pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] mutations

[Noinaj <no...@uk...>]

Orla,

This is simply, for the most part.  Here is what I do. =20

Load your *.pdb file.  Then under WIZARD in the menu bar, select =
MUTAGENESIS.  Then pretty much, follow directions.  In the PyMOL VIEWER =
window, it will ask you to ' pick a residue.'  Once you pick a residue, =
select the type of residue you want to mutate to by left clicking on [No =
Mutation] button and holding down (under Mutagenesis).  This brings up a =
list of residues that you can then select from.  Once you select the =
residue you want, hit APPLY, then DONE.  If everything was done =
correctly, you should see your mutated residue. =20

There are probably other ways to do this, but I hope this helps.  If you =
would like screenshots of the steps, just let me know. =20



Cheers,
Nick


  ----- Original Message -----=20
  From: Orla O'Sullivan=20
  To: pym...@li...=20
  Sent: Tuesday, April 18, 2006 11:31 AM
  Subject: [PyMOL] mutations


  Hi all

  I'm a newbie to Pymol and so far have been very impressed. However I =
have tried to mutate some residues in my structure and have hit a brick =
wall.

  Has anyone done this with pymol and let me know how to do it?

  =20

  Regards=20

  =20

  Orla=20

  =20

  Dr.Orla O'Sullivan

  Research Officer

  Biotechnology

  =20

  =20

  Moorepark Food Research Centre
  Teagasc

  Moorepark
  Fermoy, Co. Cork
  Ireland

  =20

  Tel:       +353 - (0)25 - 42344

  =20

[PyMOL] (small) Pymol feature request--filter for edit settings window

[Michelle G. <mic...@ya...>]

While we're discussing ways to make our favorite program a little 
better, I had an idea I thought I'd throw out there...

While making some figures the other day, I found myself scrolling 
endlessly through the edit settings menu (under Setting --> Edit All) a 
number of times, mostly to locate a relatively small number of settings 
related to ray tracing. This got me thinking about a way to improve 
access to the many wonderful features that have been added to PyMOL.

The solution I came up with is a filter line which could be placed 
directly above the window listing all the settings. Users could then 
type a word, say "ray" or "cartoon", and only the settings containing 
this word would be shown.

The best example of a program containing this feature is the 
"about:config" window in Firefox. When you open a browser and type 
"about:config" instead of an address, a window containing hundreds of 
settings appears. At the top is a filter bar which you can use to pare 
down the number of settings listed below.

I think this would be a great addition to PyMOL and would help users 
familiarize themselves with the many new settings which have been (and 
will be) implemented. :)

Perhaps others have even better solutions to this problem. The use of a 
filter is just the first idea which came to my mind. I think it would be 
relatively easy to implement, although my python programming skills are 
somewhat limited.

Thanks,
Michelle Gill

[PyMOL] mutations

[Orla O'S. <Orl...@te...>]

Hi all

I'm a newbie to Pymol and so far have been very impressed. However I
have tried to mutate some residues in my structure and have hit a brick
wall.

Has anyone done this with pymol and let me know how to do it?

=20

Regards=20

=20

Orla=20

=20

Dr.Orla O'Sullivan

Research Officer

Biotechnology

=20

=20

Moorepark Food Research Centre
Teagasc

Moorepark
Fermoy, Co. Cork
Ireland

=20

Tel:       +353 - (0)25 - 42344

=20

Re: [PyMOL] another question about ca trace model.

[Noinaj <no...@uk...>]

Tiger,

Unfortunately I don't have much experience with this procedure.  But one 
thing came to mind, you can manually assign secondary structure within 
DEEPVIEW/SWISS PDB Viewer [EDIT].  Not sure how many pdb files you have 
generated for the morph, but if nothing else works, you could try manually 
assigning secondary structures and see how that works out.  Yep, a huge pain 
in the buttocks I know, but it should work, in theory.

Best of Luck.


Cheers,
Nick



----- Original Message ----- 
From: "Geng Tian" <gen...@ho...>
To: <pym...@li...>
Sent: Tuesday, April 18, 2006 6:24 AM
Subject: [PyMOL] another question about ca trace model.


> Hi, there:
> I am trying to make a movie following the intruction at 
> http://ginsberg.med.virginia.edu/~dcoop/Help/morph.html
> From Lsqman, I got a serial of PDB files morphing between two 
> conformations. These PDB files contain only alpha carbon and non-hydrogen 
> side-chain atoms. Then I used DSSP to include the secondary structure 
> information ito the PDB files. In the pymol, after set cartoon_trace, 1 
> the helix and loop showed up nicely. But all the strands are missing. I 
> tried several setting about cartoon but just can't get them out. Do you 
> have any idea how to solve this problem.
> Thank you.
> Tiger
>
> _________________________________________________________________
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>
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[PyMOL] another question about ca trace model.

