Re: [PyMOL] Installing in Linux

[Robert Campbell]

Hello Peter,

Which Linux distribution are you using?  If you are using one of the 
Debian-based versions like Ubuntu, then PyMOL is likely available in the 
distribution's repository.  Then you could use the package management system to 
install it or simply type in a terminal window:

  sudo apt-get install pymol

Depending on which distribution you are using there may be other steps involved 
to allow it to find PyMOL.

Cheers,
Rob

On Mon, 2022-02-14 13:05  -0500,  Peter Kahn  wrote:

> Greetings,
> 
> I've downloaded the Pymol package of executable files and had no
> trouble installing in Windows but don't know how to proceed in Linux?
>  Can anyone point me in the right direction?
> 
> Thanks,
> Peter



-- 
Robert L. Campbell, Ph.D.
Undergraduate Chair (Acting), Biochemistry Program
Academic Advisor, BHSc Program
Assistant Professor, Dept. of Biomedical & Molecular Sciences, Botterell Hall 
Rm 644
Queen's University, Kingston, ON K7L 3N6  Canada
tel: 613-533-6821   http://pldserver1.biochem.queensu.ca/~rlc


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Re: [PyMOL] list_hb.py

[Robert Campbell]

Hi Evgeny and Chen,

Unfortunately, if Chen wants the list of atoms that form H-bonds, "distance" 
only provides a displayed object and only returns the average distance between 
all atoms.  Also unfortunately, that script list_hb.py (which I wrote) uses the 
find_pairs function which warns that it "only checks atom orientation, not atom 
type" (https://pymolwiki.org/index.php/Find_pairs).  It is difficult therefore 
to provide list_hb.py with two selections that can only result in real H-bonds 
without actually figuring out for yourself which pairs of atoms should H-bond!

Cheers,
Rob

On Thu, 2021-04-08 16:50  +0200,  Evgeny Osipov  wrote:

> Hi Chen,
> you can use distance command or cmd.distance for scripting purposes.
> Just specify mode 2 in order to search for polar contacts:
> https://pymolwiki.org/index.php/Distance
> 
> пн, 22 мар. 2021 г. в 18:53, Chen, Qiang :
> 
> > Hi, Pymol Users,
> >
> > I used this script to find hydrogen-bond in protein, list_hb.py.
> >
> > list_hb all, all, write_distances_file=hb
> >
> > I find there are some pairs are clearly not hydrogen bonds, e.g.
> > A/VAL`257/O/774A/MET`261/O/8342.87
> >
> > Also, the angle is not right for certain pair
> >
> > A/HIS`400/NE2/2977B/GLN`403/OE1/70932.66
> >
> > In the protein, the angle between NE2-H-OE1 is 100.8 deg
> >
> > Any suggestion to find out the correct hydrogen-bonding pairs?
> >
> > Thanks!
> > ___
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> > Unsubscribe:
> > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> >  



-- 
Robert L. Campbell, Ph.D.
Academic Advisor, BHSc Program
Assistant Professor, Dept. of Biomedical & Molecular Sciences, 
Queen's University, Kingston, ON K7L 3N6  Canada
Botterell Hall Rm 644 Tel: 613-533-6821
  http://pldserver1.biochem.queensu.ca/~rlc


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Re: [PyMOL] How to iterate commands in pymol

[Robert Campbell]

Hi Zuben,

You need to import the colorbyrmsd.py script within your script, then you can 
call it that way.  For example your script could say:

import colorbyrmsd as cbr

for obj in seleobjs:
  cmd.enable(obj)
  cbr.colorbyrmsd(obj,target)

Cheers,
Rob

On Sat, 2020-10-31 20:36  +,  "Brown, Zuben"  
wrote:

> Hi,
> 
> I'd like to iterate using a script in pymol but one of the commands
> I'd like to use does not have an associated cmd.API. For example, how
> do I run:
> 
> for obj in seleobjs:
> cmd.enable(obj)
> colorbyrmsd(obj, target)   <--- This third line doesn't work since
> colorbyrmsd does not have a cmd.colorbyrmsd.
> 
> Is there a way I can run something like:
> cmd.executecommand("colorbyrmsd {0}, target".format(obj))  ?
> 
> Best regards,
> 
> Zuben



-- 
Robert L. Campbell, Ph.D.
Academic Advisor, BHSc Program
Assistant Professor, Dept. of Biomedical & Molecular Sciences, 
Queen's University, Kingston, ON K7L 3N6  Canada
Botterell Hall Rm 644 Tel: 613-533-6821
  http://pldserver1.biochem.queensu.ca/~rlc


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Re: [PyMOL] Effect of different align method

[Robert Campbell]

Hello Sunyeping,

I would first point out that if you align on chain A of each molecule, then 
chain B of ASFV aligns with chain C of MTUB and vice versa.  In other words you 
don't have the same assignment of chain ids in your trimer.  The alignment of 
just alpha carbons of chain A with "align" gives an RMSD of 1.78 Å for 81 atoms 
and for "super" gives an RMSD of 1.746 Å for 81 atoms. That may be the best 
that you can do, but if you want to align the whole trimer than you need to 
rename chain B to chain C and chain C to chain B for one of your molecules.

You can do that renaming within PyMOL with these commands:

PyMOL>alter MTUB_trimer & c. B, chain="D"
PyMOL>alter MTUB_trimer & c. C, chain="B"
PyMOL>alter MTUB_trimer & c. D, chain="C"

(I'm just using "D" as an intermediate name here)

If you do that, then aligning all alpha carbons gives an RMSD of 2.189 Å for 
"align" and 1.845 Å for "super".

