Re: [PyMOL] attach_amino_acid
Kirk,
Just FYI, you are outside the realm of what PyMOL has been designed to do
(so far). Regardless,
editor.attach_amino_acid("junk/94/C","trp")
seems to work with current versions (0.99rev8 and the latest 1.00 beta
code).
Cheers,
Warren
_
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Kirk Vander
Meulen
Sent: Friday, February 02, 2007 1:44 PM
To: PyMOL-users@lists.sourceforge.net
Subject: [PyMOL] attach_amino_acid
I'm having some trouble getting this function to work correctly.
My pdb is called junk and residue 94 is the c-terminus, and I want to add a
tryptophan to it- here's my input
editor.attach_amino_acid('junk & resi 94 & name c', 'trp')
The result is that the tryptophan is built, but it's not bonded (it's a
separate object, actually). Could anyone tell me what I'm doing wrong?
Thanks,
Kirk
[PyMOL] attach_amino_acid
I'm having some trouble getting this function to work correctly.
My pdb is called junk and residue 94 is the c-terminus, and I want to add a
tryptophan to it- here's my input
editor.attach_amino_acid('junk & resi 94 & name c', 'trp')
The result is that the tryptophan is built, but it's not bonded (it's a
separate object, actually). Could anyone tell me what I'm doing wrong?
Thanks,
Kirk
Re: [PyMOL] 1letter code by default
From: Warren DeLano > Andrea, > > What do you mean exactly? Hi all, sorry i realized that i didn't explain clearly my question. I was wondering if there was a possibility to put the residue labels by default in 1-letter code,let's say Q65 instead of GLN-65..doing the selection with the left button of the mouse and putting the labels with the right button -->label-->residues. Thanks Andrea
Re: [PyMOL] selecting Na+ in pymol
Hi Warren,
Actually, I tried to use select .., r. na\+ as the second option, but
that didn't work for me (Pymol 0.99b on Suse 9.2).
Oh, and I owe you an elaborate answer still on the mail from a while
ago. But that got a bit buried.. sorry ;)
Tsjerk
On 2/2/07, DeLano Scientific wrote:
Tsjerk & Abhinav,
> Actually, it was a bit surprising to me to see you're right.
+ is the default list separator in selections. For example:
select posi, ARG+HIS+LYS/
select backbone, n. N+CA+C+O
That is why it needs to be escaped with a backslash.
Commas can also be used, but only within parentheses -- otherwise the parser
gets confused, since commas are also used to separate command arguments.
select backbone, (n. N,CA,C,O)
Also, be aware when using backslashes inside a Python string that they are
also a string escape character, so it is best to use two of them "\\+".
However, a single slash happens to work in this case for some bizzare
reason.
In other words, the PyMOL command:
select selectionname, r. na\+
has a true Python equivalent of
cmd.select("selectionname","r. na\\+")
not
cmd.select("selectionname","r. na\+")
which actually works, but probably shouldn't.
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:del...@delsci.info
> -Original Message-
> From: pymol-users-boun...@lists.sourceforge.net
> [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf
> Of Tsjerk Wassenaar
> Sent: Friday, February 02, 2007 2:23 AM
> To: Abhinav Verma
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] selecting Na+ in pymol
>
> Hi Abhi,
>
> Actually, it was a bit surprising to me to see you're right.
> Now, for showing/hiding, it has been dealt with in the code,
> by allowing the "+" to be left out. However, for selecting
> (and alter_ing) that doesn't go, apparently. A workaround is to use
>
> cmd.select("selectionname","r. na\+") or
> cmd.select("selectionname","n. na\+")
>
> Alternatively, you can change the residue/atomnames using:
>
> cmd.alter("r. na\+","resn='Na'") or cmd.alter("n. na\+","name='Na'")
>
> All of these worked for me. Of course, it would be good to
> have this dealt with properly in the same way as for showing/hiding.
>
> Hope it helps,
>
> Tsjerk
>
> On 2/2/07, Abhinav Verma wrote:
> > Hallo,
> > I have an annoying problem. I have pdb file with Na+ atoms
> defined as
> >
> > ATOM 1 Na+ Na+53 -1.106 7.854 52.244
> 1.00 0.00 Na
> >
> > now if want to select these Na+ with
> >
> > PyMOL>select n. na+
> > Selector: selection "sele" defined with 0 atoms.