[Geng T. <gen...@ho...>]

Hi, there:
I am trying to make a movie following the intruction at 
http://ginsberg.med.virginia.edu/~dcoop/Help/morph.html
From Lsqman, I got a serial of PDB files morphing between two conformations. 
These PDB files contain only alpha carbon and non-hydrogen side-chain atoms. 
Then I used DSSP to include the secondary structure information ito the PDB 
files. In the pymol, after set cartoon_trace, 1 the helix and loop showed up 
nicely. But all the strands are missing. I tried several setting about 
cartoon but just can't get them out. Do you have any idea how to solve this 
problem.
Thank you.
Tiger

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Re: [PyMOL] Default directory and browsing

[Peter A. M. <pa...@co...>]

There are two ways to do this.  Either start pymol from the command line
in your working directory, or use .pymolrc to automatically change to this
directory (something like os.chdir('~/working_directory') should do it).

Pete

> Would it be possible to add setting to pymol for a default working
directory?
> Along with this, perhaps a setting that, by default, ignores hidden
directories?  As it now stands, whenever I fire up pymol on linux, I
have
> to
> navigate down a huge list of hidden directories to find the directory, then
> the subdirectory, within which my pdbs and pses reside.  Pymol doesn't
remember this so every time I start it, it is the same thing all over
again.
>


Pete Meyer
Fu Lab
BMCB grad student
Cornell University

[PyMOL] Default directory and browsing

[Praedor A. <pr...@ya...>]

Would it be possible to add setting to pymol for a default working director=
y? =20
Along with this, perhaps a setting that, by default, ignores hidden=20
directories?  As it now stands, whenever I fire up pymol on linux, I have t=
o=20
navigate down a huge list of hidden directories to find the directory, then=
=20
the subdirectory, within which my pdbs and pses reside.  Pymol doesn't=20
remember this so every time I start it, it is the same thing all over again.

It would help immensely if pymol did not display hidden dot directories and=
=20
had a default working directory so it starts up ready to go right away.

praedor
=2D-=20
The Reichstag fire is to Hitler as 9/11 is to Bush

RE: [PyMOL] saving files in pymol

[Thomas S. <ts...@ex...>]

Along these lines, PyMOL also allows one to quit the program without
prompting that you may have unsaved work (i.e., the session has changed
since the last time a .pse file was written).  Is this also easily
implemented?=20

-Tom


-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Warren
DeLano
Sent: Saturday, April 15, 2006 11:08 AM
To: Paulo Martel
Cc: pym...@li...
Subject: RE: [PyMOL] saving files in pymol

Paulo,

Thank you for the simple and helpful suggestion -- this is exactly the
kind of input that can enable us to improve the software with a trivial
amount of effort on everyone's part.

PyMOL will now issue a warning if you save a PDB file using an extension
it does not recognize. =20

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...
> [mailto:pym...@li...] On Behalf Of Paulo=20
> Martel
> Sent: Friday, April 14, 2006 6:45 PM
> Cc: pym...@li...
> Subject: [PyMOL] saving files in pymol
>=20
>=20
> Hello,
>=20
> one thing I find a little bit annoying: the "save" command in Pymol=20
> will accept any of <file>.<ext>, and if the <ext> is unknown, it will=20
> simple save a pdb file. While some people may find this a useful=20
> feature, I think it is quite dangerous. For instance, suppose I'm=20
> trying to save "work.pse" and mistakenly type "work.psf", without=20
> noticing it. If I close Pymol, I will end up with a pdb file called=20
> "work.psf", and all my session work goes down the drain. This is not=20
> an hypothetical situation, it happened a couple of times, to my great=20
> dismay. What do you think, Warren ?...
>=20
> Regards,
> Paulo
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting=20
> language that extends applications into web and mobile media. Attend=20
> the live webcast and join the prime developer group breaking into this

> new coding territory!
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dat=3D121642
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>=20
>=20
>=20
>=20


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Re: [PyMOL] changing individual sphere sizes

[Tsjerk W. <ts...@gm...>]

Hi Laura,

You can change the van der Waals radii of atoms using

alter selection, vdw=3Dnewradius

Alternatively, you can use the setting sphere_scale (set
sphere_scale,factor), which changes all radii by the given factor. Note tha=
t
you need to create different objects to use different factors for
sphere_scale.

Cheers,

Tsjerk

On 4/14/06, Laura Dutca <du...@ia...> wrote:
>
> Hello,
> I need to have  spheres or dots of different sizes on a RNA ribbon. We ar=
e
> trying to show that residues modify at a smaller or larger extent. So, I
> need to
> have at different places differently sized spheres.
> Hopefully I was explicetly enough.
> Thank you,
> Laura
>
>
> Laura Dutca
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> -------------------------------------------------------
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> language
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> webcast
> and join the prime developer group breaking into this new coding
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=3D121642
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>



--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

RE: [PyMOL] saving files in pymol

[Warren D. <wa...@de...>]

Paulo,

Thank you for the simple and helpful suggestion -- this is exactly the =
kind of input that can enable us to improve the software with a trivial =
amount of effort on everyone's part.