Cheers,
Rob

On Wed, 2020-06-17 21:04  +0800,  sunyeping via PyMOL-users 
 wrote:

> Hello Julien Cappèle,
>Thank you for your response. I didn't mean to keep the input file
> in secrete. I have changed the access right to them, so you can
> download them freely. Best, Yeping Sun
> --
> From:Julien CAPPELE 
> Sent At:2020 Jun. 17 (Wed.) 17:05
> To:孙业平 
> Subject:Re: [PyMOL] Effect of different align method
> 
> Hello Sunyeping,
> 
> I would suggest you to try TM-align, and a very good way to use it
> for multi-protein alignment is to use their server mTM-align.
> TM-align is a very robust alignment tool that will in most of the
> case, give you a better structural based alignment with low to zero
> input from the sequence.
> https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fyanglab.nankai.edu.cn%2FmTM-align%2Fdata=02%7C01%7Crobert.campbell%40queensu.ca%7C4e290e0f1c4044d3b1fc08d812bf8cca%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279961201881850sdata=EOgyXD4A%2FemFaZHj6eRrx1h3nc%2BoCOHr94cFzpmIE3o%3Dreserved=0
>  
> 
> Also, if you are not working on secret stuff, you can give me access
> so I can rework the output files from mTM-align server to give you a
> RMSD-colored alignment in PyMOL.
> 
> On PyMOL only, I didn't try to implement TM-align because I use
> Windows, but the developers said that a linux implementation could be
> possible if you are a bit familiar with compiling softwares.
> 
> -
> Julien Cappèle
> Doctorant - 2ème année - ED C2MP
> Université de Lorraine
> CRM² - UMR CNRS 7036
> julien.capp...@univ-lorraine.fr
> Tel: (+33)6 99 18 59 03
> -
> 
> Le mer. 17 juin 2020 à 05:06, sunyeping via PyMOL-users
>  a écrit : Dear pymol users,
> 
> I am trying to align two very similar trimeric molecules. I tried
> different alignment commands including "align", "cealign" and
> "super", but none of them gives satisfying effect. Athough the
> backbone conformations and orientations of two two molecules look
> very similar, there are obvious displacements between them after
> alignment with these three commands. The rmsd of the two molecules
> for these three methods are 2.250, 4.682, 2.206 and 2.206,
> respectively. I wonder whether there is any better alignment command
> or there are any parameters that can be passed to these three
> alignment commands to improve the effects. Could you help me check
> this? The pdb files of these two molecules, the image for the two
> molecules after using "super" command, and the alignment effect in
> the publication I mentioned can be found at the following link.
> 
> https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1ff3XgTexgdul-SezUz75dVoCx2cL5YPL%2Fview%3Fusp%3Dsharingdata=02%7C01%7Crobert.campbell%40queensu.ca%7C4e290e0f1c4044d3b1fc08d812bf8cca%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279961201881850sdata=72dx0AyAPoHLvV4iXbEhmoGY18cXymzJRRWUqC7gdjE%3Dreserved=0
> 
> With many thanks.
> 
> ___
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> 



-- 
Robert L. Campbell, Ph.D.
Academic Advisor, BHSc Program
Assistant Professor, Dept. of Biomedical & Molecular Sciences, 
Queen's University, Kingston, ON K7L 3N6  Canada

Re: [PyMOL] hydrogen bond list for a series of files

[Robert Campbell]

Hi,

I would make one minor change to your script -- the command "run list_hb.py" 
needs to be run only once at the beginning of the script so:

# multiple_hb.py
from pymol import cmd
from glob import glob
cmd.do("run list_hb.py")

for file in glob("model.000.*.pdb"):
print(file)
#file_list = [f'{m:02d}'  for m in  list(range(0,30,1))]
cmd.load(file)
obj=cmd.get_object_list('all')
print(obj)
#chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
cmd.do("list_hb chain F, chain A:E,
write_distances_file=hb_"+str(obj[0])+".txt") cmd.delete("all”)

Cheers,
Rob

On Tue, 2020-06-16 20:23  +,  "Chen, Qiang"  wrote:

> This script will have a memory issue. My pymol will stuck if I have
> more than 3 files be processed. file_list = [f'{m:02d}'  for m in
> list(range(1,30,1))] [cmd.do("load
> model.000."+str(k)+"_minimized.pdb") for k in file_list]
> object_list=cmd.get_object_list('(model.000.*_minimized)')
> chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')] run
> C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py
> [cmd.do("list_hb chain F, chain A:E,
> write_distances_file=hb_"+str(file)+".txt") for file in object_list ]
> 
> I modified from the sample script here
> 
> https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.pymolwiki.org%2Findex.php%2FProcess_All_Files_In_Directorydata=02%7C01%7Crobert.campbell%40queensu.ca%7C5a300643d81e4d7ea3f608d812359b34%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279368764004254sdata=p5tXmvSD1QCS%2BdIXyJv58rEBk9GCIRtl8BFSnamwoNs%3Dreserved=0
> 
> Save the following lines in a file named as, eg. multiple_hb.py and
> make sure list_hb.py in the working directory of searching directory.
> 
> Then run multiple_hb.py in the pymol command line.
> 
> from pymol import cmd
> from glob import glob
> 
> for file in glob("model.000.*.pdb"):
> print(file)
> #file_list = [f'{m:02d}'  for m in  list(range(0,30,1))]
> cmd.load(file)
> obj=cmd.get_object_list('all')
> print(obj)
> #chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
> cmd.do("run list_hb.py")
> cmd.do("list_hb chain F, chain A:E,
> write_distances_file=hb_"+str(obj[0])+".txt") cmd.delete("all”)
> 
> 
> On Jun 16, 2020, at 11:15 AM,
> pymol-users-requ...@lists.sourceforge.net
> wrote:
> 
> Send PyMOL-users mailing list submissions to
> pymol-users@lists.sourceforge.net
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fpymol-usersdata=02%7C01%7Crobert.campbell%40queensu.ca%7C5a300643d81e4d7ea3f608d812359b34%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279368764004254sdata=9UIjcsPwiUC9PmwQ4mcTi1%2F4%2BIGx9jQKarXsh7dfpGk%3Dreserved=0
> or, via email, send a message with subject or body 'help' to
> pymol-users-requ...@lists.sourceforge.net
> 
> You can reach the person managing the list at
> pymol-users-ow...@lists.sourceforge.net
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
> 
> 
> Today's Topics:
> 
>   1. Re: hydrogen bond list for a series of files
>  (Mooers, Blaine H.M.  (HSC))
>   2. Re: hydrogen bond list for a series of files (Chen, Qiang)
> 
> 
> --
> 
> Message: 1
> Date: Tue, 16 Jun 2020 14:51:38 +
> From: "Mooers, Blaine H.M.  (HSC)" 
> To: "Chen, Qiang" , "pymol-users@lists.sourceforge.net"
> 
> Subject: Re: [PyMOL] hydrogen bond list for a series of files
> Message-ID:
> <87dcc6c40b22804192b6892e6429ec5fdbefd...@countach.hsc.net.ou.edu>
> Content-Type: text/plain; charset="Windows-1252"
> 
> Hi Charlie,
> 
> This will give the desired list.
> 
> file_list = [f'{m:02d}'  for m in  list(range(1,30,1))]
> print(file_list)
> 
> Best regards,
> 
> Blaine
> 
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> 
> 
> From: Chen, Qiang [q...@pitt.edu]
> Sent: Tuesday, June 16, 2020 9:26 AM
> To: Mooers, Blaine H.M.  (HSC); pymol-users@lists.sourceforge.net
> Subject: [EXTERNAL] Re: hydrogen bond list for a series of files
> 
> Hi, Blaine,
> 
> Then the question becomes how to generate a list with 30 or 300
> numbers.
> 
> Will this work?
> file_list=list(range(00, 30))
> 
> Thanks!
> 
> Charles
> 
> 
> 
> From: Mooers, Blaine H.M. (HSC) 
> Sent: Tuesday, June 16, 2020 9:57 AM
> To: Chen, Qiang ; pymol-users@lists.sourceforge.net
>  Subject: RE: hydrogen bond list
> for a series of files
> 
> Hi Charles,
> 
> You are right and I am wrong about the files 

