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

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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
>
> _________________________________________________________________
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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/
> >
> >
> >
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> > language
> > that extends applications into web and mobile media. Attend the live
> > webcast
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> > territory!
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=3D121642
> > _______________________________________________
> > PyMOL-users mailing list
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> >
>
>
>
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> 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] 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

[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

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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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
>
>_________________________________________________________________
>Express yourself instantly with MSN Messenger! Download today - it's FREE! 
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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!
>     > 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
>     >
>
>
>
>     -------------------------------------------------------
>     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
>
>
>
>
>   --
>
>   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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