PyMOL will now issue a warning if you save a PDB file using an extension =
it does not recognize. =20

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Paulo Martel
> Sent: Friday, April 14, 2006 6:45 PM
> Cc: pym...@li...
> Subject: [PyMOL] saving files in pymol
>=20
>=20
> Hello,
>=20
> one thing I find a little bit annoying: the "save" command in=20
> Pymol will accept any of <file>.<ext>, and if the <ext> is=20
> unknown, it will simple save a pdb file. While some people=20
> may find this a useful feature, I think it is quite=20
> dangerous. For instance, suppose I'm trying to save=20
> "work.pse" and mistakenly type "work.psf", without noticing=20
> it. If I close Pymol, I will end up with a pdb file called=20
> "work.psf", and all my session work goes down the drain. This=20
> is not an hypothetical situation, it happened a couple of=20
> times, to my great dismay. What do you think, Warren ?...
>=20
> Regards,
> Paulo
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking=20
> scripting language that extends applications into web and=20
> mobile media. Attend the live webcast and join the prime=20
> developer group breaking into this new coding territory!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&
dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

RE: [PyMOL] saving files in pymol

[Geng T. <gen...@ho...>]

Sorry, wrong thread.
This should be my answer to laura's question about different sphere size.
Too excited to be of a little help here.
Tiger










>From: "Geng Tian" <gen...@ho...>
>To: pm...@ua...
>CC: pym...@li...
>Subject: RE: [PyMOL] saving files in pymol
>Date: Sat, 15 Apr 2006 05:08:57 +0000
>
>Hi, Paulo:
>I hope these entries from my old pml file might help you:
>
>select c11, resi 11 and chain c
>show sphere, c11
>alter c11, vdw=vdw*0.2
>
>select c124, resi 124 and chain c
>show sphere, c124
>alter c124, vdw=vdw*2
>
>Tiger
>
>
>
>
>
>
>
>>From: Paulo Martel <pm...@ua...>
>>CC: pym...@li...
>>Subject: [PyMOL] saving files in pymol
>>Date: Sat, 15 Apr 2006 02:40:39 +0100
>>
>>
>>Hello,
>>
>>one thing I find a little bit annoying: the "save" command in Pymol will 
>>accept any of <file>.<ext>, and if the <ext> is unknown,
>>it will simple save a pdb file. While some people may find this a useful 
>>feature, I think it is quite dangerous. For instance, suppose
>>I'm trying to save "work.pse" and mistakenly type "work.psf", without 
>>noticing it. If I close Pymol, I will end up with a pdb file
>>called "work.psf", and all my session work goes down the drain. This is 
>>not an hypothetical situation, it happened a couple of times, to
>>my great dismay. What do you think, Warren ?...
>>
>>Regards,
>>Paulo
>>
>>
>>
>>-------------------------------------------------------
>>This SF.Net email is sponsored by xPML, a groundbreaking scripting 
>>language
>>that extends applications into web and mobile media. Attend the live 
>>webcast
>>and join the prime developer group breaking into this new coding 
>>territory!
>>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642
>>_______________________________________________
>>PyMOL-users mailing list
>>PyM...@li...
>>https://lists.sourceforge.net/lists/listinfo/pymol-users
>
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>
>-------------------------------------------------------
>This SF.Net email is sponsored by xPML, a groundbreaking scripting language
>that extends applications into web and mobile media. Attend the live 
>webcast
>and join the prime developer group breaking into this new coding territory!
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RE: [PyMOL] saving files in pymol

[Geng T. <gen...@ho...>]

Hi, Paulo:
I hope these entries from my old pml file might help you:

select c11, resi 11 and chain c
show sphere, c11
alter c11, vdw=vdw*0.2

select c124, resi 124 and chain c
show sphere, c124
alter c124, vdw=vdw*2

Tiger







>From: Paulo Martel <pm...@ua...>
>CC: pym...@li...
>Subject: [PyMOL] saving files in pymol
>Date: Sat, 15 Apr 2006 02:40:39 +0100
>
>
>Hello,
>
>one thing I find a little bit annoying: the "save" command in Pymol will 
>accept any of <file>.<ext>, and if the <ext> is unknown,
>it will simple save a pdb file. While some people may find this a useful 
>feature, I think it is quite dangerous. For instance, suppose
>I'm trying to save "work.pse" and mistakenly type "work.psf", without 
>noticing it. If I close Pymol, I will end up with a pdb file
>called "work.psf", and all my session work goes down the drain. This is not 
>an hypothetical situation, it happened a couple of times, to
>my great dismay. What do you think, Warren ?...
>
>Regards,
>Paulo
>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by xPML, a groundbreaking scripting language
>that extends applications into web and mobile media. Attend the live 
>webcast
>and join the prime developer group breaking into this new coding territory!
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>_______________________________________________
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Re: [PyMOL] question about ca trace

[Geng T. <gen...@ho...>]

Hi, there:
The problem was temporarily solved by putting each monomer in a separated 
file and load into pymol. Hiding the two residues doesn't work. The weird 
linkage will just jump to the next residues.
Thank you all.
Tiger