Re: [PyMOL] Extract all phi and psi angles

[Robert Campbell]

Hi Neena,

If you give a different selection, then phi_psi will give you a list of phi/psi 
angles for all residues in the selection.

For example if your protein object is called "obj_1", then typing

phi_psi obj_1

will provide a list of phi_psi values to the terminal:

PyMOL>phi_psi obj_1
 LYS-3:(  -63.3,  -75.6 )
 GLY-4:(  -62.6,  -32.9 )
 GLU-5:(  -31.7,  -58.7 )
 GLU-6:(  -57.3,  -23.4 )
 LEU-7:(  -74.7,  -18.6 )
 PHE-8:( -106.0,6.4 )
 THR-9:(  -59.8,  -16.1 )
 GLY-10:   ( -140.4, -166.5 )

or you can assign the list to a dictionary variable with:

p = cmd.phi_psi('obj_1')

where p will be a dictionary with keys representing the residue numbers and 
pointing to a list of the phi/psi values for that residue.

Cheers,
Rob

-- 
Robert L. Campbell, Ph.D.
Assistant Professor, Dept. of Biomedical & Molecular Sciences, 
Queen's University, Kingston, ON K7L 3N6  Canada
  http://pldserver1.biochem.queensu.ca/~rlc


On Sat, 2020-05-09 11:08  -0400,  Neena Susan Eappen  
wrote:

> Hi Jarrett,
> 
> Thank you for your reply. However, that command gives phi and psi
> angles for only one atom (when only one atom is selected). Is there
> one command we can use to extract all phi and psi angles?
> 
> Thanks,
> Neena
> 
> 
> 
> On Mon, 27 Apr 2020 at 22:01, Jarrett Johnson <
> jarrett.john...@schrodinger.com> wrote:  
> 
> > Hi Neena,
> >
> > Is this command sufficient?
> >
> > https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpymol.org%2Fdokuwiki%2Fdoku.php%3Fid%3Dcommand%3Aphi_psidata=02%7C01%7Crobert.campbell%40queensu.ca%7C220f11d984f74518dfe208d7f42b243e%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637246338451090438sdata=Y8U07iXlCYJ%2BE0GN2Oh04QSE7n68NPH5d2fc%2BaUhdSk%3Dreserved=0
> >
> > Best,
> > Jarrett J
> >
> > On Mon, Apr 27, 2020 at 9:45 PM Neena Susan Eappen <  
> > neenasusan...@gmail.com> wrote:  
> >  
> >> Hello PyMOL users,
> >>
> >> How to extract all peptide dihedral angles (phi and psi) in PyMOL?
> >>
> >> Many thanks,
> >> Neena
> >> ___
> >> PyMOL-users mailing list
> >> Archives:
> >> https://can01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.netdata=02%7C01%7Crobert.campbell%40queensu.ca%7C220f11d984f74518dfe208d7f42b243e%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637246338451090438sdata=%2F%2F%2BSyfR20FyqY2GFMhZVbBe0CHtQuoSLCIUMsBHgoLs%3Dreserved=0
> >> Unsubscribe:
> >> https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribedata=02%7C01%7Crobert.campbell%40queensu.ca%7C220f11d984f74518dfe208d7f42b243e%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637246338451090438sdata=gcqmQ9A%2BOEJMPVf3ubqWWGEh6DzZv95XVXXJULabe2w%3Dreserved=0
> >>  
> >
> >
> >
> > --
> >
> > *Jarrett Johnson* | Senior Developer
> > [image: Schrodinger Logo]
> > 
> >  






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Re: [PyMOL] Drawing lines between residues

[Robert Campbell]

Hi Jorge,

I have written a script that will draw lines between arbitrary pairs of atoms 
using CGO cylinders.  The script is called "draw_links.py" and can be found on 
my script page:

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

Besides listing the pairs of atoms to connect you can control the colour and 
radius of the CGO cylinders with a command like:

draw_links mol1 & chain A & name CA & resi 1+6+7+8, mol1 & chain A & name CA & 
resi 10+16+17+18 

and that would connect the alpha carbons of residue 1 with 10, 6 with 16, 7 
with 17 and 8 with 18.


Cheers,
Rob

On Thu, 2019-10-17 16:31  +0200,  Jorge Fernández de Cossío Díaz 
 wrote:

> Hi all.
> 
> I have a list of pairs of residues. I want to draw lines between the
> residues in each pair. The lines can have different colors. So in the
> end I would like to achieve a figure like this one:
> 
> 
> [image: 2019-10-15.png]
> 
> What commands can I use to get this done in PyMOL?
> 
> Thanks



-- 
Robert L. Campbell, Ph.D.
Adjunct Assistant Professor, Dept. of Biomedical & Molecular Sciences, 
Botterell Hall Rm 644
Queen's University, Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
  http://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] Pymol recolour B factors

[Robert Campbell]

Hi Mark,

In that data2bfactor.py script (which I wrote) you need to provide the 
molecular object name, not a file name.  In other words in your example you 
should load the 1d3z.pdb file as an object (defaults to 1d3z as object name).  
Then after using the run command to load the script into your pymol session 
then you can type:

data2b_res 1d3z, shift_to_b.txt

The other script you mention works the same way.  The pdb file needs to be 
loaded into PyMOL as a molecular object first.

