RE: [PyMOL] alternative method for loading coordinates
Tina, If you're willing to switch into Python, there is an undocumented "read_pdbstr" function which can take a PDB file as a string variable. See modules/pymol/importing.py for the code. Temporary files are unnecessary. However, I'm not sure that I completely understand your question. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Tina Li > Sent: Tuesday, September 09, 2003 9:43 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] alternative method for loading coordinates > > Hello, > > Is there an alternative loading PDB coordinates, other than "load "? > Let's say after threading against a large database of protein templates, I > need one PyMOL script generated for each of the templates. I could as well > generate one PDB file for each to load, but it would be difficult to > manage > the few thousands of them. Is it possible to have the coordinates included > as > part of the PyMOL script and say, "load this like how you load a PDB" so > that > the later commands can work with whatever comes earlier in the file? > > Thanks, > > Tina > > > > > --- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Re: PyMOL-users digest, Vol 1 #408 - 11 msgs
Hi List! I'm glad to see others enjoying MDK 9.1. But pymol rpm for RH is a friend of MDK, I suggest you use pymol-0_90-bin-linux-libc6-i386.tgz It works terrifically for me. Dear Warren, realy great job! If possible, a proper pymol rpm for MDK 9.1 would be very welcome, since I believe there's many MDK users of pymol like me and Dan. Cheers, Alan Silvae On Tue, 9 Sep 2003, Warren L. DeLano wrote: > Dan, > > Opinions may vary, but I see RPMs are pretty heavily tied to the > distribution. The kind of errors you're seeing are to be expected when > trying to install cross-distribution. > > RPM doesn't look at the file system (AFAIK), it looks in the RPM > database for the names of (Redhat-specific) known dependency packages. > > You also need the Python megawidgets (pmw) -- there should be an > RPM for this... > > How many other PyMOL users are using Mandrake? Perhaps there > are enough users to justify at least one official mdk package release? > > Cheers, > Warren - This mail sent through IMP: http://horde.org/imp/
[PyMOL] alternative method for loading coordinates
Hello, Is there an alternative loading PDB coordinates, other than "load "? Let's say after threading against a large database of protein templates, I need one PyMOL script generated for each of the templates. I could as well generate one PDB file for each to load, but it would be difficult to manage the few thousands of them. Is it possible to have the coordinates included as part of the PyMOL script and say, "load this like how you load a PDB" so that the later commands can work with whatever comes earlier in the file? Thanks, Tina
RE: [PyMOL] pymol problems with Mandrake 9.1
Thanks for this Warren, but now I get a fresh set of error messages (still
no menus) with no obvious explanation along the lines of missing package
xxx.
Exception in thread Thread-1:
Traceback (most recent call last):
File "/usr/lib/python2.2/threading.py", line 408, in __bootstrap
self.run()
File "/usr/lib/python2.2/threading.py", line 396, in run
apply(self.__target, self.__args, self.__kwargs)
File
"/usr/lib/python2.2/site-packages/pymol/modules/pmg_tk/__init__.py", li
ne 33, in run
PMGApp(balloon_state='both').run()
File
"/usr/lib/python2.2/site-packages/pymol/modules/pmg_tk/AbstractApp.py",
line 53, in __init__
self.__createInterface()
File
"/usr/lib/python2.2/site-packages/pymol/modules/pmg_tk/AbstractApp.py",
line 256, in __createInterface
self.createInterface()
File "/usr/lib/python2.2/site-packages/pymol/modules/pmg_tk/PMGApp.py",
line
227, in createInterface
self.createButtons()
File "/usr/lib/python2.2/site-packages/pymol/modules/pmg_tk/PMGApp.py",
line
75, in createButtons
btn_reset = self.buttonAdd(row2,'Zoom',lambda: cmd.do("_ zoom"))
File "/usr/lib/python2.2/site-packages/pymol/modules/pmg_tk/PMGApp.py",
line
66, in buttonAdd
command=cmd,padx=0,pady=0)
File "/usr/lib/python2.2/site-packages/Pmw/Pmw_1_1/lib/PmwBase.py", line
455
, in createcomponent
raise ValueError, 'Component "%s" already exists' % componentName
ValueError: Component "button" already exists
Any ideas?
Thanks again
Daniel
+-+
| Dr Daniel John Rigden |
| CENARGEN/EMBRAPA | e-mail: dan...@cenargen.embrapa.br |
| Parque Estacao Biologica | http://www.cenargen.embrapa.br |
| PqEB - Final - Av. W3 Norte | Phone: +55 (61)448-4741|
| 70770-900, Brasilia-D.F.-BRAZIL | Fax:+55 (61)340-3658|
+-+
On Tue, 9 Sep 2003, Warren L. DeLano wrote:
> Dan,
>
> Opinions may vary, but I see RPMs are pretty heavily tied to the
> distribution. The kind of errors you're seeing are to be expected when
> trying to install cross-distribution.