> >
> > Any ideas how to select them?
> >
> > I tried renaming them to Na and then select n. na which works. So I
> > assume the problem is "+" which is used for add in pymol.
> > I also tried n. "na+" which did not work either.
> >
> >
> > thanks in advance,
> > Abhi.
> >
> >
> --
> > --- Using Tomcat but need to do more? Need to support web services,
> > security?
> > Get stuff done quickly with pre-integrated technology to
> make your job
> > easier.
> > Download IBM WebSphere Application Server v.1.0.1 based on Apache
> > Geronimo
> >
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=1216
> > 42 ___
> > PyMOL-users mailing list
> > PyMOL-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> >
>
>
> --
> 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
>
> --
> ---
> Using Tomcat but need to do more? Need to support web
> services, security?
> Get stuff done quickly with pre-integrated technology to make
> your job easier.
> Download IBM WebSphere Application Server v.1.0.1 based on
> Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&;
dat=121642
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
--
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
[PyMOL] comparing proteins structures
Hi all! Does anyone know how to overlay two proteins structures? thanks! best Filo
Re: [PyMOL] selecting Na+ in pymol
Tsjerk & Abhinav,
> Actually, it was a bit surprising to me to see you're right.
+ is the default list separator in selections. For example:
select posi, ARG+HIS+LYS/
select backbone, n. N+CA+C+O
That is why it needs to be escaped with a backslash.
Commas can also be used, but only within parentheses -- otherwise the parser
gets confused, since commas are also used to separate command arguments.
select backbone, (n. N,CA,C,O)
Also, be aware when using backslashes inside a Python string that they are
also a string escape character, so it is best to use two of them "\\+".
However, a single slash happens to work in this case for some bizzare
reason.
In other words, the PyMOL command:
select selectionname, r. na\+
has a true Python equivalent of
cmd.select("selectionname","r. na\\+")
not
cmd.select("selectionname","r. na\+")
which actually works, but probably shouldn't.
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:del...@delsci.info
> -Original Message-
> From: pymol-users-boun...@lists.sourceforge.net
> [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf
> Of Tsjerk Wassenaar
> Sent: Friday, February 02, 2007 2:23 AM
> To: Abhinav Verma
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] selecting Na+ in pymol
>
> Hi Abhi,
>
> Actually, it was a bit surprising to me to see you're right.
> Now, for showing/hiding, it has been dealt with in the code,
> by allowing the "+" to be left out. However, for selecting
> (and alter_ing) that doesn't go, apparently. A workaround is to use
>
> cmd.select("selectionname","r. na\+") or
> cmd.select("selectionname","n. na\+")
>
> Alternatively, you can change the residue/atomnames using:
>
> cmd.alter("r. na\+","resn='Na'") or cmd.alter("n. na\+","name='Na'")
>
> All of these worked for me. Of course, it would be good to
> have this dealt with properly in the same way as for showing/hiding.
>
> Hope it helps,
>
> Tsjerk
>
> On 2/2/07, Abhinav Verma wrote:
> > Hallo,
> > I have an annoying problem. I have pdb file with Na+ atoms
> defined as
> >
> > ATOM 1 Na+ Na+53 -1.106 7.854 52.244
> 1.00 0.00 Na
> >
> > now if want to select these Na+ with
> >
> > PyMOL>select n. na+
> > Selector: selection "sele" defined with 0 atoms.
> >
> > Any ideas how to select them?
> >
> > I tried renaming them to Na and then select n. na which works. So I
> > assume the problem is "+" which is used for add in pymol.
> > I also tried n. "na+" which did not work either.
> >
> >
> > thanks in advance,
> > Abhi.
> >
> >
> --
> > --- Using Tomcat but need to do more? Need to support web services,
> > security?
> > Get stuff done quickly with pre-integrated technology to
> make your job
> > easier.
> > Download IBM WebSphere Application Server v.1.0.1 based on Apache
> > Geronimo
> >
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=1216
> > 42 ___
> > PyMOL-users mailing list
> > PyMOL-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> >
>
>
> --
> 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
>
> --
> ---
> Using Tomcat but need to do more? Need to support web
> services, security?