Cheers,
Rob

On Fri, 2019-03-22 11:36  +,  Dr Mark Bostock  wrote:

> Hello,
> 
> I'm trying to recolour the B factors in a pymol file with chemical
> shift differences (from NMR data). There's a nice script here for
> this http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
> (data2bfactor.py) and also a simpler one here 
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffigshare.com%2Farticles%2FPymol_script_loadBfacts_py%2F1176991data=02%7C01%7Crobert.campbell%40queensu.ca%7C664f1bfa0c934c52f40108d6aebdf161%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C1%7C636888528158871468sdata=jDmJ4NSc%2F%2BXy5IG%2BRCCsQOmqh1Xj9l4j6gTMEmJB6Zc%3Dreserved=0.
> 
> In both cases after loading the script with the run command, when I
> execute the script I get the following error
> 
> data2b_res 1d3z.pdb, shift_to_b.txt
> Selector-Error: Invalid selection name "1d3z.pdb".
> ( 1d3z.pdb )<--
> 
> The pdb file and list of new b-factor values are in the same
> directory and can be filled in with tab-completion. I've also tried
> using the full file path but get a similar error. I've tried with a
> couple of different pdb files as well so it's not just a problem with
> that particular pdb file.
> 
> I'd be grateful if anyone has any experience with this or suggestions
> as to what is going wrong.
> 
> Thanks in advance,
> 
> Mark
> 
> 
> 
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Tel: 613-533-6821
  http://pldserver1.biochem.queensu.ca/~rlc


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Re: [PyMOL] ExecutivesSymexp-Error: No Symmetry loaded!

[Robert Campbell]

Hi Leila,

You need the "CRYST1" line from the template pdb file.  That is where PyMOL 
gets the symmetry information from.

Cheers,
Rob

On Wed, 2017-06-21 09:29  +0200,  leila karami  wrote:

> Dear PYMOL users,
> 
> I have done a homology modelling using swiss model. Template pdb file
> contain 3 chains (A, B, C). I used only chain A for homology
> modelling as template.
> 
> There is a symmetry operator in template pdb file (temp.pdb). I want
> to use symexp to obtain dimeric structure for modeled pdb file
> (model.pdb).
> 
> I manually added following records (from temp.pdb) at the first of the
> modeled pdb file:
> ===
> REMARK 290
> REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
> REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
> REMARK 290
> REMARK 290  SYMOP   SYMMETRY
> REMARK 290 NNNMMM   OPERATOR
> REMARK 290   1555   X,Y,Z
> REMARK 290   2555   -X,Y,-Z
> REMARK 290   3555   X+1/2,Y+1/2,Z
> REMARK 290   4555   -X+1/2,Y+1/2,-Z
> REMARK 290
> REMARK 290 WHERE NNN -> OPERATOR NUMBER
> REMARK 290   MMM -> TRANSLATION VECTOR
> REMARK 290
> REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
> REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
> REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
> REMARK 290 RELATED MOLECULES.
> REMARK 290   SMTRY1   1  1.00  0.00  0.000.0
> REMARK 290   SMTRY2   1  0.00  1.00  0.000.0
> REMARK 290   SMTRY3   1  0.00  0.00  1.000.0
> REMARK 290   SMTRY1   2 -1.00  0.00  0.000.0
> REMARK 290   SMTRY2   2  0.00  1.00  0.000.0
> REMARK 290   SMTRY3   2  0.00  0.00 -1.000.0
> REMARK 290   SMTRY1   3  1.00  0.00  0.00   88.99000
> REMARK 290   SMTRY2   3  0.00  1.00  0.00   28.29500
> REMARK 290   SMTRY3   3  0.00  0.00  1.000.0
> REMARK 290   SMTRY1   4 -1.00  0.00  0.00   88.99000
> REMARK 290   SMTRY2   4  0.00  1.00  0.00   28.29500
> REMARK 290   SMTRY3   4  0.00  0.00 -1.000.0
> REMARK 290
> CRYST1  177.980   56.590   83.220  90.00 116.58  90.00 C 1 2 1  12
> ORIGX1  1.00  0.00  0.000.0
> ORIGX2  0.00  1.00  0.000.0
> ORIGX3  0.00  0.00  1.000.0
> SCALE1  0.005619  0.00  0.0028110.0
> SCALE2  0.00  0.017671  0.000.0
> SCALE3  0.00  0.00  0.0134360.0
> 
> ===
> 
> After using symexp sym,model,(model),1 in command line, I encountered
> with:
> 
> ExecutivesSymexp-Error: No Symmetry loaded!
> 
> temp.pdb and model.pdb files are in following links:
> 
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fs%2Ft8m1nrkx2s69wi9%2Fmodel.pdb%3Fdl%3D0=02%7C01%7Crobert.campbell%40queensu.ca%7C6261ebf5a5494e8b230808d4b877938b%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636336271090533556=g6I122L2C0o%2FAObHdjC9xXwoiPUx8J9MfupIpPp07ZM%3D=0
> 
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fs%2Fmt7toc0wtenr779%2Ftemp.pdb%3Fdl%3D0=02%7C01%7Crobert.campbell%40queensu.ca%7C6261ebf5a5494e8b230808d4b877938b%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636336271090533556=6U5D%2BZOPnIAx3X61eeK77XLW23mroFnaM8sxiX7n1Ow%3D=0
> 
> Any help will be highly appreciated.
> 
> Best,
> Leila




-- 
Robert L. Campbell, Ph.D.
Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
  http://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] ExecutivesSymexp-Error: No Symmetry loaded!

[Robert Campbell]

Hi Leila,

I responded too quickly without reading carefully!  Adding those lines should 
have worked (but only the CRYST1 line is needed).  Your model.pdb file that you 
linked to on Dropbox does not have the CRYST1 line.  Adding that line works for 
me.

