[PyMOL] (no subject)

[Len Banaszak]

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[PyMOL] (no subject)

[Jose Arturo Sanchez Paz]

Please unsubscribe me.

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[PyMOL] (no subject)

[P Divya]

Please unsubscribe me 
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[PyMOL] (no subject)

[ragini sinha]

Pls unsubscribe me
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Re: [PyMOL] (no subject)

[David Hall]

For some reason, the people doing brew have decided to stop supporting
compiling tcl-tk with X11 support. Not 100% sure, but I'm pretty certain
pymol cannot use tcl-tk with aqua.

If you already had pymol installed, this seems to eliminate the external
gui. If you didn't, new installations of pymol will now crash randomly.

Here's how I got to the old version that worked

$ cd /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/
$ git checkout 46e1ef94247cd2fb9555b724c051e8907996 -- tcl-tk.rb
$ cd ../../homebrew-science/
Edit the pymol.rb file so that it depends on "tcl-tk" instead of
"homebrew/dupes/tcl-tk"

$ brew remove tcl-tk python pymol
$ brew install pymol
$ brew pin tcl-tk

Really, I uninstalled all my homebrew packages and then reinstalled
everything because some of their changes over the last 6 months had made
things oddly broken. If you want to do the same, you can try this:

$ brew list > installed
$  wrote:

> Hi,
> pymol external gui menus missing, I have compiled pymol in mac os by using
> brew.
>
> Anyone can provide some suggestions?
>
> Jacky
>
> --
> Lei Zhao, Ph.D. & M.D.
> Associate Professor
> National Clinical Research Center for Normal Aging and Geriatric
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>
>
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[PyMOL] (no subject)

[jacky zhao]

Hi,
pymol external gui menus missing, I have compiled pymol in mac os by using
brew.

Anyone can provide some suggestions?

Jacky

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National Engineering Research Center for Antibody Medicine
The Key Lab of Normal Aging and Geriatric
PLA General Hospital
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P.R.China
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Re: [PyMOL] (no subject)

[Vivien Schoonenberg]

This worked! Thank you Leandro and Jed!

 

From: jedg...@gmail.com [mailto:jedg...@gmail.com] On Behalf Of Jed Goldstone
Sent: Tuesday, April 4, 2017 11:35
To: Vivien Schoonenberg 
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] (no subject)

 

Try using

remove not alt +A

to remove alternative conformations.

Jed

 

On Mon, Apr 3, 2017 at 11:47 AM, Vivien Schoonenberg 
mailto:vivienschoonenb...@gmail.com> > wrote:

Hi there,

 

I’m saving the sequences from each chain of the PDB via pymol with 

>>save something.fasta, chain A

 

This is the same sequence that is shown in pymol and seems to correspond to the 
structure I am looking at.

However, when I loaded new B-factors in my structure, I noticed something funny 
happened. The list which I made corresponding to the sequence I saved earlier 
was too short. 

I  found out by iterating that some residues repeated themselves(>>iterate 
(chain A and n. CA), print resn). They carry the same residue number, and are 
not shown in the sequence. However, when I load my B-factors my list shifts 
because of these repeats, making it too short for the complete chain and 
loading the wrong value onto residues. 

 

Does anyone know why this happens and how I can fix this?

 

Thank you,

Vivien


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(508) 685-2253 (cell/home) (508) 289-4823 (work/WHOI)

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Re: [PyMOL] (no subject)

[Jed Goldstone]

Try using

remove not alt +A

to remove alternative conformations.

Jed

On Mon, Apr 3, 2017 at 11:47 AM, Vivien Schoonenberg <
vivienschoonenb...@gmail.com> wrote:

> Hi there,
>
>
>
> I’m saving the sequences from each chain of the PDB via pymol with
>
> >>save something.fasta, chain A
>
>
>
> This is the same sequence that is shown in pymol and seems to correspond
> to the structure I am looking at.
>
> However, when I loaded new B-factors in my structure, I noticed something
> funny happened. The list which I made corresponding to the sequence I saved
> earlier was too short.
>
> I  found out by iterating that some residues repeated themselves(>>iterate
> (chain A and n. CA), print resn). They carry the same residue number, and
> are not shown in the sequence. However, when I load my B-factors my list
> shifts because of these repeats, making it too short for the complete chain
> and loading the wrong value onto residues.
>
>
>
> Does anyone know why this happens and how I can fix this?
>
>
>
> Thank you,
>
> Vivien
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>



-- 
-
Jed Goldstone, PhD
Research Specialist
Woods Hole Oceanographic Institution
Redfield 3-52 MS #32
Woods Hole, MA  02543
http://www.whoi.edu/hpb/Site.do?id=481
(508) 685-2253 (cell/home) (508) 289-4823 (work/WHOI)
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Re: [PyMOL] (no subject)

[Leandro Bortot]

Hi,

 You probably have a pdb file which has multiple possible conformations
for some residues. You can check this by visual inspection of such
residues. They have two side chains coming from the same CA. In the text
file you can see the conformations marked as A and B in the residue name
field, e.g. APHE BPHE.

 If that is the case, you have to choose one of them either manually or
with some other molecular modeling software, e.g. gromacs.

I hope it helps!
Regards,
Leandro



On Mon, Apr 3, 2017 at 5:47 PM, Vivien Schoonenberg <
vivienschoonenb...@gmail.com> wrote:

> Hi there,
>
>
>
> I’m saving the sequences from each chain of the PDB via pymol with
>
> >>save something.fasta, chain A
>
>
>
> This is the same sequence that is shown in pymol and seems to correspond
> to the structure I am looking at.
>
> However, when I loaded new B-factors in my structure, I noticed something
> funny happened. The list which I made corresponding to the sequence I saved
> earlier was too short.
>
> I  found out by iterating that some residues repeated themselves(>>iterate
> (chain A and n. CA), print resn). They carry the same residue number, and
> are not shown in the sequence. However, when I load my B-factors my list
> shifts because of these repeats, making it too short for the complete chain
> and loading the wrong value onto residues.
>
>
>
> Does anyone know why this happens and how I can fix this?
>
>
>
> Thank you,
>
> Vivien
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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[PyMOL] (no subject)

[Vivien Schoonenberg]

Hi there,

 

I'm saving the sequences from each chain of the PDB via pymol with 

>>save something.fasta, chain A

 

This is the same sequence that is shown in pymol and seems to correspond to
the structure I am looking at.

However, when I loaded new B-factors in my structure, I noticed something
funny happened. The list which I made corresponding to the sequence I saved
earlier was too short. 

I  found out by iterating that some residues repeated themselves(>>iterate
(chain A and n. CA), print resn). They carry the same residue number, and
are not shown in the sequence. However, when I load my B-factors my list
shifts because of these repeats, making it too short for the complete chain
and loading the wrong value onto residues. 

 

Does anyone know why this happens and how I can fix this?

 

Thank you,

Vivien

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[PyMOL] (no subject)

[Dan Lin]

Dear all:

It appears that pymol only interpolates motions that include rotations by
moving the object along an arc. I would like to make a movie that does not
do this, but rather, moves the object along a straight line while rotating
the object. Unfortunately, I'm absolutely at a loss about how I could do
this. Would anybody have any suggestions about where to look for this
information?

Thanks,
Dan
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[PyMOL] (no subject)

[Raag Saluja]

Hi!

What is the command for superimposing a .gro file and a .pdb file in PyMOL?

I tried opening the .gro file and then loading the .pdb file. Consequently,
I could only see the latter and not the former.

Thank you in advance!
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Raag
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[PyMOL] (no subject)

[Dak Aboah Monrovia]

daka...@yahoo.com--
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Re: [PyMOL] (no subject)

[Edward A. Berry]

On 04/19/2015 02:08 AM, leila karami wrote:
> Dear Marcelo
>
> Thanks for your quick answer.
>
> Unfortunately, I can't open the link (https://www.pymol.org/citing) you 
> suggested me.

perhaps your firewall or browser is blocking the https: connection or rejecting 
the certificate?
Try http: instead- they seem to reach the same content.
Just don't give your taxpayer ID number or bank password!