>From: "Noinaj" <no...@uk...>
>To: "Tsjerk Wassenaar" 
><ts...@gm...>,<pym...@li...>
>Subject: Re: [PyMOL] question about ca trace
>Date: Fri, 14 Apr 2006 11:23:52 -0400
>
>Tsjerk,
>
>Nice point, and probably easier to just create new objects in Pymol.
>
>
>
>nick
>
>
>   ----- Original Message -----
>   From: Tsjerk Wassenaar
>   To: pym...@li...
>   Sent: Friday, April 14, 2006 4:29 AM
>   Subject: Re: [PyMOL] question about ca trace
>
>
>   Hi Tiger,
>
>   Nick is largely right. The cause for the link to show up is that pymol 
>just traces through all c-alphas in the object, regardless of chains or 
>distances. So, selecting the linked residues and hiding the trace should 
>solve your problem. Also, creating two files will do the trick. 
>Alternatively, you can create two objects and draw the trace for each of 
>these.
>
>   Cheers,
>
>   Tsjerk
>
>
>   On 4/13/06, Noinaj <no...@uk...> wrote:
>     Tiger,
>
>     I am no expert by far, but can you select the linkage?  If so, just 
>select
>     and hide.  Also, you might try just hiding the two residues that are 
>linked,
>     this might get rid of the link and you probably wouldn't notice the 
>missing
>     residues unless it is a small protein.  alternatively, and probably 
>the best
>     solution is to edit the pdb file to create two individual files, one 
>for
>     each dimer (this can be done in any text editor).  then open both in 
>Pymol
>     and you should then be able to edit independently.
>
>     The problem may be, and again I remind you that I am no expert, that 
>these
>     atoms are two close to each other and may be getting mistaken for a 
>covalent
>     interaction, can't tell without actually seeing though.
>
>     Hope any or all of this helps.  Good Luck!
>
>
>
>     Cheers,
>     Nick
>
>
>
>
>
>
>     ----- Original Message -----
>     From: "Geng Tian" <gen...@ho... >
>     To: <pym...@li...>
>     Sent: Thursday, April 13, 2006 3:19 PM
>     Subject: [PyMOL] question about ca trace
>
>
>     > Hi, There:
>     > I have a pdb file for a dimer. only coordinates of alph carbons are 
>in the
>     > pdb. In the pymol, I
>     > set cartoon_trace, 1
>     > and
>     > show cartoon
>     > each monomer is fine but a weird linkage showed up between the last
>     > residue of chain a and first residue of chain b. I just can't remove 
>this
>     > ugly linkage. Do you have any idea? Thank you. Actually I tried 
>ribbon
>     > mode and no this weird linkage but I like the figure qualify of the
>     > cartoon.
>     > Tiger
>     >
>     > _________________________________________________________________
>     > Express yourself instantly with MSN Messenger! Download today - it's 
>FREE!
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>     >
>     >
>     > -------------------------------------------------------
>     > This SF.Net email is sponsored by xPML, a groundbreaking scripting
>     > language
>     > that extends applications into web and mobile media. Attend the live
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>     > 
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>     >
>
>
>
>     -------------------------------------------------------
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>language
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>
>
>
>
>   --
>
>   Tsjerk A. Wassenaar, M.Sc.
>   Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
>   Dept. of Biophysical Chemistry
>   University of Groningen
>   Nijenborgh 4
>   9747AG Groningen, The Netherlands
>   +31 50 363 4336

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[PyMOL] saving files in pymol

[Paulo M. <pm...@ua...>]

Hello,

one thing I find a little bit annoying: the "save" command in Pymol will 
accept any of <file>.<ext>, and if the <ext> is unknown,
it will simple save a pdb file. While some people may find this a useful 
feature, I think it is quite dangerous. For instance, suppose
I'm trying to save "work.pse" and mistakenly type "work.psf", without 
noticing it. If I close Pymol, I will end up with a pdb file
called "work.psf", and all my session work goes down the drain. This is 
not an hypothetical situation, it happened a couple of times, to
my great dismay. What do you think, Warren ?...

Regards,
Paulo

[PyMOL] changing individual sphere sizes

[L. D. <du...@ia...>]

Hello, 
I need to have  spheres or dots of different sizes on a RNA ribbon. We are
trying to show that residues modify at a smaller or larger extent. So, I need to
have at different places differently sized spheres. 
Hopefully I was explicetly enough. 
Thank you, 
Laura
 

Laura Dutca

Re: [PyMOL] question about ca trace

[Noinaj <no...@uk...>]

Tsjerk,

Nice point, and probably easier to just create new objects in Pymol. =20



nick


  ----- Original Message -----=20
  From: Tsjerk Wassenaar=20
  To: pym...@li...=20
  Sent: Friday, April 14, 2006 4:29 AM
  Subject: Re: [PyMOL] question about ca trace


  Hi Tiger,

  Nick is largely right. The cause for the link to show up is that pymol =
just traces through all c-alphas in the object, regardless of chains or =
distances. So, selecting the linked residues and hiding the trace should =
solve your problem. Also, creating two files will do the trick. =
Alternatively, you can create two objects and draw the trace for each of =
these.