Cheers,
Rob

On Wed, 2017-06-21 09:29  +0200,  leila karami  wrote:

> Dear PYMOL users,
> 
> I have done a homology modelling using swiss model. Template pdb file
> contain 3 chains (A, B, C). I used only chain A for homology
> modelling as template.
> 
> There is a symmetry operator in template pdb file (temp.pdb). I want
> to use symexp to obtain dimeric structure for modeled pdb file
> (model.pdb).
> 
> I manually added following records (from temp.pdb) at the first of the
> modeled pdb file:
> ===
> REMARK 290
> REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
> REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
> REMARK 290
> REMARK 290  SYMOP   SYMMETRY
> REMARK 290 NNNMMM   OPERATOR
> REMARK 290   1555   X,Y,Z
> REMARK 290   2555   -X,Y,-Z
> REMARK 290   3555   X+1/2,Y+1/2,Z
> REMARK 290   4555   -X+1/2,Y+1/2,-Z
> REMARK 290
> REMARK 290 WHERE NNN -> OPERATOR NUMBER
> REMARK 290   MMM -> TRANSLATION VECTOR
> REMARK 290
> REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
> REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
> REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
> REMARK 290 RELATED MOLECULES.
> REMARK 290   SMTRY1   1  1.00  0.00  0.000.0
> REMARK 290   SMTRY2   1  0.00  1.00  0.000.0
> REMARK 290   SMTRY3   1  0.00  0.00  1.000.0
> REMARK 290   SMTRY1   2 -1.00  0.00  0.000.0
> REMARK 290   SMTRY2   2  0.00  1.00  0.000.0
> REMARK 290   SMTRY3   2  0.00  0.00 -1.000.0
> REMARK 290   SMTRY1   3  1.00  0.00  0.00   88.99000
> REMARK 290   SMTRY2   3  0.00  1.00  0.00   28.29500
> REMARK 290   SMTRY3   3  0.00  0.00  1.000.0
> REMARK 290   SMTRY1   4 -1.00  0.00  0.00   88.99000
> REMARK 290   SMTRY2   4  0.00  1.00  0.00   28.29500
> REMARK 290   SMTRY3   4  0.00  0.00 -1.000.0
> REMARK 290
> CRYST1  177.980   56.590   83.220  90.00 116.58  90.00 C 1 2 1  12
> ORIGX1  1.00  0.00  0.000.0
> ORIGX2  0.00  1.00  0.000.0
> ORIGX3  0.00  0.00  1.000.0
> SCALE1  0.005619  0.00  0.0028110.0
> SCALE2  0.00  0.017671  0.000.0
> SCALE3  0.00  0.00  0.0134360.0
> 
> ===
> 
> After using symexp sym,model,(model),1 in command line, I encountered
> with:
> 
> ExecutivesSymexp-Error: No Symmetry loaded!
> 
> temp.pdb and model.pdb files are in following links:
> 
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fs%2Ft8m1nrkx2s69wi9%2Fmodel.pdb%3Fdl%3D0=02%7C01%7Crobert.campbell%40queensu.ca%7C6261ebf5a5494e8b230808d4b877938b%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636336271090533556=g6I122L2C0o%2FAObHdjC9xXwoiPUx8J9MfupIpPp07ZM%3D=0
> 
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fs%2Fmt7toc0wtenr779%2Ftemp.pdb%3Fdl%3D0=02%7C01%7Crobert.campbell%40queensu.ca%7C6261ebf5a5494e8b230808d4b877938b%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636336271090533556=6U5D%2BZOPnIAx3X61eeK77XLW23mroFnaM8sxiX7n1Ow%3D=0
> 
> Any help will be highly appreciated.
> 
> Best,
> Leila




-- 
Robert L. Campbell, Ph.D.
Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
  http://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] Scripting coloring method via own calculations

[Robert Campbell]

Hello Peleg,

I think there are other possibilities, but my data2bfactor.py script will do 
that for you.  You create a file with whitespace-separated columns (spaces 
and/or tabs) in which each line contains:

chain resi resn name data 

(i.e. chain, residue number, residue name, atom name and value to be applied to 
the B-factor column).

The number can also be applied to the occupancy column instead if you want to 
keep the B-factor intact.

Then you can use the spectrum command or my color_b.py script to colour each 
atom according to the data value.  My color_b.py script has a few more options 
than the spectrum command, including the ability to define a custom colour 
gradient scheme.

You can find my scripts here:

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

Cheers,
Rob

On Tue, 2017-02-14 17:12  +0100,  Peleg Bar-Sapir  wrote:

> Hello,
> 
> I wish to write a script that will take the molecule loaded in PyMol,
> and color the molecule according to values I will calculate using the
> molecules' parameters (in the end there will be one floating number
> per atom). Then, I would like to display that using surface mode.
> 
> Could anyone direct me to a way of doing that? I saw scripts coloring
> by atom type, but I'm not sure how to apply it for a molecule already
> loaded in PyMol.
> 
> Best,
> 
> Peleg




-- 
Robert L. Campbell, Ph.D.
Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
  http://pldserver1.biochem.queensu.ca/~rlc

--
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Re: [PyMOL] Fw: symmetry and pdb remark

[Robert Campbell]

Hello Smith,

I had a look at the two structures.  In some crystallographic space groups 
there are alternate choices for the origin that are all equivalent. It appears 
that this is what you are seeing here.

If you look carefully at the mates generated separately for 2zam and 2zan, they 
are equivalent in their position and orientation relative to the original 
coordinates for each structure.  There is simply a translational shift along 
two axes that relates the coordinates of 2zam and its mates to 2zan and its 
mates.

There is a slight difference in the unit cell dimensions as well, which could 
make very small differences in the packing contacts.