>
> Thanks in advance.
>
>
> --
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Re: [PyMOL] (no subject)

[Marcelo Marcet]

Hi Leila,

No problem, here is the content of the site. If you need the reference manager 
files (BibTex or EndNote files), I am happy to email them to you as well.

Cheers,
Marcelo





Citation Format
Please cite PyMOL, AxPyMOL and JyMOL as shown below. Be sure to edit the 
version number in accordance with your usage.  If you use BibTex or EndNote, 
download the handy citation files below.

PyMOL
The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.
 

JyMOL
The JyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.
 

AxPyMOL

The AxPyMOL Molecular Graphics Plugin for PowerPoint, Version 1.7.4 
Schrödinger, LLC.
 

BibTex Files
PyMOL BibTex Entries [.bib] 
For help with BibTex see:

http://en.wikipedia.org/wiki/BibTeX 
http://www.bibtex.org/Using/ 
EndNote Files
PyMOL EndNote Entries [.xml]  
(right-click and save this file to your computer; most browsers dont' render 
XML nicely)




> On Apr 19, 2015, at 12:08 AM, leila karami  wrote:
> 
> Dear Marcelo
> 
> Thanks for your quick answer.
> 
> Unfortunately, I can't open the link (https://www.pymol.org/citing 
> ) you suggested me.
> 
> Thanks in advance.
> --
> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
> Develop your own process in accordance with the BPMN 2 standard
> Learn Process modeling best practices with Bonita BPM through live exercises
> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF___
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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Re: [PyMOL] (no subject)

[Jordan Willis]

PyMOL
The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.
 

JyMOL
The JyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.
 

AxPyMOL

The AxPyMOL Molecular Graphics Plugin for PowerPoint, Version 1.7.4 
Schrödinger, LLC.


> On Apr 18, 2015, at 11:08 PM, leila karami  wrote:
> 
> Dear Marcelo
> 
> Thanks for your quick answer.
> 
> Unfortunately, I can't open the link (https://www.pymol.org/citing 
> ) you suggested me.
> 
> Thanks in advance.
> --
> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
> Develop your own process in accordance with the BPMN 2 standard
> Learn Process modeling best practices with Bonita BPM through live exercises
> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF___
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[PyMOL] (no subject)

[leila karami]

Dear Marcelo

Thanks for your quick answer.

Unfortunately, I can't open the link (https://www.pymol.org/citing) you
suggested me.

Thanks in advance.
--
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Re: [PyMOL] (no subject)

[Marcelo Marcet]

Hi Leila,

Take a look at the link below:

https://www.pymol.org/citing 

Cheers,
Marcelo




> On Apr 18, 2015, at 11:55 PM, leila karami  wrote:
> 
> Dear all
> 
> How to cite pymol in my paper?
> 
> Thanks.
> --
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[PyMOL] (no subject)

[leila karami]

Dear all

How to cite pymol in my paper?

Thanks.
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[PyMOL] (no subject)

[Pawe? Gniewek]

Hi all,

I wonder if it's possible to fill the space (like in the case of
nucleotide's ring) between three arbitrary/selected atoms.

I'm trying to render an object which is not a biomolecule so
"cartoon_ring_mode" is no use for me.

Cheers,
pawel
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Re: [PyMOL] (no subject)

[Thomas Holder]

Hi Aliya,

yes, likely there is a clash. But that's hard to tell without seeing your data.

Cheers,
  Thomas

On 01 Jul 2014, at 11:34, Aliya Holland  
wrote:
> Hello,
> 
> I just created an animation of a conformational change of a specific domain 
> on a molecule. During the animation the domain rotates just as it should,  
> however other parts of the molecule moves with the conformation change. I was 
> wondering if that was part of the PyMOL programming or if there was a clash 
> between the end domain and the rotating section. Why would there be movement 
> in the entire molecule when only one section of it is morphing. 
> 
> Thank you 
> 
> A

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[PyMOL] (no subject)

[Aliya Holland]

Hello,

I just created an animation of a conformational change of a specific domain
on a molecule. During the animation the domain rotates just as it should,
 however other parts of the molecule moves with the conformation change. I
was wondering if that was part of the PyMOL programming or if there was a
clash between the end domain and the rotating section. Why would there be
movement in the entire molecule when only one section of it is morphing.

Thank you

A
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Re: [PyMOL] (no subject)

[Gianluigi Caltabiano]

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Re: [PyMOL] (no subject)

[Davi de Miranda Fonseca]

My PyMOL 1.5.0.5 works fine in Windows 8 (64 bits).

Try the following:
- Press Windows Key + Q
- This should open the search apps thingy, type pymol
- It should show all PyMOL shortcuts, try the "PyMOL + Tcl-Tk GUI + Console"
- Does PyMOL still refuses to open? Did you get any error message?

On 20/03/2013 03:11, Thomas Holder wrote:
> Hi Nina Marie,
>
> I haven't tested that thoroughly, but for me Incentive PyMOL 1.5.0.5
> runs fine on Windows 8.
>
> Cheers,
>Thomas
>
> Wolf, Nina Marie wrote, On 03/19/13 21:11:
>> Hi,
>>
>> I recently upgraded my computer to windows 8. Since then, pymol will not
>> open. Is the latest version of pymol incompatible with windows 8? Or is
>> there something I can do to get it working on my computer?


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Re: [PyMOL] (no subject)

[Thomas Holder]

Hi Nina Marie,

I haven't tested that thoroughly, but for me Incentive PyMOL 1.5.0.5
runs fine on Windows 8.

Cheers,
  Thomas

Wolf, Nina Marie wrote, On 03/19/13 21:11:
> Hi,
> 
> I recently upgraded my computer to windows 8. Since then, pymol will not
> open. Is the latest version of pymol incompatible with windows 8? Or is
> there something I can do to get it working on my computer?

-- 
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PyMOL Developer
Schrödinger Contractor

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[PyMOL] (no subject)

[Wolf, Nina Marie]

 Hi,

I recently upgraded my computer to windows 8. Since then, pymol will not
open. Is the latest version of pymol incompatible with windows 8? Or is
there something I can do to get it working on my computer?



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Re: [PyMOL] (no subject)

[Jason Vertrees]

Hi Mary,

Just a hint for any future lists you might be on: most modern email
lists, including pymol-users, have footers with links to subscription
options. You simply click that to get to a subscription page where you
can unsubscribe.

In this case, I removed you from the list to save you the hassle.

Cheers,

-- Jason

On Mon, Nov 26, 2012 at 5:30 PM, Mary Hall  wrote:
> How do I remove myself from the PyMOL users list? I'd like to stop receiving
> emails.
>
> Thank you.
>
> M. Hall
>
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[PyMOL] (no subject)

[Mary Hall]

How do I remove myself from the PyMOL users list? I'd like to stop
receiving emails.

Thank you.

M. Hall

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[PyMOL] (no subject)

[Mintu Chandra]

I have downloaded the pymol linux version in my kubuntu 12.4 , but while
> installing, it is asking for -Kubuntu 11.04 _Natty Narwhal_ - Release i386
> (20110427.1). Please suggest me what shoul i do???
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[PyMOL] (no subject)

[guridis]

 This message was sent using IMBB - WebMail.


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Re: [PyMOL] (no subject)

[Thomas Holder]

Hi Noloofar and Lina,

>> I would like to calculate partial charges of my pdb. Is it possible to do it
> 
> In pymol:
> 
> Action-> compute -> partial charge sum

this doesn't calculate partial charges, sorry.