  Cheers,

  Tsjerk


  On 4/13/06, Noinaj <no...@uk...> wrote:
    Tiger,

    I am no expert by far, but can you select the linkage?  If so, just =
select
    and hide.  Also, you might try just hiding the two residues that are =
linked,
    this might get rid of the link and you probably wouldn't notice the =
missing=20
    residues unless it is a small protein.  alternatively, and probably =
the best
    solution is to edit the pdb file to create two individual files, one =
for
    each dimer (this can be done in any text editor).  then open both in =
Pymol=20
    and you should then be able to edit independently.

    The problem may be, and again I remind you that I am no expert, that =
these
    atoms are two close to each other and may be getting mistaken for a =
covalent
    interaction, can't tell without actually seeing though.=20

    Hope any or all of this helps.  Good Luck!



    Cheers,
    Nick






    ----- Original Message -----
    From: "Geng Tian" <gen...@ho... >
    To: <pym...@li...>
    Sent: Thursday, April 13, 2006 3:19 PM
    Subject: [PyMOL] question about ca trace


    > Hi, There:=20
    > I have a pdb file for a dimer. only coordinates of alph carbons =
are in the
    > pdb. In the pymol, I
    > set cartoon_trace, 1
    > and
    > show cartoon
    > each monomer is fine but a weird linkage showed up between the =
last=20
    > residue of chain a and first residue of chain b. I just can't =
remove this
    > ugly linkage. Do you have any idea? Thank you. Actually I tried =
ribbon
    > mode and no this weird linkage but I like the figure qualify of =
the=20
    > cartoon.
    > Tiger
    >
    > _________________________________________________________________
    > Express yourself instantly with MSN Messenger! Download today - =
it's FREE!
    > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
    >
    >
    >
    > -------------------------------------------------------
    > This SF.Net email is sponsored by xPML, a groundbreaking scripting =

    > language
    > that extends applications into web and mobile media. Attend the =
live
    > webcast
    > and join the prime developer group breaking into this new coding
    > territory!
    > =
http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&dat=3D=
121642
    > _______________________________________________
    > PyMOL-users mailing list
    > PyM...@li...
    > https://lists.sourceforge.net/lists/listinfo/pymol-users
    >



    -------------------------------------------------------=20
    This SF.Net email is sponsored by xPML, a groundbreaking scripting =
language
    that extends applications into web and mobile media. Attend the live =
webcast
    and join the prime developer group breaking into this new coding =
territory!=20
    =
http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&dat=3D=
121642
    _______________________________________________=20
    PyMOL-users mailing list
    PyM...@li...
    https://lists.sourceforge.net/lists/listinfo/pymol-users=20




  --=20

  Tsjerk A. Wassenaar, M.Sc.
  Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
  Dept. of Biophysical Chemistry
  University of Groningen
  Nijenborgh 4
  9747AG Groningen, The Netherlands
  +31 50 363 4336

RE: [PyMOL] question about ca trace

[Warren D. <wa...@de...>]

FYI: all. =20

This is a bug that has been fixed in the source and will not occur with =
future releases.