>
> RPM doesn't look at the file system (AFAIK), it looks in the RPM
> database for the names of (Redhat-specific) known dependency packages.
>
> You also need the Python megawidgets (pmw) -- there should be an
> RPM for this...
>
> How many other PyMOL users are using Mandrake? Perhaps there
> are enough users to justify at least one official mdk package release?
>
> Cheers,
> Warren
>
>
> --
> mailto:war...@delanoscientific.com
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154
> Fax (650)-593-4020
>
> > -Original Message-
> > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> > ad...@lists.sourceforge.net] On Behalf Of Daniel John Rigden
> > Sent: Tuesday, September 09, 2003 12:49 AM
> > To: pymol-users@lists.sourceforge.net
> > Subject: [PyMOL] pymol problems with Mandrake 9.1
> >
> > Hi everyone
> >
> > Having previously used RedHat I've just put Mandrake 9.1 on my latest
> > machine (ease of installation, disk partitioning). To my surprise
> > (naively perhaps) the standard RH-derived RPMs on the pymol site lead
> to
> > chains of missing dependencies that I don't reach the bottom of.
> > Eventually I got pymol working kind-of with
> >
> > pymol-0.82-2mdk.i586.rpm
> >
> > preceded by
> >
> > python-numeric-22.0-2mdk.i586.rpm
> >
> > I dealt with some Tkinter error messages by installing the appropriate
> rpm
> > but now I have
> >
> > Traceback (most recent call last):
> > File
> "/usr/lib/python2.2/site-packages/pymol/modules/pymol/__init__.py",
> > lin
> > e 74, in exec_str
> > exec s in globals(),globals()
> > File "", line 1, in ?
> > File
> "/usr/lib/python2.2/site-packages/pymol/modules/pymol/__init__.py",
> > lin
> > e 129, in launch_gui
> > __import__(invocation.options.gui)
> > File
> > "/usr/lib/python2.2/site-packages/pymol/modules/pmg_tk/__init__.py",
> li
> > ne 22, in ?
> > from PMGApp import *
> > File
> "/usr/lib/python2.2/site-packages/pymol/modules/pmg_tk/PMGApp.py",
> > line
> > 18, in ?
> > from AbstractApp import AbstractApp
> > File
> >
> "/usr/lib/python2.2/site-packages/pymol/modules/pmg_tk/AbstractApp.py",
> > line 16, in ?
> > import Pmw
> > ImportError: No module named Pmw
> >
> > How to proceed?
> >
> > 2) More generally, am I doomed to use out-of-date versions of programs
> > (pymol and perhaps others), having made myself dependent on
> > Mandrake-specific rpms that won't keep up with new releases? The
> > dependency chains when trying to install RH rpms were quite tricky and
> > included some complaints about libraries that I could even see in /lib
> !
> > That completely flummoxed me.
> >
> > Thanks in advance
> >
> > Dan
RE: [PyMOL] pymol problems with Mandrake 9.1
Dan, Opinions may vary, but I see RPMs are pretty heavily tied to the distribution. The kind of errors you're seeing are to be expected when trying to install cross-distribution. RPM doesn't look at the file system (AFAIK), it looks in the RPM database for the names of (Redhat-specific) known dependency packages. You also need the Python megawidgets (pmw) -- there should be an RPM for this... How many other PyMOL users are using Mandrake? Perhaps there are enough users to justify at least one official mdk package release? Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Daniel John Rigden > Sent: Tuesday, September 09, 2003 12:49 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] pymol problems with Mandrake 9.1 > > Hi everyone > > Having previously used RedHat I've just put Mandrake 9.1 on my latest > machine (ease of installation, disk partitioning). To my surprise > (naively perhaps) the standard RH-derived RPMs on the pymol site lead to > chains of missing dependencies that I don't reach the bottom of. > Eventually I got pymol working kind-of with > > pymol-0.82-2mdk.i586.rpm > > preceded by > > python-numeric-22.0-2mdk.i586.rpm > > I dealt with some Tkinter error messages by installing the appropriate rpm > but now I have > > Traceback (most recent call last): > File "/usr/lib/python2.2/site-packages/pymol/modules/pymol/__init__.py", > lin > e 74, in exec_str > exec s in globals(),globals() > File "", line 1, in ? > File "/usr/lib/python2.2/site-packages/pymol/modules/pymol/__init__.py", > lin > e 129, in launch_gui > __import__(invocation.options.gui) > File > "/usr/lib/python2.2/site-packages/pymol/modules/pmg_tk/__init__.py", li > ne 22, in ? > from PMGApp import * > File "/usr/lib/python2.2/site-packages/pymol/modules/pmg_tk/PMGApp.py", > line > 18, in ? > from AbstractApp import AbstractApp > File > "/usr/lib/python2.2/site-packages/pymol/modules/pmg_tk/AbstractApp.py", > line 16, in ? > import Pmw > ImportError: No module named Pmw > > How to proceed? > > 2) More generally, am I doomed to use out-of-date versions of programs > (pymol and perhaps others), having made myself dependent on > Mandrake-specific rpms that won't keep up with new releases? The > dependency chains when trying to install RH rpms were quite tricky and > included some complaints about libraries that I could even see in /lib ! > That completely flummoxed me. > > Thanks in advance > > Daniel > > > > > +--- -- > + > | Dr Daniel John Rigden > | > | CENARGEN/EMBRAPA | e-mail: dan...@cenargen.embrapa.br > | > | Parque Estacao Biologica | http://www.cenargen.embrapa.br > | > | PqEB - Final - Av. W3 Norte | Phone: +55 (61)448-4741 > | > | 70770-900, Brasilia-D.F.-BRAZIL | Fax:+55 (61)340-3658 > | > +--- -- > + > > > > > > > --- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] incorporation of unusual amino acids