This does:
Action -> generate -> vacuum electrostatics

But better would be to use pdb2pqr:
http://www.poissonboltzmann.org/pdb2pqr

>> I have another question too, when aligning two structure in Pymol, there is
>> a RMSD for the total structure, is there any command to calculate the RMSD
>> for a specific region of the alignment.

If the two structures have the same sequence (same atom identifiers) and 
you don't need an "alignment", you can use rms_cur.

http://pymolwiki.org/index.php/Rms_Cur

Cheers,
   Thomas

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Re: [PyMOL] (no subject)

[lina]

On Sun, Sep 4, 2011 at 8:37 PM, niloofar niknam
 wrote:
>
>
> Deal list,
> I would like to calculate partial charges of my pdb. Is it possible to do it

In pymol:

Action-> compute -> partial charge sum


> by Pymol? If not, Is anyone know any server
> or  software to do it?
> I have another question too, when aligning two structure in Pymol, there is
> a RMSD for the total structure, is there any command to calculate the RMSD
> for a specific region of the alignment.
> Any offer would be appreciated.
> kind regards.
> Niloofar
>
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>



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lina

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[PyMOL] (no subject)

[niloofar niknam]

 
Deal list,
I would like to calculate partial charges of my pdb. Is it possible to do it by 
Pymol? If not, Is anyone know any server 

or  software to do it?

I have another question too, when aligning two structure in Pymol, there is a 
RMSD for the total structure, is there any command to calculate the RMSD for a 
specific region of the alignment.

Any offer would be appreciated.

kind regards.

Niloofar
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Re: [PyMOL] (no subject)

[Nat Echols]

On Fri, May 28, 2010 at 10:49 AM, Thomas Juettemann wrote:

> Hi Chris,
>
> the emails are only sent to you because you subscribed to the pymol-users
> list.
> If you don't want them anymore you need to unsubscribe.
>
> Click on "Show details" at the top of this email. Click then on:
> unsubscribe Unsubscribe from this mailing-list
>
> That will do the magic.


Or click on the link at the bottom of *every email sent to the list*:


> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>
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Re: [PyMOL] (no subject)

[Thomas Juettemann]

Hi Chris,

the emails are only sent to you because you subscribed to the pymol-users list.
If you don't want them anymore you need to unsubscribe.

Click on "Show details" at the top of this email. Click then on:
unsubscribe Unsubscribe from this mailing-list

That will do the magic.


On Fri, May 28, 2010 at 10:42, Christian De Ford  wrote:
> Please stop sending me daily emails its very annoying, i would
> appreciate if you erase me from the list
> Thank you!
> --
>
>
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[PyMOL] (no subject)

[Christian De Ford]

Please stop sending me daily emails its very annoying, i would
appreciate if you erase me from the list
Thank you!
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[PyMOL] (no subject)

[Joel Tyndall]

PS is it possible to run two versions at once on a PC (a quick test failed)


_

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Re: [PyMOL] (no subject)

[Warren DeLano]

Rotem,

Try starting with the script below.  It will produce output like:

PRO A 1Chi-1:   20.6
GLN A 2Chi-1: -178.8
LEU A 5Chi-1:  -64.6
TRP A 6Chi-1:  -55.6
GLN A 7Chi-1:  -59.6
ARG A 8Chi-1:  -83.1
PRO A 9Chi-1:   34.9
LEU A 10   Chi-1:  -53.5
...

Cheers,
Warren

---

load $TUT/1hpv.pdb

select chi1, polymer & (br. */N) & (br. */CA) & (br. */CB) & (br. */CG)

N  = cmd.index("chi1 & */N ") 

CA = cmd.index("chi1 & */CA")

CB = cmd.index("chi1 & */CB")

CG = cmd.index("chi1 & */CG")

LABEL = []

iterate chi1 & */CA, LABEL.append(resn+" "+chain+" "+resi)

I = range(len(LABEL))

CHI1 = [0] * len(I)

for i in I: CHI1[i] = cmd.get_dihedral(N[i],CA[i],CB[i],CG[i])

for i in I: print "%-10s Chi-1: %6.1f" % (LABEL[i],CHI1[i])




From: Rotem Sertchook [mailto:rotem.sertch...@weizmann.ac.il] 
Sent: Tuesday, March 24, 2009 12:11 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] (no subject)

Hi,
I'm looking for a way to calculate set of torsion angels from selected residues 
(for example Chi1 dihedral of all His residues). Is it possible to write PyMOL 
script for such task ? Any hints to write such script will be appreciated!
 
Thank you
Rotem
 





--
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Weizmann Institute of Science,
Rehovot 76100, Israel.
--

Re: [PyMOL] (no subject)

[gilleain torrance]

Hi,

I think that it probably is possible to do this from within pymol, and
probably quite convenient for single molecules.

However, there are two other possible approaches, which would be
helpful for multiple molecules.

Firstly, there is a program called 'dang' made by the Richardson group:

http://kinemage.biochem.duke.edu/software/dang.php

and secondly, might I humbly submit that I have a program I call
'Tailor' that is intended for measuring and analysing (to a limited
extent) selected parts of proteins:

http://tailor.sourceforge.net/docs/index.html

gilleain

On Tue, Mar 24, 2009 at 7:06 AM, Rotem Sertchook
 wrote:
> Hi,
> I'm looking for a way to calculate set of torsion angels from selected
> residues (for example Chi1 dihedral of all His residues). Is it possible to
> write PyMOL script for such task ? Any hints to write such script will be
> appreciated!
>
> Thank you
> Rotem
>
>
>
>
>
>
> --
> Rotem Sertchook, Ph.D.
> Bioinformatics Unit, Biological Services
> Weizmann Institute of Science,
> Rehovot 76100, Israel.
> --
>
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[PyMOL] (no subject)

[Rotem Sertchook]

Hi,
I'm looking for a way to calculate set of torsion angels from  
selected residues (for example Chi1 dihedral of all His residues). Is  
it possible to write PyMOL script for such task ? Any hints to write  
such script will be appreciated!


Thank you
Rotem







--
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Bioinformatics Unit, Biological Services
Weizmann Institute of Science,
Rehovot 76100, Israel.
--

Re: [PyMOL] (no subject)

[Warren DeLano]

Justin,

Sorry about that...

"svn update" and rebuild.

I believe the warning is gone now.  It should only print if you
specifically request certain stereo modes.

Cheeers,
Warren
 

> -Original Message-
> From: Justin Lecher [mailto:j.lec...@fz-juelich.de] 
> Sent: Thursday, February 19, 2009 5:42 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] (no subject)
> 
> Hello all especially Warren,
> 
> What does
> 
> "Sorry, time-sequential stereo 3D not available"
> 
> mean. It is printed out when I start pymol. I am using current HEAD.
> 
> Thanks justin
> 
> 
> --
> Justin Lecher
> Institute for  Neuroscience and Biophysics INB 2 - Molecular 
> Biophysics II Research centre Juelich GmbH,
> 52425 Juelich,Germany
> phone: +49 2461 61 5385
> 
> 
> 
> 

[PyMOL] (no subject)

[Justin Lecher]

Hello all especially Warren,

What does

"Sorry, time-sequential stereo 3D not available"

mean. It is printed out when I start pymol. I am using current HEAD.

Thanks justin


-- 
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Institute for  Neuroscience and Biophysics
INB 2 - Molecular Biophysics II
Research centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385




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Description: OpenPGP digital signature

[PyMOL] (no subject)

[Grigoryan Hasmik]

hasg...@yahoo.com

   
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Re: [PyMOL] (no subject)

[DeLano Scientific]

Martin,

No, sorry, you will need an external tool to do this.