Cheers,
Warren


--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Tsjerk Wassenaar
> Sent: Friday, April 14, 2006 5:04 AM
> To: pym...@li...
> Subject: Re: [PyMOL] question about ca trace
>=20
> Hi Tiger,
>=20
> Nick is largely right. The cause for the link to show up is=20
> that pymol just traces through all c-alphas in the object,=20
> regardless of chains or distances. So, selecting the linked=20
> residues and hiding the trace should solve your problem.=20
> Also, creating two files will do the trick. Alternatively,=20
> you can create two objects and draw the trace for each of these.
>=20
> Cheers,
>=20
> Tsjerk
>=20
>=20
> On 4/13/06, Noinaj <no...@uk...> wrote:
>=20
> 	Tiger,
> =09
> 	I am no expert by far, but can you select the linkage? =20
> If so, just select
> 	and hide.  Also, you might try just hiding the two=20
> residues that are linked,
> 	this might get rid of the link and you probably=20
> wouldn't notice the missing=20
> 	residues unless it is a small protein.  alternatively,=20
> and probably the best
> 	solution is to edit the pdb file to create two=20
> individual files, one for
> 	each dimer (this can be done in any text editor).  then=20
> open both in Pymol=20
> 	and you should then be able to edit independently.
> =09
> 	The problem may be, and again I remind you that I am no=20
> expert, that these
> 	atoms are two close to each other and may be getting=20
> mistaken for a covalent
> 	interaction, can't tell without actually seeing though.=20
> =09
> 	Hope any or all of this helps.  Good Luck!
> =09
> =09
> =09
> 	Cheers,
> 	Nick
> =09
> =09
> =09
> =09
> =09
> =09
> 	----- Original Message -----
> 	From: "Geng Tian" <gen...@ho... >
> 	To: <pym...@li...>
> 	Sent: Thursday, April 13, 2006 3:19 PM
> 	Subject: [PyMOL] question about ca trace
> =09
> =09
> 	> Hi, There:=20
> 	> I have a pdb file for a dimer. only coordinates of=20
> alph carbons are in the
> 	> pdb. In the pymol, I
> 	> set cartoon_trace, 1
> 	> and
> 	> show cartoon
> 	> each monomer is fine but a weird linkage showed up=20
> between the last=20
> 	> residue of chain a and first residue of chain b. I=20
> just can't remove this
> 	> ugly linkage. Do you have any idea? Thank you.=20
> Actually I tried ribbon
> 	> mode and no this weird linkage but I like the figure=20
> qualify of the=20
> 	> cartoon.
> 	> Tiger
> 	>
> 	>=20
> _________________________________________________________________
> 	> Express yourself instantly with MSN Messenger!=20
> Download today - it's FREE!
> 	>=20
> http://messenger.msn.click-url.com/go/onm00200471ave/direct/01
> / <http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/>=20
> 	>
> 	>
> 	>
> 	> -------------------------------------------------------
> 	> This SF.Net email is sponsored by xPML, a=20
> groundbreaking scripting=20
> 	> language
> 	> that extends applications into web and mobile media.=20
> Attend the live
> 	> webcast
> 	> and join the prime developer group breaking into this=20
> new coding
> 	> territory!
> 	>=20
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&
dat=3D121642 <http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944> =
&bid=3D241720&dat=3D121642>=20
> 	> _______________________________________________
> 	> PyMOL-users mailing list
> 	> PyM...@li...=20
> <mailto:PyM...@li...>=20
> 	> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 	>
> =09
> =09
> =09
> 	-------------------------------------------------------=20
> 	This SF.Net email is sponsored by xPML, a=20
> groundbreaking scripting language
> 	that extends applications into web and mobile media.=20
> Attend the live webcast
> 	and join the prime developer group breaking into this=20
> new coding territory!=20
> =09
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&
dat=3D121642
> 	_______________________________________________=20
> 	PyMOL-users mailing list
> 	PyM...@li...
> 	https://lists.sourceforge.net/lists/listinfo/pymol-users=20
> =09
>=20
>=20
>=20
>=20
> --=20
>=20
> Tsjerk A. Wassenaar, M.Sc.
> Groningen Biomolecular Sciences and Biotechnology Institute=20
> (GBB) Dept. of Biophysical Chemistry University of Groningen=20
> Nijenborgh 4 9747AG Groningen, The Netherlands
> +31 50 363 4336
>=20
>=20

Re: [PyMOL] question about ca trace

[Tsjerk W. <ts...@gm...>]

Hi Tiger,

Nick is largely right. The cause for the link to show up is that pymol just
traces through all c-alphas in the object, regardless of chains or
distances. So, selecting the linked residues and hiding the trace should
solve your problem. Also, creating two files will do the trick.
Alternatively, you can create two objects and draw the trace for each of
these.

Cheers,

Tsjerk

On 4/13/06, Noinaj <no...@uk...> wrote:
>
> Tiger,
>
> I am no expert by far, but can you select the linkage?  If so, just selec=
t
> and hide.  Also, you might try just hiding the two residues that are
> linked,
> this might get rid of the link and you probably wouldn't notice the
> missing
> residues unless it is a small protein.  alternatively, and probably the
> best
> solution is to edit the pdb file to create two individual files, one for
> each dimer (this can be done in any text editor).  then open both in Pymo=
l
> and you should then be able to edit independently.
>
> The problem may be, and again I remind you that I am no expert, that thes=
e
> atoms are two close to each other and may be getting mistaken for a
> covalent
> interaction, can't tell without actually seeing though.
>
> Hope any or all of this helps.  Good Luck!
>
>
>
> Cheers,
> Nick
>
>
>
>
>
>
> ----- Original Message -----
> From: "Geng Tian" <gen...@ho...>
> To: <pym...@li...>
> Sent: Thursday, April 13, 2006 3:19 PM
> Subject: [PyMOL] question about ca trace
>
>
> > Hi, There:
> > I have a pdb file for a dimer. only coordinates of alph carbons are in
> the
> > pdb. In the pymol, I
> > set cartoon_trace, 1
> > and
> > show cartoon
> > each monomer is fine but a weird linkage showed up between the last
> > residue of chain a and first residue of chain b. I just can't remove
> this
> > ugly linkage. Do you have any idea? Thank you. Actually I tried ribbon
> > mode and no this weird linkage but I like the figure qualify of the
> > cartoon.
> > Tiger
> >
> > _________________________________________________________________
> > Express yourself instantly with MSN Messenger! Download today - it's
> FREE!
> > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
> >
> >
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by xPML, a groundbreaking scripting
> > language
> > that extends applications into web and mobile media. Attend the live
> > webcast
> > and join the prime developer group breaking into this new coding
> > territory!
> > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&dat=
=3D121642
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting
> language
> that extends applications into web and mobile media. Attend the live
> webcast
> and join the prime developer group breaking into this new coding
> territory!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&dat=
=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>



--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

Re: [PyMOL] question about ca trace

[Noinaj <no...@uk...>]

Tiger,

I am no expert by far, but can you select the linkage?  If so, just select 
and hide.  Also, you might try just hiding the two residues that are linked, 
this might get rid of the link and you probably wouldn't notice the missing 
residues unless it is a small protein.  alternatively, and probably the best 
solution is to edit the pdb file to create two individual files, one for 
each dimer (this can be done in any text editor).  then open both in Pymol 
and you should then be able to edit independently.