Cheers,
Rob

On Thu, 2017-02-02 12:37  +0800,  Smith Liu  wrote:

> Dear All,
> 
> 
> Here I make my question much clear.
> 
> 
> For both PDB 2zan and 2zam, they are for the same protein, they
> conformation were similar except that 2zam was apo and 2zam was ATP
> binding. 2zaz was got by soaking the 2zam crystal with ATP. Both were
> P65 space group
> 
> 
> However by getting the mate coordinates of 2zam and 2zan by Coot or
> Chimera, you will find their 6 mates arrange differently ( viewed by
> Chimera or by Pymol). For 2zan, the 6 mates were separated with each
> other, but for 2zam the 6 mates were connected. Can you explain to me
> why  their 6 mates arrange differently?
> 
> 
> What is more, by pymol I align 2zan onto 2zam, and I get the PDB for
> 2zan fitted to 2zam (no any text information from the pdb file left
> after pymol saving, except the coordinates). Then I add all the text
> information from 2zan (except the coordinates) to the PDB for 2zan
> fitted to 2zam, and then I get the mate coordinates by Chimera or
> Coort and then view the mates got by Chimera or Coot for the text
> information added PDB for 2zan fitted to 2zam, I find the 6 mates
> arrange like 2zam, rather like 2zan (viewed by Chimera). Thus, will
> you please explain which remark information decide the mate
> arrangement, as in the  remark added PDB for 2zan fitted to 2zam? Why
> after pymol alignment, the same remark information leads to different
> mates arrangement?
> 
> 
> I am looking forward to getting a reply from you.
> 
> 
> Smith
> 
> 
> 
> 
> 
> 
> 
>  Forwarding messages 
> From: "Smith Liu" 
> Date: 2017-02-02 12:06:16
> To: pymol-users@lists.sourceforge.net
> Subject: symmetry and pdb remark
> 
> Dear All,
> 
> 
> 
> I have a symmetry problem, which I hope I can get your help.
> 
> 
> 
> For both PDB 2zan and 2zam, they are for the same protein, they
> conformation were similar except that 2zam was apo and 2zam was ATP
> binding. 2zaz was got by soaking the 2zam crystal with ATP. Both were
> P65 space group
> 
> 
> However by getting the mates of 2zam and 2zan, you will find their 6
> mates arrange differently ( viewed by Chimera). Can you explain to me
> why  their 6 mates arrange differently?
> 
> 
> What is more, by pymol I align 2zan onto 2zam, and I get the PDB for
> 2zan fitted to 2zam (no any remark information left after pymol
> saving). Then I add all the remark information from 2zan to the PDB
> for 2zan fitted to 2zam, and then I view the mates for the remark
> added PDB for 2zan fitted to 2zam, I find the 6 mates arrange like
> 2zam, rather like 2zan (viewed by Chimera).
> 
> 
> Thus, will you please explain which remark information decide the
> mate arrangement, as in the  remark added PDB for 2zan fitted to
> 2zam? Why after pymol alignment, the same remark information leads to
> different mates arrangement?
> 
> 
> I am looking forward to getting a reply from you.
> 
> 
> Smith



-- 
Robert L. Campbell, Ph.D.
Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
  http://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] Function signature

[Robert Campbell]

Hi Martin,

If you simply want to be able to have the function operate on any
selection, simply do this:


def zoom_custom(position):
  cmd.zoom(position)

cmd.extend("zoom_custom", zoom_custom)

This allows you to type:

zoom_custom resi 117

or any other more complicated selection syntax without any parentheses.
Perhaps I am missing something in your specific requirements?

Cheers,
Rob

 On Sun, 2016-04-17 20:18  +0200,  Martin
Hediger  wrote:

> Dear all
> 
> In PyMOL, the syntax for eg. zooming in on residue 110 of a protein
> would be
> 
> zoom resi 117
> 
> I have a pymol script where I define a function that also zooms in on
> a residue (it's simple, only to illustrate the point):
> 
> def zoom_custom(position):
>  cmd.zoom("resi" + " " + str(position))
> cmd.extend("zoom_custom", zoom_custom)
> 
> However, when I want to call it from the PyMOL promt, i have to use
> 
> zoom_custom(117)
> 
> i.e. using parenthesis. How do i need to design the function such
> that I can enter it as above?
> 
> Thanks and best regards
> Martin
> 
> --
> Find and fix application performance issues faster with Applications
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-- 
Robert L. Campbell, Ph.D.
Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
  http://pldserver1.biochem.queensu.ca/~rlc

--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
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Re: [PyMOL] efficiency assigning b-factors

[Robert Campbell]

Hi Jordan et al.,

Yes one can use the alter command with a whole selection at once and
it is much faster. I hadn't realized that until Thomas Holder helped fix
my script that appears to do what you were wanting to do:

 http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/data2bfactor.py

The B-factor data is read in and assigned to a dictionary by the
atom_data_extract function elsewhere in the script (indexed either by
chain and residue number, or by chain and ID) and then it is applied
like this:

b_dict = atom_data_extract(data_file)
quiet = int(quiet) == 1

def b_lookup(chain, resi, name, ID, b):
def _lookup(chain, resi, name, ID):
if resi in b_dict[chain] and isinstance(b_dict[chain][resi], dict):
return b_dict[chain][resi][name][0]
else:
# find data by ID
return b_dict[chain][int(ID)][0]
try:
if not chain in b_dict:
chain = ''
b = _lookup(chain, resi, name, ID)
if not quiet: print '///%s/%s/%s new: %f' % (chain, resi, name, b)
except KeyError:
if not quiet: print '///%s/%s/%s keeping: %f' % (chain, resi, name, 
b)
return b
stored.b = b_lookup

cmd.alter(mol, '%s=stored.b(chain, resi, name, ID, %s)' % (prop, prop))
cmd.rebuild()

Hope that helps.

Cheers,
Rob

On Tue, 2015-06-16 11:10 EDT, Tsjerk Wassenaar tsje...@gmail.com
wrote:

 Hi Jordan,
 
 The answer is something like (assuming reading from a file):
 
 newb=[float(i) for i in open(stuff.dat).read().split()]
 alter n. ca, b=newb.pop()
 spectrum b
 
 Hope it helps,
 
 Tsjerk
 
 On Tue, Jun 16, 2015 at 10:25 AM, Jordan Willis
 jwillis0...@gmail.com wrote:
 
  Hi Tsjerk,
 
  It seems everyone is pointing to this (
  http://www.pymolwiki.org/index.php/Color#Reassigning_B-Factors_and_Coloring)
  which I somehow missed. However, they seem to be altering one
  residue at a time like I’m doing.
 
 
  Jordan
 
  On Jun 15, 2015, at 11:59 PM, Tsjerk Wassenaar tsje...@gmail.com
  wrote:
 
  Hi Jordan,
 
  Yes, although I don't have the answer at hand, it has been given on
  the user list several times. You can find it in the archives.
 