Uwe, > We plan a research project where we want to stepwise incorporate D-amino > acids into a peptide. To determine the exchanges it would be very useful > if > PyMol could assist. > If I might dream I would like to have D-amino acids (and maybe other un- > usual amino acids) available in the mutation-tool; You can flip residue 5 from L to D with the following two commands edit 5/ca invert 5/n, 5/c > some simple energy > minimization / bond relaxation; storing the resulting molecule in PDB- > format. Sculpting can relax VDW/bond/angle strain, but it is not energy minimization by any means. > Can I hope ? Is this something others find useful as well ? We'd all like to see a real forcefield in PyMOL, but no one has written the code yet. Cheers, Warren
RE: [PyMOL] individual surfaces?
Dirk, The trick for displaying "contact" surfaces in PyMOL is to create separate objects for each surface: create res431, resi 431 create res440, resi 440 show surface, res431 or res440 For CPK, you don't need to do this show spheres, resi 431+440 Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Dirk Kostrewa > Sent: Monday, September 08, 2003 11:15 PM > To: PyMOLBB > Subject: [PyMOL] individual surfaces? > > Dear PyMol users, > > I'm currently trying to display individual surfaces around different > selections of a molecule to show how they contact each other. However, > either > I get only the last surface displayed or a joined surface using the > command > examples below: > > this one gives only the surface of residue 440 > > show surface, ( resid 431 ) > flag ignore, ( not resid 431 ) > show surface, ( resid 440 ) > flag ignore, ( not resid 440 ) > rebuild > > whereas this one gives the joint surface of residues 431 and 440 > > show surface, ( resid 431 or resid 440 ) > flag ignore, ( not ( resid 431 or resid 440 ) ) > rebuild > > How can I display the individual surfaces separately? > > Alternatively, is there a command to display atoms in a CPK > representation? > > Best regards, > > Dirk. > > -- > > > Dirk Kostrewa > Paul Scherrer Institut > Life Sciences, OSRA/007 > CH-5232 Villigen PSI, Switzerland > E-mail: dirk.kostr...@psi.ch > Phone: +41-56-310-4722 > Fax: +41-56-310-4556 > WWW: http://www.sb.psi.ch > > > > > --- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] pymol problems with Mandrake 9.1
Hi everyone Having previously used RedHat I've just put Mandrake 9.1 on my latest machine (ease of installation, disk partitioning). To my surprise (naively perhaps) the standard RH-derived RPMs on the pymol site lead to chains of missing dependencies that I don't reach the bottom of. Eventually I got pymol working kind-of with pymol-0.82-2mdk.i586.rpm preceded by python-numeric-22.0-2mdk.i586.rpm I dealt with some Tkinter error messages by installing the appropriate rpm but now I have Traceback (most recent call last): File "/usr/lib/python2.2/site-packages/pymol/modules/pymol/__init__.py", lin e 74, in exec_str exec s in globals(),globals() File "", line 1, in ? File "/usr/lib/python2.2/site-packages/pymol/modules/pymol/__init__.py", lin e 129, in launch_gui __import__(invocation.options.gui) File "/usr/lib/python2.2/site-packages/pymol/modules/pmg_tk/__init__.py", li ne 22, in ? from PMGApp import * File "/usr/lib/python2.2/site-packages/pymol/modules/pmg_tk/PMGApp.py", line 18, in ? from AbstractApp import AbstractApp File "/usr/lib/python2.2/site-packages/pymol/modules/pmg_tk/AbstractApp.py", line 16, in ? import Pmw ImportError: No module named Pmw How to proceed? 2) More generally, am I doomed to use out-of-date versions of programs (pymol and perhaps others), having made myself dependent on Mandrake-specific rpms that won't keep up with new releases? The dependency chains when trying to install RH rpms were quite tricky and included some complaints about libraries that I could even see in /lib ! That completely flummoxed me. Thanks in advance Daniel +-+ | Dr Daniel John Rigden | | CENARGEN/EMBRAPA | e-mail: dan...@cenargen.embrapa.br | | Parque Estacao Biologica | http://www.cenargen.embrapa.br | | PqEB - Final - Av. W3 Norte | Phone: +55 (61)448-4741| | 70770-900, Brasilia-D.F.-BRAZIL | Fax:+55 (61)340-3658| +-+
[PyMOL] incorporation of unusual amino acids
We plan a research project where we want to stepwise incorporate D-amino acids into a peptide. To determine the exchanges it would be very useful if PyMol could assist. If I might dream I would like to have D-amino acids (and maybe other un- usual amino acids) available in the mutation-tool; some simple energy minimization / bond relaxation; storing the resulting molecule in PDB- format. Can I hope ? Is this something others find useful as well ? Best regards Uwe Hobohm
Re: [PyMOL] individual surfaces?