> Get stuff done quickly with pre-integrated technology to make
> your job easier.
> Download IBM WebSphere Application Server v.1.0.1 based on
> Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&;
dat=121642
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] mesure line width
Hi Andrea, * andrea carotti [2007-02-02 14:13] wrote: > Hi all, > is there the possibility to change the line width of the distance > measure between two atoms? set dash_width, 3 If you like using a white background like I do, you can also change the dash color using the "Setting... -> Color..." menu item. Scroll down to "dash" and double click on it to bring up the "Modify Color" window. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 http://adelie.biochem.queensu.ca/~rlc
Re: [PyMOL] OSx X11 Pymol Clicking problem
Scott, > I have had this problem for the past few weeks, and it has been > difficult to diagnose the cause. The problem is that in the X11 version of pymol run on my mactel osx laptop does not interpret my three button mouse click properly. When I click on a given atom in the UI, it selects something else, often far away from the the > intended selection. This is more of an annoyance, since I can > visualize molecule, but the wizards and click menus are basically non- functional. I've sees slightly similar problems (mouse selection with stereo enabled using the fglrx driver for ati firegl cards doesn't work; same selection with stereo off works fine). > > If anyone out there has any suggestions I would love to hear them. > I don't have any solutions for you, but the graphics card driver (or X11 configuration) might be a good place to start poking around for troubleshooting. Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
[PyMOL] mesure line width
Hi all, is there the possibility to change the line width of the distance measure between two atoms? Thanks Andrea -- Andrea Carotti Dipartimento di Chimica e Tecnologia del Farmaco Via del Liceo, 1 06123 Perugia, Italy phone: +39 075 585 5169 fax: +39 075 585 5161
Re: [PyMOL] selecting Na+ in pymol
Hi Abhi,
Actually, it was a bit surprising to me to see you're right. Now, for
showing/hiding, it has been dealt with in the code, by allowing the
"+" to be left out. However, for selecting (and alter_ing) that
doesn't go, apparently. A workaround is to use
cmd.select("selectionname","r. na\+") or
cmd.select("selectionname","n. na\+")
Alternatively, you can change the residue/atomnames using:
cmd.alter("r. na\+","resn='Na'") or cmd.alter("n. na\+","name='Na'")
All of these worked for me. Of course, it would be good to have this
dealt with properly in the same way as for showing/hiding.
Hope it helps,
Tsjerk
On 2/2/07, Abhinav Verma wrote:
Hallo,
I have an annoying problem. I have pdb file with Na+ atoms defined as
ATOM 1 Na+ Na+53 -1.106 7.854 52.244 1.00 0.00 Na
now if want to select these Na+ with
PyMOL>select n. na+
Selector: selection "sele" defined with 0 atoms.
Any ideas how to select them?
I tried renaming them to Na and then select n. na which works. So I assume
the problem is "+" which is used for add in pymol.
I also tried n. "na+" which did not work either.
thanks in advance,
Abhi.
-
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job
easier.
Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users
--
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
[PyMOL] selecting Na+ in pymol
Hallo, I have an annoying problem. I have pdb file with Na+ atoms defined as ATOM 1 Na+ Na+53 -1.106 7.854 52.244 1.00 0.00 Na ATOM 2 Na+ Na+54 -0.106 3.854 27.244 1.00 0.00 Na ATOM 3 Na+ Na+55 1.894 -6.146 62.244 1.00 0.00 Na ATOM 4 Na+ Na+56 8.894 -5.146 42.244 1.00 0.00 Na ATOM 5 Na+ Na+57 -4.106 4.854 13.244 1.00 0.00 Na ATOM 6 Na+ Na+58 -10.106 -6.146 42.244 1.00 0.00 Na ATOM 7 Na+ Na+59 -7.106 5.854 35.244 1.00 0.00 Na ATOM 8 Na+ Na+60 4.894 4.854 49.244 1.00 0.00 Na ATOM 9 Na+ Na+61 9.894 -3.146 22.244 1.00 0.00 Na now if want to select these Na+ with PyMOL>select n. na+ Selector: selection "sele" defined with 0 atoms. Any ideas how to select them? I tried renaming them to Na and then select n. na which works. So I assume the problem is "+" which is used for add in pymol. I also tried n. "na+" which did not work either. thanks in advance, Abhi.