Cheers,
Warren


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> -Original Message-
> From: pymol-users-boun...@lists.sourceforge.net 
> [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf 
> Of Martin Sztacho
> Sent: Monday, April 16, 2007 3:51 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] (no subject)
> 
> Hello,
>  I would like to ask about building phosphate group at Tyr 
> residue. Is there any posibility to do it at PyMOL programe?
> Thank you for answer
> Martin Sztacho
> 
> --
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[PyMOL] (no subject)

[Martin Sztacho]

Hello, 
 I would like to ask about building phosphate group at Tyr residue. Is there 
any posibility to do it at PyMOL programe?
Thank you for answer
Martin Sztacho

Re: [PyMOL] (no subject)

[Tsjerk Wassenaar]

Dear Bernhard,

The user manual is quite informative where it comes to making
selections. There is not a polar/nonpolar grouping made for you, but
you can easily select the residues based on their names (resn or r.).

select basic, (resn lys,his,arg)

As a side note, on this as well as all other user lists, it is
preferred that you set a subject line which reflects the question
you're asking. Since many of us are dedicating our own time to
answering, we usually make a preselection of the mails we could
possibly provide an answer to. Mails without subject are likely to be
thrown away unread.

Cheers,

Tsjerk


On 2/23/07, Bernhard Kleine  wrote:

Hello and good morning,

being newly arrived in this list, I am a molecular biologist working
recently in endocrinology and epigenetics and living in the black forest
in the south west of germany.

Since I am not fully content with the picture quality which I can get
with Rasmol, I am trying to use PyMOL. However, since I try to adopt my
rasmol script for use in PyMOL, I am unable to find how to select
individual amino acids, or e.g. polar or basic residues. I am quite
convinced that such shortcuts exist. But either the refmanual oder the
usermanual lack mentioning any typ of aminoacids, so far as I can say
(searching with Acrobat reader).

It would be a pleasure if anyone could point me to the proper
information.

Thanks a lot

Bernhard
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Utrecht University
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F: +31-30-2537623

[PyMOL] (no subject)

[Bernhard Kleine]

Hello and good morning,

being newly arrived in this list, I am a molecular biologist working
recently in endocrinology and epigenetics and living in the black forest
in the south west of germany.

Since I am not fully content with the picture quality which I can get
with Rasmol, I am trying to use PyMOL. However, since I try to adopt my
rasmol script for use in PyMOL, I am unable to find how to select
individual amino acids, or e.g. polar or basic residues. I am quite
convinced that such shortcuts exist. But either the refmanual oder the
usermanual lack mentioning any typ of aminoacids, so far as I can say
(searching with Acrobat reader).

It would be a pleasure if anyone could point me to the proper
information.

Thanks a lot

Bernhard
-- 
Bernhard Kleine
mail b...@gmx.net
linux-user Nr. 411598

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61BF C842 4D18 6C1D 9C2A



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Re: [PyMOL] (no subject)

[gilleain torrance]

Hi,

I don't know how simple you want it, but python lets you print just like:

   print cmd.distance(a, b)

assuming that a and b are strings that are atom selections. See

  http://www.pymolwiki.org/index.php/Translate_And_Measure

for a more complex example! :)

gilleain


On 11/7/06, Giacomo Bastianelli  wrote:


Dear Users,

I would like with a simple script to export
some data regarding distances.
Do any of you know how to write an output with
all distances that I set up?

Thanks in advance

Giacomo



Giacomo Bastianelli

EIMID Ph.D Fellow (www.eimid.org)

Marie Curie EST

gbast...@pasteur.fr

Unité de Bioinformatique Structurale

Institut Pasteur

25-28 Rue de Dr.Roux

75015 Paris, France

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[PyMOL] (no subject)

[Giacomo Bastianelli]

Dear Users,
 
I would like with a simple script to export
some data regarding distances.
Do any of you know how to write an output with
all distances that I set up?
 
Thanks in advance
 
Giacomo
 

Giacomo Bastianelli

EIMID Ph.D Fellow (www.eimid.org  )

Marie Curie EST

gbast...@pasteur.fr

Unité de Bioinformatique Structurale

Institut Pasteur

25-28 Rue de Dr.Roux

75015 Paris, France

 

[PyMOL] (no subject)

[mati]

hello all
pymol draw lines between near atom with no real connection between them!
I wanted to know if there is a way to prevent pymol of making the  
bonds (lines)

between atom and that pymol will connect atom only by a specific request
(like a connect line in the pdb file)
CONECT  416  778  (which means connect atoms 416 778)
thank you very much
mati

Re: [PyMOL] (no subject)

[Donglu Xie]

Hi Warren,

Thank you very much. Under the help of one of PyMol users, at last figure
out the right configuration. It needs "AllowDFPStereo" on in LCD and
""XineramaStereoFlipping" on in CRT. Following is the part I changed:

== begin the partial xorg.conf 

# for CRT
Section "Device"
Identifier  "Videocard0"
Driver  "nvidia"
VendorName  "Videocard vendor"
BoardName   "NVIDIA Quadro FX3400"
BusID   "PCI:5:0:0"
Option  "Stereo" "3"
Screen 0
Option "UBB"   "1"
Option "NoPowerConnectorCheck"
Option   "XineramaStereoFlipping" "1"
EndSection


# for LCD
Section "Device"
Identifier  "Videocard1"
Driver  "nvidia"
VendorName  "Videocard vendor"
BoardName   "NVIDIA Quadro FX3400"
BusID   "PCI:5:0:0"
Screen  1
Option "UBB"   "1"
Option "Stereo"   "3"
Option "NoPowerConnectorCheck"
Option   "AllowDFPStereo" "1"
EndSection

== end 

Bests,
-Donglu


> Donglue,
>
> My suspicion is that stereo and windows spanning multiple displays may
> be mutually exclusive, possibly because the displays aren't necessarily
> sync'd on the VBL, or because the LCD context may not be stereo-capable.
>
> Cheers,
> Warren
>
> -Original Message-
> From: pymol-users-boun...@lists.sourceforge.net
> [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Donglu
> Xie
> Sent: Saturday, July 15, 2006 9:36 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] (no subject)
>
> Hi Dear Pymol-users,
>
> Sorry about this long message. I am struggling to configure X Windwo to
> enable stereo.
>
> Two monitors are connected with the NVIDIA GPU Quadro FX 3400 card. One
> monitor is ViewSonic VP2030b LCD, another is ViewSonic G225fb CRT. Try
> to
> configure X widnow to enable stereo with Xinerama on so that application
> can cross the screen boundaries. There is no any error or warning
> message
> in Xorg.0.log (xorg.conf is below). However, when tried to run stereo
> application, such as PyMol or Coot, it doesn't work. It came out with
> different error messages.
>
> In PyMol, error is following:
> X Error of failed request:  BadValue (integer parameter out of range for
> operation)
>   Major opcode of failed request:  78 (X_CreateColormap)
>   Value in failed request:  0x0
>   Serial number of failed request:  14
>   Current serial number in output stream:  16
>  PyMOL: abrupt program termination.
>
> In Coot, the error is
> Gdk-ERROR **: BadValue (integer parameter out of range for operation)
>   serial 390 error_code 2 request_code 78 minor_code 0
>
> Googling doesn't get much useful information.
>
> I also tried to use Twinview. The stereo works well. However, the
> application interface cannot move cross the screen boundaries.
>
> The Xinerama enabled setting works perfect with systems connected with a
> CRT and a LCD monitors
> (2.4.20-6smp #1 SMP Thu Feb 27 09:36:38 EST 2003 i686 athlon i386
> GNU/Linux)
> (NVIDIA Quadro4 750 XGL).
>
> The system with stereo problem is
> 2.6.9-34.0.1.ELlargesmp #1 SMP Wed May 17 17:19:07 EDT 2006 x86_64
> x86_64
> x86_64 GNU/Linux
>
> xorg.conf and partial of Xorg.0.log files is below.
>
> Any help or suggestion is appreciated.
> Best,
> -Donglu Xie
>
> xorg.conf is following
> =
> Section "ServerLayout"
> Identifier "Dual Layout"
> Option "Xinerama" "true"
> Screen 0  "Screen0"
> Screen 1 "Screen1" RightOf "Screen0"
> InputDevice"Mouse0" "CorePointer"
> InputDevice"Keyboard0" "CoreKeyboard"
> EndSection
>
> Section "Files"
> RgbPath  "/usr/X11R6/lib/X11/rgb"
> FontPath "unix/:7100"
> EndSection
>
> Section "Module"
> Load  "dbe"
> Load  "extmod"
> Load  "fbdevhw"
> Load  "glx"
> Load  "glx"
> Load  "record"
> Load  "freetype"
> Load  "type1"
> #   Load  "dri"
> EndSection
>
> Section "InputDevice"
>

[PyMOL] (no subject)

[Donglu Xie]

Hi Dear Pymol-users,

Sorry about this long message. I am struggling to configure X Windwo to
enable stereo.