Am Dienstag, 9. September 2003 09:14 schrieb Dirk Kostrewa: > Dear PyMol users, > > I'm currently trying to display individual surfaces around different > selections of a molecule to show how they contact each other. The trick is to define the selections as individual objects: create obj1, (resi 431) create obj2, (resi 440) show surface, obj1 show surface, obj2 results in two separate surface objects. Regards, Kristian Rother > However, > either I get only the last surface displayed or a joined surface using the > command examples below: > > this one gives only the surface of residue 440 > > show surface, ( resid 431 ) > flag ignore, ( not resid 431 ) > show surface, ( resid 440 ) > flag ignore, ( not resid 440 ) > rebuild > > whereas this one gives the joint surface of residues 431 and 440 > > show surface, ( resid 431 or resid 440 ) > flag ignore, ( not ( resid 431 or resid 440 ) ) > rebuild > > How can I display the individual surfaces separately? > > Alternatively, is there a command to display atoms in a CPK representation? > > Best regards, > > Dirk. ---
Re: [PyMOL] individual surfaces?
Hi Dirk, The best way to go there is to create two objects. One of one part of the protein and one of the other, and show the surfaces of each of them. Good luck, Tsjerk Dirk Kostrewa wrote: Dear PyMol users, I'm currently trying to display individual surfaces around different selections of a molecule to show how they contact each other. However, either I get only the last surface displayed or a joined surface using the command examples below: this one gives only the surface of residue 440 show surface, ( resid 431 ) flag ignore, ( not resid 431 ) show surface, ( resid 440 ) flag ignore, ( not resid 440 ) rebuild whereas this one gives the joint surface of residues 431 and 440 show surface, ( resid 431 or resid 440 ) flag ignore, ( not ( resid 431 or resid 440 ) ) rebuild How can I display the individual surfaces separately? Alternatively, is there a command to display atoms in a CPK representation? Best regards, Dirk. -- ~ -- :) -- :) Tsjerk A. Wassenaar, M.Sc. -- :) Molecular Dynamics Group -- :) Dept. of Biophysical Chemistry -- :) University of Groningen -- :) Nijenborgh 4 -- :) 9747 AG Groningen -- :) The Netherlands -- :) ~ -- :) -- :) Hi! I'm a .signature virus! -- :) Copy me into your ~/.signature to help me spread! -- :) ~
[PyMOL] individual surfaces?
Dear PyMol users, I'm currently trying to display individual surfaces around different selections of a molecule to show how they contact each other. However, either I get only the last surface displayed or a joined surface using the command examples below: this one gives only the surface of residue 440 show surface, ( resid 431 ) flag ignore, ( not resid 431 ) show surface, ( resid 440 ) flag ignore, ( not resid 440 ) rebuild whereas this one gives the joint surface of residues 431 and 440 show surface, ( resid 431 or resid 440 ) flag ignore, ( not ( resid 431 or resid 440 ) ) rebuild How can I display the individual surfaces separately? Alternatively, is there a command to display atoms in a CPK representation? Best regards, Dirk. -- Dirk Kostrewa Paul Scherrer Institut Life Sciences, OSRA/007 CH-5232 Villigen PSI, Switzerland E-mail: dirk.kostr...@psi.ch Phone: +41-56-310-4722 Fax: +41-56-310-4556 WWW: http://www.sb.psi.ch