  Cheers,
 
  Tsjerk
  On Jun 16, 2015 08:16, Jordan Willis jwillis0...@gmail.com
  wrote:
 
  Hi,
 
  I have a dictionary that has a bunch of values I want to assign to
  b-factors in order to color by. In my script:
 
  for residue in data:
 cmd.alter(“resi
  {}”.format(residue[‘resnum’]),”b={}”.format(residue[‘value’]))
 
  This executes the alter command for each residue. For some reason,
  its taking forever in my script. Is there something inherently
  inefficient about alter? And is there anyway to fix it? Perhaps,
  assign a bunch of b-factors at once.
 
  Jordan
 
 
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-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical  Molecular Sciences, Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
robert.campb...@queensu.ca  http://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] Backbone RMSD

[Robert Campbell]

Hello Amita,

On Wed, 2014-09-10 09:41  EDT,  Amita Rani Sahoo amita.r.sa...@gmail.com
wrote:

 Dear Pymol users,
 
 I want to calculate backbone RMSD of proteins having two different
 conformations (For example 2RH1 and 1F88). With the align command it
 calculates the executive RMSD, but i need backbone RMSD. Please advise
 something.

You simply need to include a selection on the command line.  At the PyMOL
prompt, you could type

  align 2hr1  backbone, 1f88  backbone

Cheers,
Rob


-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical  Molecular Sciences
Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] command question RE printing out distances to text file

[Robert Campbell]

Hi Suzanne,

You can also get the distance printed in the external GUI or terminal window
by using the cmd.distance version of the command.  So either you can
assign the distance to a variable and print it or you can print the result
directly.

Assuming you have two selections, sele1 and sele2 specifying the atoms of
interest you could do something like this:

  d = cmd.distance(sele1,sele2)
  print sele1,sele2,d


Cheers,
Rob

On Mon, 2014-06-09
13:13 EDT, Thomas Holder thomas.hol...@schrodinger.com wrote:

 Hi Suzanne,
 
 you can use the get_distance command. It doesn't generate a distance
 object but prints the distance to the external window.
 
 http://pymolwiki.org/index.php/Get_Distance
 
 Cheers,
   Thomas
 
 On 06 Jun 2014, at 23:03, Lapolla, Suzanne M (HSC)
 suzanne-lapo...@ouhsc.edu wrote:
 
  Fellow Pymol Users:
  I may have asked this question before...but if so have forgotten. I am
  measuring distances between 2 atoms in 2 different objects using the
  distance command, and it is working perfectly, but I wonder if there is
  a command I can use/add so that those distances can be printed in the
  external gui as well as being shown in the viewer. I will be doing lots
  of these at the same time and the screen will get crowded. Thank you in
  advance.
 




-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical  Molecular Sciences
Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] command question RE printing out distances to text file

[Robert Campbell]

Hi Suzanne,

You can also get the distance printed in the external GUI or terminal window
by using the cmd.distance version of the command.  So either you can
assign the distance to a variable and print it or you can print the result
directly.

Assuming you have two selections, sele1 and sele2 specifying the atoms of
interest you can do:

  d = cmd.distance(sele1,sele2)
  print sele1,sele2,d


Cheers,
Rob

On Mon, 2014-06-09
13:13 EDT, Thomas Holder thomas.hol...@schrodinger.com wrote:

 Hi Suzanne,
 
 you can use the get_distance command. It doesn't generate a distance
 object but prints the distance to the external window.
 
 http://pymolwiki.org/index.php/Get_Distance
 
 Cheers,
   Thomas
 
 On 06 Jun 2014, at 23:03, Lapolla, Suzanne M (HSC)
 suzanne-lapo...@ouhsc.edu wrote:
 
  Fellow Pymol Users:
  I may have asked this question before...but if so have forgotten. I am
  measuring distances between 2 atoms in 2 different objects using the
  distance command, and it is working perfectly, but I wonder if there is
  a command I can use/add so that those distances can be printed in the
  external gui as well as being shown in the viewer. I will be doing lots
  of these at the same time and the screen will get crowded. Thank you in
  advance.
 




-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical  Molecular Sciences
Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] ccp4 question

[Robert Campbell]

Dear Stefan,

On Tue, 2014-02-04 14:44  EST,  Stefan Ivanov
stefan.iva...@postgrad.manchester.ac.uk wrote:

 Dear Pymolers,
 
 I tried to run ncont on a pdb structure and got a .ncont file as output,
 but the only thing the file contains is an error message (see below). I
 tried copying default.def into the working directory, but couldn't get
 the darn thing to work. If someone can help I'd appreciate it.

You might have better luck asking on the ccp4bb, but I'll try to answer...

 --
 
  CCP4 library signal ccp4_general:Cannot open default.def (Error)
raised in ccp4fyp 
  
  ###
  ###
  ###
  ### CCP4 6.4: NCONTversion 6.4 : ##
  ###
  User: unknown  Run date:  3/ 2/2014 Run time: 16:00:09 
 
 
  Please reference: Collaborative Computational Project, Number 4. 1994.
  The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50,
 760-763. as well as any specific reference in the program write-up.
 
 
  
 --
 
  * ERROR #40 READ:
 
  Logical file name not found.

You haven't told us how you tried to run it, but the error tells you
that it is not finding your .pdb file.  Did you run it on the command
line?  If so, did you type something like:

ncont xyzin file.pdb

The standard command line format for CCP4 programs is such that coordinate
files are indicated by the xyzin (and xyzout) logical names. 

It can also be run from the ccp4i interface. Did you try that?

Cheers,
Rob

-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical  Molecular Sciences
Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] combining multiple objects into one multistate object

[Robert Campbell]

Hi Jed,

On Thu, 2014-01-16 10:28  EST,  Jed Goldstone jgoldst...@whoi.edu wrote:

 I know this seems silly, but I can't figure out how to combine multiple 
 separate objects into one multistate object. I have a set of Modeler 
 models loaded from a single pdb file, automagically separated into 
 separate objects that have been aligned, and I want to combine them into 
 one object in order to run Robert Cambell's rmsf_states script (and, 
 also since it's just easier to compare and manipulate).