Two monitors are connected with the NVIDIA GPU Quadro FX 3400 card. One
monitor is ViewSonic VP2030b LCD, another is ViewSonic G225fb CRT. Try to
configure X widnow to enable stereo with Xinerama on so that application
can cross the screen boundaries. There is no any error or warning message
in Xorg.0.log (xorg.conf is below). However, when tried to run stereo
application, such as PyMol or Coot, it doesn't work. It came out with
different error messages.

In PyMol, error is following:
X Error of failed request:  BadValue (integer parameter out of range for
operation)
  Major opcode of failed request:  78 (X_CreateColormap)
  Value in failed request:  0x0
  Serial number of failed request:  14
  Current serial number in output stream:  16
 PyMOL: abrupt program termination.

In Coot, the error is
Gdk-ERROR **: BadValue (integer parameter out of range for operation)
  serial 390 error_code 2 request_code 78 minor_code 0

Googling doesn't get much useful information.

I also tried to use Twinview. The stereo works well. However, the
application interface cannot move cross the screen boundaries.

The Xinerama enabled setting works perfect with systems connected with a
CRT and a LCD monitors
(2.4.20-6smp #1 SMP Thu Feb 27 09:36:38 EST 2003 i686 athlon i386 GNU/Linux)
(NVIDIA Quadro4 750 XGL).

The system with stereo problem is
2.6.9-34.0.1.ELlargesmp #1 SMP Wed May 17 17:19:07 EDT 2006 x86_64 x86_64
x86_64 GNU/Linux

xorg.conf and partial of Xorg.0.log files is below.

Any help or suggestion is appreciated.
Best,
-Donglu Xie

xorg.conf is following
=
Section "ServerLayout"
Identifier "Dual Layout"
Option "Xinerama" "true"
Screen 0  "Screen0"
Screen 1 "Screen1" RightOf "Screen0"
InputDevice"Mouse0" "CorePointer"
InputDevice"Keyboard0" "CoreKeyboard"
EndSection

Section "Files"
RgbPath  "/usr/X11R6/lib/X11/rgb"
FontPath "unix/:7100"
EndSection

Section "Module"
Load  "dbe"
Load  "extmod"
Load  "fbdevhw"
Load  "glx"
Load  "glx"
Load  "record"
Load  "freetype"
Load  "type1"
#   Load  "dri"
EndSection

Section "InputDevice"
Identifier  "Keyboard0"
Driver  "kbd"
Option  "XkbModel" "pc105"
Option  "XkbLayout" "us"
EndSection

Section "InputDevice"
Identifier  "Mouse0"
Driver  "mouse"
Option  "Protocol" "IMPS/2"
Option  "Device" "/dev/input/mice"
Option  "ZAxisMapping" "4 5"
Option  "Emulate3Buttons" "yes"
EndSection

Section "Monitor"
Identifier   "LCD"
VendorName   "Viewsonic"
ModelName"VP2030b"
HorizSync24.0 - 92.0
VertRefresh  50.0 - 85.0
Option  "dpms"
EndSection

Section "Monitor"
Identifier   "CRT"
VendorName   "Viewsonic"
ModelName"G225fb"
HorizSync30.0 - 130.0
VertRefresh  50.0 - 160.0
Option  "dpms"
Modeline "1600x1200_99.00"  277.61  1600 1728 1904 2208  1200 1201
1204 1270  -HSync +Vsync
EndSection

Section "Device"
Identifier  "Videocard0"
Driver  "nvidia"
VendorName  "Videocard vendor"
BoardName   "NVIDIA Quadro FX3400"
#VideoRam262144
BusID   "PCI:5:0:0"
Option  "Stereo" "3"
Screen 0
Option "NoPowerConnectorCheck"
EndSection

Section "Device"
Identifier  "Videocard1"
Driver  "nvidia"
VendorName  "Videocard vendor"
BoardName   "NVIDIA Quadro FX3400"
#VideoRam262144
BusID   "PCI:5:0:0"
Screen  1
Option "NoPowerConnectorCheck"
EndSection

Section "Screen"
Identifier "Screen1"
Device "Videocard1"
Monitor"LCD"
DefaultDepth 24
SubSection "Display"
   Viewport   0 0
Depth 24
Modes"1600x1200" "1400x1050" "1280x1024" "1280x960"
"1152x864" "1024x768" "800x600" "640x480"
EndSubSection
EndSection

Section "Screen"
Identifier "Screen0"
Device "Videocard0"
Monitor"CRT"
DefaultDepth 24
SubSection "Display"
Viewport 0 0
Depth 24
Modes"1600x1200_99.00" "1600x1200" "1400x1050"
"1280x1024" "1024x768" "800x600" "640x480"
EndSubSection
EndSection

 end of xorg.conf ==


Partial of Xorg.0.log

(II) Module glx: vendor="NVIDIA Corporation"
(II) Module nvidia: vendor="NVIDIA Corporation"
(II) NVIDIA dlloader X Driver  1.0-8756  Wed Mar 29 15:14:16 PST 2006
(II) NVIDIA Unified Driver for all Supported NVIDIA GPUs
(--) Chipset NVIDIA GPU found
(--)

[PyMOL] (no subject)

[Gabrielle Malo]

 Hello all, 

I am a new PyMOL user trying to prepare figures for publication.  I'm confused 
about the difference between the isomesh level of the 'mesh' in PyMOL and the 
contour level of the electron density map that I read in from CCP4.  For 
example, for one of my figures I created a 3sigma Fo-Fc omit map and read it in 
to PyMOL.  In order to make the density lovely I used the 'map_double' command  
and created a second 'mesh'.  I then adjusted each of these 'mesh' to a 'level' 
of 4.  Does this mean that my omit map is actually now contoured to 4sigma, or 
are the two not related?  

Thanks for any help,

Gabrielle

[PyMOL] (no subject)

[O. J. Ganesh]

 
 
Hey again PyMOL gurus,

>* O. J. Ganesh  [2006-05-18 16:09] wrote:
>> 
>> Hey PyMOL gurus:
>> 
>> I have a 'perfect' helix. Is there some way to 'loosen' all of the
>> angles in the helix so instead of 3.6 residues per turn, I could
>> have, say, 8 residues per turn. My goal is to make the helix more
>> 'coil-like'. Is this possible?
>
>Well, if you know the phi/psi angles you like, then you could just build
>it and specify those angles with my build_seq.py script:
>
>http://adelie.biochem.queensu.ca/~rlc/work/pymol/build_seq.py
>
>You can specify the phi, psi angles on the command line. Alternatively,
>you can create a file of resname, phi, psi and build it with:
>
>http://adelie.biochem.queensu.ca/~rlc/work/pymol/build_seq_phi_psi.py
>
>if you don't want the phi/psi angles to be the same for every residue.
>
>Cheers,
>Rob
 
Thanks Robert Campbell,
I've actually used the build_seq_phi_psi.py script before, and it is WONDERFUL! 
  I can (and probably will) use it in this case also.   I was just checking to 
see if there wasn't an easier way to do this within PyMOL...   Something that 
would take a selection of a pdb structure and generally 'loosen' or 'relax' it. 
  (I know it sounds vague.)
 
