisation and 
commandline
From: Christian Seifert <cseifert@bp...> - 2006-11-13 02:07

 Hi,
 
 I found a critical and reproducible bug using the 0.99rc6-binarys on my
 machine.
 
 Stepps:
 - starting pymol from a kde terminal with user-rights
 - loading a pdb-file (e.g. 1K5D from pdb-database)
 - rotate the molecule with the mouse in any direction
 - hitting "Esc" to get to the commandline-mode
 - hitting "Esc" again to get back to the visualisation-mode
 - trying to rotate the molecule again with the mouse
 
 The programm crashes, the two windows of pymol disappear and my
 terminal-window show the following error:
 
 >./pymol: line 14:  7110 Speicherzugriffsfehler  $PYMOL_PATH/pymol.exe "$@"
 
 "Speicherzugriffsfehler" is the german word for segmentation fault.
 
 There is nothing in dmseg.
 
 The full output:
 >cseifert@lexx ~/pymol $ ./pymol
 >
 > PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC.
 >
 > A current PyMOL Maintenance and/or Support Subscription may be required
 > for legal use of this Build beyond a finite honor-system evaluation period.
 > Please visit http://www.pymol.org/funding.html for more information.
 >
 > This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc6.
 > OpenGL graphics engine:
 >  GL_VENDOR: ATI Technologies Inc.
 >  GL_RENDERER: ATI MOBILITY FireGL V5200 Pentium 4 (SSE2) (FireGL) (GNU_ICD)
 >  GL_VERSION: 2.0.5946 (8.27.10)
 > Detected 2 CPUs.  Enabled multithreaded rendering.
 >HEADER    SIGNALING PROTEIN/SIGNALING ACTIVATOR   10-OCT-01   1K5D
 >TITLE     CRYSTAL STRUCTURE OF RAN-GPPNHP-RANBP1-RANGAP COMPLEX
 >COMPND    MOL_ID: 1;
 >COMPND   2 MOLECULE: GTP-BINDING NUCLEAR PROTEIN RAN;
 >COMPND   3 CHAIN: A, D, G, J;
 >COMPND   4 SYNONYM: RAN, TC4, RAN GTPASE, ANDROGEN RECEPTOR-
 >COMPND   5 ASSOCIATED PROTEIN 24;
 >COMPND   6 ENGINEERED: YES;
 >COMPND   7 MOL_ID: 2;
 >COMPND   8 MOLECULE: RAN-SPECIFIC GTPASE-ACTIVATING PROTEIN;
 >COMPND   9 CHAIN: B, E, H, K;
 >COMPND  10 SYNONYM: RANBP1, RAN BINDING PROTEIN 1;
 >COMPND  11 ENGINEERED: YES;
 >COMPND  12 MUTATION: YES;
 >COMPND  13 MOL_ID: 3;
 >COMPND  14 MOLECULE: RAN GTPASE ACTIVATING PROTEIN 1;
 >COMPND  15 CHAIN: C, F, I, L;
 >COMPND  16 SYNONYM: RANGAP, PROTEIN RNA1;
 >COMPND  17 ENGINEERED: YES
 > ObjectMolecule: Read secondary structure assignments.
 > ObjectMolecule: Read crystal symmetry information.
 > Symmetry: Found 1 symmetry operators.
 > CmdLoad: "/home/cseifert/Desktop/1K5D.pdb" loaded as "1K5D".
 >./pymol: line 14:  7110 Speicherzugriffsfehler  $PYMOL_PATH/pymol.exe "$@"
 
 Thanks,
 
 Christian Seifert.

My preference would be for something implemented in
Python/C. The project could start with a clean,
extensible (it should be easy to add new molecules)
and modular Python library and then start replacing
some functions with C equivalents. I would like a
library that doesn't use inheritance, or use it at
less as possible (it makes too difficult to read code)
which could only
contain descriptions of molecules and maybe perform
some basic operations (functions could be and are
implemented in other libraries) Even when the library
wolud be in Python, It should be easy to "plug" C
functions into it so we would not loose in
performance. It should also be as similar to chempy as
possible so pymol  could be easily ported to it.
I don't know how well chempy fits with the avobe
description, because, due of the lack of
documentation, I only use it in a very basic way.
Maybe It only needs minor changes and documentation to
become the standar in chemical objects for Python.