The problem may be, and again I remind you that I am no expert, that these 
atoms are two close to each other and may be getting mistaken for a covalent 
interaction, can't tell without actually seeing though.

Hope any or all of this helps.  Good Luck!



Cheers,
Nick






----- Original Message ----- 
From: "Geng Tian" <gen...@ho...>
To: <pym...@li...>
Sent: Thursday, April 13, 2006 3:19 PM
Subject: [PyMOL] question about ca trace


> Hi, There:
> I have a pdb file for a dimer. only coordinates of alph carbons are in the 
> pdb. In the pymol, I
> set cartoon_trace, 1
> and
> show cartoon
> each monomer is fine but a weird linkage showed up between the last 
> residue of chain a and first residue of chain b. I just can't remove this 
> ugly linkage. Do you have any idea? Thank you. Actually I tried ribbon 
> mode and no this weird linkage but I like the figure qualify of the 
> cartoon.
> Tiger
>
> _________________________________________________________________
> Express yourself instantly with MSN Messenger! Download today - it's FREE! 
> http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting 
> language
> that extends applications into web and mobile media. Attend the live 
> webcast
> and join the prime developer group breaking into this new coding 
> territory!
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

[PyMOL] question about ca trace

[Geng T. <gen...@ho...>]

Hi, There:
I have a pdb file for a dimer. only coordinates of alph carbons are in the 
pdb. In the pymol, I
set cartoon_trace, 1
and
show cartoon
each monomer is fine but a weird linkage showed up between the last residue 
of chain a and first residue of chain b. I just can't remove this ugly 
linkage. Do you have any idea? Thank you. Actually I tried ribbon mode and 
no this weird linkage but I like the figure qualify of the cartoon.
Tiger

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today - it's FREE! 
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/

Re: [PyMOL] pqr file

[Noinaj <no...@uk...>]

Chun,

Here is another site to check out.  It is Michael Lerner's site, the guy who 
brings us the APBS PyMol Plugin.  He mentions some information about the 
plugin and also has contact info in case the website doesn't answer your 
question.

http://www-personal.umich.edu/~mlerner/PyMOL/

At a quick glance, it seems to use AMBER force field.  I know that the 
pdb2pqr server has several parameters for you to choose from, so you might 
check out the plugin and see how Michael sets those to run within PyMOL. 
You can check that using any text editor such as Notepad.

Again, hope this helps.



Cheers,
Nick

----- Original Message ----- 
From: "Noinaj" <no...@uk...>
To: "Chun Tang" <tcs...@gm...>
Sent: Wednesday, April 12, 2006 10:45 AM
Subject: Re: [PyMOL] pqr file


> Chun,
>
> You might check out the web site below, it probably contains all 
> information that you might need and contact information for things not 
> explained online.
>
> http://apbs.sourceforge.net/
>
> Hope this helps.
>
>
>
> Cheers,
> Nick
>
>
>
> ----- Original Message ----- 
> From: "Chun Tang" <tcs...@gm...>
> To: <pym...@li...>
> Sent: Tuesday, April 11, 2006 6:39 PM
> Subject: [PyMOL] pqr file
>
>
> Hi there,
>
> When one uses the APBS plugin of pymol to generate a pqr file, how
> dose it assign the partial charges to the atoms, what force field is
> it based on? Thank you.
>
> Chun
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting 
> language
> that extends applications into web and mobile media. Attend the live 
> webcast
> and join the prime developer group breaking into this new coding 
> territory!
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> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

[PyMOL] Re: pqr file

[Chun T. <tcs...@gm...>]

I probably didn't make myself clear in my last email.

What I meant is that there is an option in pymol APBS tool that allows one
to use pymol to generate pqr file from pdb file, instead of loading an pqr
file generated externally. I noticed that the electrostatic potential looks
quite different for the pqr file of the same structure generated on pdb2pqr
server. My question is how does pymol assign partial charges? I can only
find a file called apbs_tools.py under the directory of
./modules/pmg_tk/startup/ that remotely has some information.

Chun

On 4/11/06, Chun Tang <tcs...@gm...> wrote:
>
> Hi there,
>
> When one uses the APBS plugin of pymol to generate a pqr file, how
> dose it assign the partial charges to the atoms, what force field is
> it based on? Thank you.
>
> Chun
>

Re: [PyMOL] pymol on amd64?