Thanks again!

[PyMOL] (no subject)

[Orla O'Sullivan]

 

Hi  all

This probably a very stupid question but its driving me mad. I have
produced two Raster 3D scences using molscript and have loaded them into
pymol. 

What I want to do is to be able to move them on screen independent of
each other. Is this possible?

 

Regards

Orla

 

Dr.Orla O'Sullivan

Research Officer

Biotechnology

 

 

Moorepark Food Research Centre
Teagasc

Moorepark
Fermoy, Co. Cork
Ireland

 

Tel:   +353 - (0)25 - 42344

 

Re: [PyMOL] (no subject)

[Andrea Spitaleri]

Hi,
for this purpose I have used caver program. You can download it free
of charge from here  http://loschmidt.chemi.muni.cz/caver/download.php

I hope this help

Regards

andrea

2006/3/27, srilath...@jubilantbiosys.com :
> dear sir
> iam a pymol user, do we can find area & volume of active site in
> pymol
> if we can, just tell me how to do it
> thanking you
> srilatha
> Thanks & Regards
> srilatha potlapelly
> MSc Biotechnology
>  ---
> This SF.Net email is sponsored by xPML, a groundbreaking scripting language
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> https://lists.sourceforge.net/lists/listinfo/pymol-users


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

[PyMOL] (no subject)

[Srilatha_P]

dear sir iam a pymol user, do we can find area & volume of active site in pymol if we can, just tell me how to do it thanking you srilathaThanks & Regardssrilatha potlapellyMSc Biotechnology

Re: [PyMOL] (no subject)

[gilleain torrance]

Hi,

I found out how to do ... something ... like this the other day.

RE: [PyMOL] (no subject)

[EPF (Esben Peter Friis)]

Hi Blanton

You are probably looking for the "symexp" command. I don't remember the exact 
syntax, but there is a small help text. You can also try to search the mail 
archive.


Best wishes

Esben


-Original Message-
From: pymol-users-ad...@lists.sourceforge.net on behalf of Blanton Tolbert
Sent: Sat 2006-03-04 15:01
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] (no subject)
 
Hi pymol community

I would like to recapitulate the crystal packing arrangement of a  
protein structure to look for neighbor interactions.  Is it possible  
to do this in pymol?  If so, please provide me some insight.

Thanks,


Blanton Tolbert
Graduate Student
University of Rochester
Biophysics and Structural Biology
585-275-5189
blanton_tolb...@urmc.rochester.edu





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[PyMOL] (no subject)

[Blanton Tolbert]

Hi pymol community

I would like to recapitulate the crystal packing arrangement of a  
protein structure to look for neighbor interactions.  Is it possible  
to do this in pymol?  If so, please provide me some insight.


Thanks,


Blanton Tolbert
Graduate Student
University of Rochester
Biophysics and Structural Biology
585-275-5189
blanton_tolb...@urmc.rochester.edu

Re: [PyMOL] (no subject)

[Andrea Spitaleri]

Hi
try align or fit

regards

andrea

2006/3/3, srilath...@jubilantbiosys.com :
> dear all
> can we superimpose structures in pymol
> Thanks & Regards
> srilatha potlapelly
> MSc Biotechnology
> Drug discovery,
> #450,4th D Main, 12th cross,
> Mahalakshmipuram - 560086
> Bangalore
> Office: +9180-23495461-64  Extn.-1029
>  ---
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> https://lists.sourceforge.net/lists/listinfo/pymol-users


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

[PyMOL] (no subject)

[Srilatha_P]

dear all can we superimpose structures in pymolThanks & Regardssrilatha potlapellyMSc BiotechnologyDrug discovery, #450,4th D Main, 12th cross, Mahalakshmipuram - 560086 Bangalore Office: +9180-23495461-64  Extn.-1029

[PyMOL] (no subject)

[D . Bryan Prince]

To all:

I am new to PyMol, and to structure programs in general. I am trying to 
build a beta sheet from a peptide molecule in the pdb. I can't seem to 
load more than one molecule at a time, and I do not see any 
instructions related to it in the manual. I am running version 0.98 
beta 32 on a Mac G5 with the OS X (10.3.9) operating system. Any help 
would be greatly appreciated.


Many thanks,
Bryan Prince

RE: [PyMOL] (no subject)

[Warren DeLano]

Yes, the create command provide you with this ability, though at the end
of the process you end up with a new object.

create new_object, old_object1 | old_object2

In some cases, new_object can be the same name as either old_object1 or
old_object2:

create old_object1, old_object1 | old_object2

Also note that the vertical bar (the "or" operator) is optional in
recent betas, so

create old_object1, old_object1 old_object2

becomes legal.

Cheers,
Warren

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

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

> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net 
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
> Joseph Fernandez
> Sent: Sunday, September 25, 2005 11:19 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] (no subject)
> 
> There is a very useful functionality in Sybyl, whereby the 
> user can "merge" a residue from one molecular area, into 
> another molecular area.  The residue then becomes a part of 
> the latter moleculear area, without deleting it.  I wonder 
> whether there is such a functionality in PyMol.  
> 
> As an example, I have created a new object, consisting of 
> several residues that I have extracted from the active site 
> of a protein (using the create command). 
> I then deleted these residues from the original object 
> (active site of protein).  I now want to merge an additional 
> residue from the active site into the ligand object, and 
> delete the residue from the active site, but without deleting 
> the ligand object.
> 
> Any assistance on this matter would be appreciated.
> 
> Joe
> 
> 
>   
>   
> __
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> 
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> 

[PyMOL] (no subject)

[Joseph Fernandez]

There is a very useful functionality in Sybyl, whereby
the user can "merge" a residue from one molecular
area, into another molecular area.  The residue then
becomes a part of the latter moleculear area, without
deleting it.  I wonder whether there is such a
functionality in PyMol.  

As an example, I have created a new object, consisting
of several residues that I have extracted from the
active site of a protein (using the create command). 
I then deleted these residues from the original object
(active site of protein).  I now want to merge an
additional residue from the active site into the
ligand object, and delete the residue from the active
site, but without deleting the ligand object.

Any assistance on this matter would be appreciated.

Joe




__ 
Yahoo! for Good 
Donate to the Hurricane Katrina relief effort. 
http://store.yahoo.com/redcross-donate3/ 

RE: [PyMOL] (no subject)

[Warren DeLano]

Yi,

To stuff a bunch of identical object in one PDB file, you need to assign
a unique segment ID to each one.  For example:

load $PYMOL_PATH/test/dat/1tii.pdb

symexp s,1tii,1tii,5

names=cmd.get_names()
for a in range(len(names)): cmd.alter(names[a],"segi="+str(a))

save multi.pdb

Cheers,
Warren

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

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

> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net 
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of yi zhang
> Sent: Sunday, July 24, 2005 8:43 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] (no subject)
> 
> Hi, everyone,
> 
> I used symexp command in pymol to generate symmetry-related 
> molecule, something like:
> 
> cmd.symexp('sym', 'obj', 'obj',10 )
> 
> of course, I can manually save each symmetry-related molecule 
> to *.pdb file by clicking save molecule button, but how can I 
> write a script to save all of them or part of them? the 
> symmetry-related objects are not appendable.
> 
> thanks!
> 
> yi
> 
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Re: [PyMOL] (no subject)

[lieven]

On Sunday 24 July 2005 05:42, yi zhang wrote:
> cmd.symexp('sym', 'obj', 'obj',10 )
>
> of course, I can manually save each symmetry-related
> molecule to *.pdb file by clicking save molecule
> button, but how can I write a script to save all of
> them or part of them? the symmetry-related objects
> are not appendable.