It sounds an interesting project. I would probably
join if something comes out

Cheers

Raúl 


>CDK is too Java-centric in my view, and I'll be the
>first to admit that
>Python is much too slow for cheminformatics.
>
>My preference would be for a fast, clean, back-end
>cheminformatics 
>library
>with a simple C API that could be exposed to and
>interporate with 
>Java, C, C++, SQL, and .NET.  Several proprietary
>examples of this 
>design
>exist, and they are all quite successful.  

>We need an open-source equivalent!

>Cheers,
>Warren
>DeLano Scientific LLC



__________________________________________________
Correo Yahoo!
Espacio para todos tus mensajes, antivirus y antispam ¡gratis! 
Regístrate ya - http://correo.espanol.yahoo.com/ 

CDK is too Java-centric in my view, and I'll be the first to admit that
Python is much too slow for cheminformatics.

My preference would be for a fast, clean, back-end cheminformatics =
library
with a simple C API that could be exposed to and interporate with =
Python,
Java, C, C++, SQL, and .NET.  Several proprietary examples of this =
design
exist, and they are all quite successful. =20

We need an open-source equivalent!

Cheers,
Warren
DeLano Scientific LLC

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf=20
> Of Jerome Pansanel
> Sent: Monday, November 20, 2006 9:08 AM
> To: pym...@li...
> Subject: Re: [PyMOL] chempy documentation
>=20
> Hi,
>=20
> Frowns is another Python-based chemical informatics library,=20
> but is no more maintained. A great idea would be to initiate=20
> such project. We could based the design on the CDK library=20
> (http://cdk.sourceforge.net/).
>=20
> Comments or suggestions ?
>=20
> Cheers,
>=20
> Jerome Pansanel
>=20
>=20
> Le lundi 20 novembre 2006 17:14, DeLano Scientific a =E9crit=A0:
> > Bgbg,
> >
> > The idea behind chempy was that it could eventually be=20
> developed into=20
> > a Python-based chemical informatics library.  In practice, however,=20
> > its capabilites and performace are quite limited and so it=20
> mainly just=20
> > exists for use by PyMOL.  No, there is no documentation for chempy=20
> > other than the code and its usage.
> >
> > Cheers,
> >
> > DeLano Scientific LLC
> > Email Support Services
> >
> > > -----Original Message-----
> > > From: pym...@li...
> > > [mailto:pym...@li...] On=20
> Behalf Of bgbg=20
> > > bg
> > > Sent: Monday, November 20, 2006 4:59 AM
> > > To: pym...@li...
> > > Subject: [PyMOL] chempy documentation
> > >
> > > Hello, all.
> > > Is there any chempy documentation available? I've=20
> searched the web=20
> > > for a while, but couldn't find anything relevant. Do PyMol=20
> > > subscribers have access to extra documentation?
> > >
> > > Thank you
> > >
> > > --------------------------------------------------------------
> > > -----------
> > > Take Surveys. Earn Cash. Influence the Future of IT Join=20
> > > SourceForge.net's Techsay panel and you'll get the chance=20
> to share=20
> > > your opinions on IT & business topics through brief surveys - and=20
> > > earn cash=20
> > > http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge
> > > &CID=3DDEVDEV
> > > _______________________________________________
> > > PyMOL-users mailing list
> > > PyM...@li...
> > > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> >=20
> ----------------------------------------------------------------------
> > --- Take Surveys. Earn Cash. Influence the Future of IT Join=20
> > SourceForge.net's Techsay panel and you'll get the chance to share=20
> > your opinions on IT & business topics through brief surveys=20
> - and earn=20
> > cash=20
> >=20
> =
http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D=
DEV
> > DEV _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
> --------------------------------------------------------------
> -----------
> Take Surveys. Earn Cash. Influence the Future of IT Join=20
> SourceForge.net's Techsay panel and you'll get the chance to=20
> share your opinions on IT & business topics through brief=20
> surveys - and earn cash=20
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&CID=3DDEVDEV
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>=20