[Praedor A. <pr...@ya...>]

Yes, this binary works just fine.  Thanks again. =20

I am still puzzled/unhappy that I cannot get the source to build on my AMD6=
4. =20
especially given that I've checked and rechecked to make sure the=20
dependencies are met.  It isn't just pymol...if any source that SHOULD buil=
d=20
fails to build I get unhappy, having to assume that there is something hidd=
en=20
"wrong" with my system which limits my capabilities.

praedor

On Wednesday 12 April 2006 07:36 am, Andrea Spitaleri wrote:
> Hi,
> this should be a binary, so just installing it should work ...
> try also to export the lib path (export or setenv LD_LIBRARY_PATH)
>
> Regards
>
> Andrea
>
> 2006/4/12, Praedor Atrebates <pr...@ya...>:
> > Great!  Thank you.  I've just finished trying and failing to get pymol =
to
> > build again on my AMD64 Mandriva system.  It invariably fails quickly
> > with:
> >
> > layer0/Crystal.c:314:1: error: unterminated argument list invoking macro
> > "sprintf"
> > layer0/Crystal.c: In function 'CrystalDump':
> > layer0/Crystal.c:201: error: syntax error at end of input
> > layer0/Crystal.c:201: warning: unused variable '_FBstr'
> > layer0/Crystal.c:199: warning: unused variable 'i'
> > layer0/Crystal.c:198: warning: unused variable 'G'
> > error: command 'gcc' failed with exit status 1
> >
> > There must be a lib difference or gcc difference between the Mandriva
> > 2006 system and SuSE that apparently allows a 64 bit build to proceed.
> >
> > praedor
> >
> > On Wednesday 12 April 2006 04:18 am, Andrea Spitaleri wrote:
> > > Hi,
> > > few weeks ago I had a problem with pymol-32bit on my laptop 64bit usi=
ng
> > > slamd Warren built a pymol for 64bit and you can download it from her=
e:
> > > http://delsci.com/beta/
> > >
> > > In my case it worked.
> > > Regards
> > >
> > > andrea
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by xPML, a groundbreaking scripting
> > language that extends applications into web and mobile media. Attend the
> > live webcast and join the prime developer group breaking into this new
> > coding territory!
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=3D121642
> > _______________________________________________
> > PyMOL-users mailing list
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> > https://lists.sourceforge.net/lists/listinfo/pymol-users
>
> --
> "La conoscenza libera il genere umano dalla superstizione"
> J. Watson
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting langua=
ge
> that extends applications into web and mobile media. Attend the live
> webcast and join the prime developer group breaking into this new coding
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=2D-=20
The Reichstag fire is to Hitler as 9/11 is to Bush

Re: [PyMOL] pymol on amd64?

[Andrea S. <and...@gm...>]

Hi,
this should be a binary, so just installing it should work ...
try also to export the lib path (export or setenv LD_LIBRARY_PATH)

Regards

Andrea

2006/4/12, Praedor Atrebates <pr...@ya...>:
> Great!  Thank you.  I've just finished trying and failing to get pymol to
> build again on my AMD64 Mandriva system.  It invariably fails quickly wit=
h:
>
> layer0/Crystal.c:314:1: error: unterminated argument list invoking macro
> "sprintf"
> layer0/Crystal.c: In function 'CrystalDump':
> layer0/Crystal.c:201: error: syntax error at end of input
> layer0/Crystal.c:201: warning: unused variable '_FBstr'
> layer0/Crystal.c:199: warning: unused variable 'i'
> layer0/Crystal.c:198: warning: unused variable 'G'
> error: command 'gcc' failed with exit status 1
>
> There must be a lib difference or gcc difference between the Mandriva 200=
6
> system and SuSE that apparently allows a 64 bit build to proceed.
>
> praedor
>
> On Wednesday 12 April 2006 04:18 am, Andrea Spitaleri wrote:
> > Hi,
> > few weeks ago I had a problem with pymol-32bit on my laptop 64bit using
> > slamd Warren built a pymol for 64bit and you can download it from here:
> > http://delsci.com/beta/
> >
> > In my case it worked.
> > Regards
> >
> > andrea
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting langua=
ge
> that extends applications into web and mobile media. Attend the live webc=
ast
> and join the prime developer group breaking into this new coding territor=
y!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&dat=
=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


--
"La conoscenza libera il genere umano dalla superstizione"
J. Watson

Re: [PyMOL] pymol on amd64?

[Praedor A. <pr...@ya...>]

Great!  Thank you.  I've just finished trying and failing to get pymol to 
build again on my AMD64 Mandriva system.  It invariably fails quickly with:

layer0/Crystal.c:314:1: error: unterminated argument list invoking macro 
"sprintf"
layer0/Crystal.c: In function 'CrystalDump':
layer0/Crystal.c:201: error: syntax error at end of input
layer0/Crystal.c:201: warning: unused variable '_FBstr'
layer0/Crystal.c:199: warning: unused variable 'i'
layer0/Crystal.c:198: warning: unused variable 'G'
error: command 'gcc' failed with exit status 1

There must be a lib difference or gcc difference between the Mandriva 2006 
system and SuSE that apparently allows a 64 bit build to proceed.

praedor

On Wednesday 12 April 2006 04:18 am, Andrea Spitaleri wrote:
> Hi,
> few weeks ago I had a problem with pymol-32bit on my laptop 64bit using
> slamd Warren built a pymol for 64bit and you can download it from here:
> http://delsci.com/beta/
>
> In my case it worked.
> Regards
>
> andrea