I have used something like this in the past:
#--
# get symmetry mates
objs = [ n for n in cmd.get_names() if n[0:3]=="sym" ]
for obj in objs:
if cmd.get_type(obj)!="object:molecule":
print "Something's wrong!"
else:
cmd.save(obj+".pdb",obj)
#--

Hope this helps,
-- 
Lieven Buts
Ultrastructure Laboratory
Vrije Universiteit Brussel

[PyMOL] (no subject)

[yi zhang]

Hi, everyone,

I used symexp command in pymol to generate
symmetry-related molecule, something like:

cmd.symexp('sym', 'obj', 'obj',10 )

of course, I can manually save each symmetry-related
molecule to *.pdb file by clicking save molecule 
button, but how can I write a script to save all of
them or part of them? the symmetry-related objects 
are not appendable.

thanks!

yi

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Re: [PyMOL] (no subject)

[Joel Tyndall]

Check out the post on "High end graphics". This will solve the problem. 
Basically you can ray-trace your molecule at a resolution bigger tahn 
teh screen size and then cut it down afterwards effectively generating a 
high resolution graphic from a 72 dpi starting point


Cheers

J

Kolli, Madhavi wrote:


Hi,

I’ve just started using PyMol for making some figures. I’m very happy 
that it is so easy to use. However the resolution of my pictures is 
very bad even after rendering them. When I print them they are very 
pixellated. I’m sure there is something I’m not doing right. Any help, 
suggestions will be appreciated.


Thanks.

Regards,

Madhavi Kolli

Graduate Student

UMass Medical School Worcester



--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
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[PyMOL] (no subject)

[Kolli, Madhavi]

Hi,

I've just started using PyMol for making some figures.  I'm very happy
that it is so easy to use.  However the resolution of my pictures is
very bad even after rendering them.  When I print them they are very
pixellated.  I'm sure there is something I'm not doing right.  Any help,
suggestions will be appreciated.

Thanks.

Regards,

Madhavi Kolli

Graduate Student

UMass Medical School Worcester

[PyMOL] (no subject)

[Alexey V Paramonov]

Hi,

I have a problem with PyMOl 0.97 viewing pdb file with several models
(MODEL 1...ENDMDL)
I can upload somewhere (or attach?) the screenshot + pdb file to show it 
(~1.3 Mb).

[PyMOL] (no subject)

[James Stevens]

Hi,
The lab I am part of now has the licensed MacPymol incentive product. 
In response to the brilliant crystallography on OS X website maintained 
by Bill Scott, he recommends using a Powermate dial (Griffin 
Technology). I would like to follow in his footsteps, however the 
instructions he provides for configuring the system 
(http://chemistry.ucsc.edu/%7Ewgscott/xtal/powermate_pymol_osx.html) 
requires me to edit my .pymolrc file. As far as I can tell, I have no 
need for a .pymolrc file with this version and if I create one, all I 
seem to get is syntax errors.


If anyone can help me as I have little to no experience with python 
scripting.


Many thanks in advance
James 

[PyMOL] (no subject)

[ELHAM MOHAMMADI]

Hello!
I have 2 questions:
1) What is the correct/common email address to send your questions on PyMOL?
2) I have downloaded PyMOL on a PC(microsoft windows XP)using the instructions 
posted on the PyMOL site. But I am not able to get input files form the 
Internet--I simply wanted to go to the PUBMED and get the structure of a 
protein from PUBMED/web directly into the PyMOL. SO going to the external GUI 
of PyMOL , then File, then Open did not give me the option of opening the 
internet eventhough it is on our desktop. I could open other files such as :my 
computer, my files, my network places, just not the Internet!!! Does anybody 
know how to do it?
Thank you for your time and consideration,
ELham

RE: [PyMOL] (no subject)

[Warren DeLano]

Christian,

This isn't implemented yet, but it is on the to do list.

Cheers,
Warren
 

> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net 
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
> Christian Rummey
> Sent: Thursday, April 22, 2004 2:35 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] (no subject)
> 
> 
> hi ppl,
> 
> is there a way to sort the list of objects/selections in the 
> panel on the right side other than loading/selecting stuff in 
> a specific order?
> 
> simple example: I compare several ligands in a specific site, 
> and save the data as pymol sessions; after adding new 
> ligands//site conformations I'd like to sort the sites 1st, 
> then the ligands. 
> 
> any hints?
> 
> thanks a lot,
> christian
> 
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[PyMOL] (no subject)

[Christian Rummey]

hi ppl,

is there a way to sort the list of objects/selections in the panel on the
right side other than loading/selecting stuff in a specific order?

simple example: I compare several ligands in a specific site, and save the
data as pymol sessions; after adding new ligands//site conformations I'd
like to sort the sites 1st, then the ligands. 

any hints?

thanks a lot,
christian

-- 
NEU : GMX Internet.FreeDSL
Ab sofort DSL-Tarif ohne Grundgebühr: http://www.gmx.net/dsl

[PyMOL] (no subject)

[xiaofeng qian]

Hi,everybody:
 Is there someway so that I can generate several asymmetry molecules from 
one asymmetry unit in pymol?

 Thank you.

Xiaofeng

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RE: [PyMOL] (no subject)

[Warren DeLano]

Mohammed,

ray width, height
  png filename.png

for example, for a 5x4 figure at 300 dpi:

ray 1600,1200
  
  png hires.png
 (or use Save image... from the File menu after the ray command)

Cheers,
Warren


> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net 
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
> Mohammad Wadud Bhuiya
> Sent: Monday, April 05, 2004 5:53 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] (no subject)
> 
> Dear pymol usres
> 
> I want to increase the resolution of the figure but how? Save 
> file is png and resolution is very poor and print quality is 
> not good. I also make CA model by xfit and save file is 
> rasted3d and it is opened by pymol and save as png but figure 
> is not good quality for its low resolution. png file save as 
> windows resolution.  Could you suggest me how to increse 
> windows resolution I mean png resolution.
> 
> Thanks in advance
> Wadud
> 
> _
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> 
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> 

[PyMOL] (no subject)

[Mohammad Wadud Bhuiya]

Dear pymol usres

I want to increase the resolution of the figure but how? Save file is png 
and resolution is very poor and print quality is not good. I also make CA 
model by xfit and save file is rasted3d and it is opened by pymol and save 
as png but figure is not good quality for its low resolution. png file save 
as windows resolution.  Could you suggest me how to increse windows 
resolution I mean png resolution.


Thanks in advance
Wadud

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Re: [PyMOL] (no subject)

[Matt Stephenson]

Hi Blanton,

Are you running the unstable tree, or have you just copied the 
pymol-0.90-2 package to stable, you either have to enable the unstable 
tree, or copy the numeric-py22 package from the unstable to stable, it 
can be found at '/sw/fink/dists/unstable/main/finkinfo/sci'


see here;

http://fink.sourceforge.net/faq/usage-fink.php#unstable

Matt

On Wednesday, Aug 20, 2003, at 12:01 Australia/Canberra, Tolbert, 
Blanton wrote:


I was attempting to install pymol 0.9 using fink and got the following 
error

message,

Failed: Can't resolve dependency "numeric-py22" for package 
"pymol-0.90-2"

(no matching packages/versions found)

Can anyone advise me on what to do to get around this?  Thanks in 
advance.



Blanton


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[PyMOL] (no subject)

[Tolbert, Blanton]

I was attempting to install pymol 0.9 using fink and got the following error
message,

Failed: Can't resolve dependency "numeric-py22" for package "pymol-0.90-2"
(no matching packages/versions found)

Can anyone advise me on what to do to get around this?  Thanks in advance.


Blanton

Re: [PyMOL] (no subject)

[Cameron Mura]

Hi Martin,
Visit Robert Campbell's repository of PyMOL scripts 
(http://adelie.biochem.queensu.ca/~rlc/work/pymol/)...where you'll find 
Python scripts  to import into PyMOL for drawing unit cell edges 
(draw_cell.py), symmetry axes (draw_symops.py), and lots of other stuff...


   Cameron



mkienetz wrote:


Dear All,

How do I show the unit cell using pymol?

Martin

Martin Kienetz
429 MSB
Department of Biochemistry
University of Alberta
Edmonton AB
T6G 2H7
(780) 492-2422



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[PyMOL] (no subject)

[mkienetz]

Dear All,

How do I show the unit cell using pymol?

Martin

Martin Kienetz
429 MSB
Department of Biochemistry
University of Alberta
Edmonton AB
T6G 2H7
(780) 492-2422

Re: [PyMOL] (no subject)

[Kristian Rother]

Fei Xu wrote:

HI! Dr. Delano:
Would you like to tell me how I can control the size of the ball, if I
pick an atom and show it like a ball?


Dear Fei Xu:

1. You select an atom
2. You display it as a ball
3. You type:
set sphere_scale = 2.0

Here, the number is the size proportional to an original size of 1.0.

Unfortunately, settings for individual objects are not functional yet.


Kristian

[PyMOL] (no subject)

[Fei Xu]

HI! Dr. Delano:
Would you like to tell me how I can control the size of the ball, if I
pick an atom and show it like a ball?
Have a nice day!
Fei

[PyMOL] (no subject)

[wgscott]

Hi Lieven:

I don't have windows pymol or access currently to a windows machine, so 
I will have to tell you how I did it on the Mac version and then hope 
it is essentially identical with windows.


I did this about 6 months ago in order to hyperlink quicktime to 
Powerpoint in XP.  I am assuming hyperlinking to Pymol would work the 
same way, since it works the same way on a Mac.  But you never know 
with Windows since 90% of the operating system seems to be dedicated to 
preventing you from using your computer.


Open up powerpoint and create a new slide.

In it put a word or picture or something.

Then select that word or picture or whatever it is.

Go to insert > hyperlink

and then put in the full file hierarchy path to your pymol application


Then when you are in presentation mode, you click on this and it starts 
pymol.  On XP it seemed to embed it in situ (at least when I was using 
quicktime).  In OS X it changes over to the pymol display.  That's the 
basis for my claim that it works better in XP.  I apologize if this 
doesn't.


HTH,

Bill Scott




William G. Scott

Associate Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA

phone:  +1-831-459-5367 (office)
   +1-831-459-5292 (lab)
fax: +1-831-4593139  (fax)

RE: [PyMOL] (no subject)

[DeLano, Warren]

Question 1, CA-trace:  

show ribbon
set ribbon_sampling=1

(NOTE: requires all main chain atoms to be present, but not necessarily visible 
-- CA-only models will be supported later on).

Question 2, Alignment of structural homologs (requires version 0.82).

load prot1.pdb
load prot2.pdb
align prot1,prot2ca

This will perform a sequence alignment and then an iterative alpha-carbon 
superposition of matched residues.

Cheers,
Warren


-Original Message-
From: Craig Smith [mailto:boiler...@mac.com]
Sent: Wednesday, October 09, 2002 3:19 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] (no subject)


Hello, 


On the advice of a friend, I recently downloaded the OSX beta version of PyMOL. 
So far I'm very,very impressed. I have two questions: 1. How do you display a 
simple CA trace. I saw the selection for a backbone trace. 2. I want to rms-fit 
two structural homologs. How is this done in PyMOL? I tried using the fit 
command and kept getting errors. 


Thanks for you help 



Craig L. Smith, Ph. D. 
Molecular Microbiology 
Washington University School of Medicine 
660 South Euclid Box 8230 
Voice: (314) 362-9054 
Fax: (314) 362-1232 
e-mail: sm...@borcim.wustl.edu 

[PyMOL] (no subject)

[Craig Smith]

Hello,

On the advice of a friend, I recently downloaded the OSX beta version 
of PyMOL.  So far I'm very,very impressed.  I have two questions:  1.  
How do you display a simple CA trace. I saw the selection for a 
backbone trace.  2.  I want to rms-fit two structural homologs.  How is 
this done in PyMOL?  I tried using the fit command and kept getting 
errors.


Thanks for you help


Craig L. Smith, Ph. D.
Molecular Microbiology
Washington University School of Medicine
660 South Euclid Box 8230
Voice: (314) 362-9054
Fax: (314) 362-1232
e-mail: sm...@borcim.wustl.edu

[PyMOL] (no subject)

[Sona Vasudevan]

Hello All,

Need your help:

I would like to overlay a cartoon representation onto a surface
representation and would like to color certain residues that show up on
the surface representation. This is what I did and recall doing awhile ago but 
it
isn't working now. I would appreciate knowing what i am doing wrong.

Step 1: load temp.pdb

step 2: create cpy=temp

show surf, cpy

set transparency=0.5, cpy

Then I go on to color individual residues:

select t1=(resi 42)

Now I want residue 42 to be coloured say red on the surface 1.e object
cpy. Ofcourse overlaying is not the problem.

 Thanks much,

sona

Re: [PyMOL] (no subject)

[Warren L. DeLano]

On Sun, 17 Feb 2002, Nat wrote:

> From an earlier reply...
> > The easiest way to use PyMOL as a module is to use PyMOL as your Python
> > interpreter.  It isn't trivial to launch PyMOL from within a running
> > Python interpreter, but it can be done under unix (only).  See pymol.com
> > and modules/launch_pymol.py for an example of how to do it.
> 
> Got this working.  Now, I'm trying to create movie frames from the
> command line; I've got two systems I've tried this on, one SuSE
> 7.something (compiled manually), the other RedHat 7.2 (rpms).  I'm
> wondering whether this is even possible.  I've modified pymol.com to
> launch my script instead; what it does is this:
> 

You shouldn't (need to) modify any of the launch
scripts.  Just use the "-c" option to get
PyMOL running in command-line only mode.
(see "help launching for all the command-line options")

pymol.com -c script.py
pymol.com -c script.pml

Cheers,
Warrren

[PyMOL] (no subject)

[Nat]

Re: [PyMOL] (no subject)

[Warren L. DeLano]

On Thu, 22 Nov 2001, Sona Vasudevan wrote:
 
> Hi!
> 
> Just wondering if there is a way to save a pymol session like in Insight
> and setor if I want to get back to it.

PyMOL isn't quite as sophisticated as Insight II in this respect, however
the logging features can achieve session-like behavior.  It works sort-of
like Grasp but with log files that are much more straight-forward to edit
and modify, since they are written in the PyMOL command language (.pml
files) or using PyMOL's Python API (.pym files).  Example:

Select "Log..." from the file menu immediately after you start PyMOL to
start writing a ".pml" or ".pym" log file.  Go about your business.

When done, press the "Get View" button and quit the program.

To resume your "session", launch PyMOL and select "Resume..." from the
file menu.  Open your log file and *PRESTO* PyMOL should be in
the same state as when you left. Any additional actions you then take will
be appended on to the log.  

Note that any "ray", "png", or "save" operations will be repeated when you
resume the log file.  Thus, you may want to edit the log file and
remove these commands with a text editor (Notepad on Windows) before
resuming.  Perhaps it would be nice to have a setting which ignores this
kinds of commands when resuming.  Hmm...

- Warren

PS. There is only bug I know of in the logging feature of 0.68 which
affects conformational editing when logging to .pml files.  It will be
fixed in the next release, but for now just log to .pym files if you
are going to edit conformations.



 

[PyMOL] (no subject)

[Sona Vasudevan]

Hi!

Just wondering if there is a way to save a pymol session like in Insight
and setor if I want to get back to it.

Thanks.

sona




Sona Vasudevan
National Center for Biotechnology Information
National Library of Medicine
National Institutes of Health,Bldg. 38A, Rm. B2N21I,
8600 Rockville pike, Bethesda, MD 20894, USA 
Voice: (301)594-3154; Home: (703)-893-8424
Email: vasud...@ncbi.nlm.nih.gov or sona.vasude...@nih.gov
-