You probably have a reason for loading the models into separate objects,
but my first suggestion would be to just load all of the models into a
single object in the first place.  You can align them using the
intra_fit command.  I normally load my modeller models into one object
with my load_models.py script or my load_best.py script if I want them
sorted by modeller's objective function value (both scripts are also on my
web site). I like being able to see the models individually or all at once
(with set all_states, 1).

Cheers,
Rob

 
 I've searched the manual, the sourceforge list, and the wiki. Somehow 
 the command 'create' with 'target_state=-1' and 'discrete=1' seems like 
 it should do this, but all the objects end up in the first state (and 
 the cartoon representation is a subset of what it should be (other 
 representations are fine).
 I'm using incentive v1.6.0.0 on Windows 7.
 
 Jed
 




-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical  Molecular Sciences
Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] How to automate RMSD calculation for large no of structures

[Robert Campbell]

On Tue, 2014-01-07 12:05  EST,  Jed Goldstone jgoldst...@whoi.edu wrote:

 Check out Robert Campbell's Pymol script repository.
 I think align_all_to_all.py should do what you want, including exporting 
 RMSD values.
 
 http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

Actually, I think Om only wants to align the individual mutants to the
wild-type not all 500 mutants against each other which is what the above
script does.  Also, I think for 500 structure you probably don't want to
load all 500 in at one time, so it would be better to have a script that
only loads each mutant one at a time, calculates its RMSD to the wild-type
and then deletes it.

I have modified my align_all.py script to create a new one called
align_allfiles.py and added that to the above website.  It is also attached
here.  To specify the use of all atoms simply add that to the mobile and
target selections.  You can also specify PyMOL's cutoff and cycles
arguments to the align function (defaults to cycles=5, cutoff=2)

align_allfiles target_model, files=mutants*.pdb, mobile_selection=all,
   target_selection=all

It will print out a list of RMSD values for each mutant in order read in as
well as sorted by RMSD.


Cheers,
Rob

 Jed
 
 
 On 1/7/2014 11:58 AM, Om Shiv wrote:
  Hello All
 
  I am a new user to Pymol and Python.
 
  I have a PDB Structure with single chain (A) and I have modeled 500
  single point mutants of this wild structure.
 
  Now for each such 500 modeled structures, I would like to calculate RMSD
  (ALL ATOMS) with the wild type PDB structure.
 
  Can anybody help me with the script to automate calculation of 500 RMSD
  calculations using PYMOL ?
 
  Secondly, what threshold value of RMSD can be considered above which we
  can say that the mutant structure is considerably different than the
  wild type ?
 
  Thanks in advance.
 




-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical  Molecular Sciences
Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc
#! /usr/bin/env python
# original Written by Jules Jacobsen (jacob...@ebi.ac.uk). Feel free to do whatever you like with this code.
# extensively modified by Robert L. Campbell (r...@queensu.ca)

from pymol import cmd
import glob, re

def align_allfiles(target=None,files=None,mobile_selection='name ca',target_selection='name ca',cutoff=2, cycles=5,cgo_object=0):
  
  Aligns all models in a list of files to one target

  usage:
align_allfiles [target][files=filenames][target_selection=name ca][mobile_selection=name ca]
[cutoff=2][cycles=5][cgo_object=0]
where target specifies the model id you want to align all others against,
and target_selection, mobile_selection, cutoff and cycles are options
passed to the align command.  You can specify the files to load and align
using a wildcard.

By default the selection is all C-alpha atoms and the cutoff is 2 and the
number of cycles is 5.
Setting cgo_object to 1, will cause the generation of an alignment object for
each object.  They will be named like object_on_target, where object and
target will be replaced by the real object and target names.

Example:
  align_allfiles target=name1, files=model.B*.pdb, mobile_selection=c. b  n. n+ca+c+o,target_selection=c. a  n. n+ca+c+o

  
  cutoff = int(cutoff)
  cycles = int(cycles)
  cgo_object = int(cgo_object)

  file_list = glob.glob(files)
  file_list.sort()
  extension = re.compile( '(^.*[\/]|\.(pdb|ent|brk))' )
  object_list = []

  rmsd = {}
  rmsd_list = []
  for i in range(len(file_list)):
obj_name1 = extension.sub('',file_list[i])
object_list.append(extension.sub('',file_list[i]))
cmd.load(file_list[i],obj_name1)
if cgo_object:
  objectname = 'align_%s_on_%s' % (object_list[i],target)
  rms = cmd.align('%s  %s'%(object_list[i],mobile_selection),'%s  %s'%(target,target_selection),cutoff=cutoff,cycles=cycles,object=objectname)
else:
  rms = cmd.align('%s  %s'%(object_list[i],mobile_selection),'%s  %s'%(target,target_selection),cutoff=cutoff,cycles=cycles)

rmsd[object_list[i]] = (rms[0],rms[1])
rmsd_list.append((object_list[i],rms[0],rms[1]))
cmd.delete(obj_name1)

  rmsd_list.sort(lambda x,y: cmp(x[1],y[1]))
# loop over dictionary and print out matrix of final rms values
  print Aligning against:,target
  for object_name in object_list:
print %s: %6.3f using %d atoms % (object_name,rmsd[object_name][0],rmsd[object_name][1])

  print \nSorted from best match to worst:
  for r in rmsd_list:
print %s: %6.3f using %d atoms % r

cmd.extend('align_allfiles',align_allfiles)
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Re: [PyMOL] Problem Compiling v 1.6.0.0 in 64 bit Debian Testing

[Robert Campbell]

Hi Stephen,

On Tue, 2013-06-25 09:16  EDT,  Stephen P. Molnar
s.mol...@sbcglobal.net wrote:

 I have just installed the 64 bit Debian Testing distribution in an
 Oracle VM on my laptop as a test bed.
 
 I successfully compiled v 1.6.0.0 in my 6 bit Debian Wheezy production
 OS.
 
 I didn't get any error messages from my laptop installation during the
 compilation process.  However when run pymol only the viewer window
 opens!
 
 Here are the messages:
 
  Traceback (most recent call last):
File /home/computation/Apps/pymol/lib/python/pymol/__init__.py,
  line 448, in launch_gui __import__(self.invocation.options.gui)
File /home/computation/Apps/pymol/lib/python/pmg_tk/__init__.py,
  line 22, in module from PMGApp import *
File /home/computation/Apps/pymol/lib/python/pmg_tk/PMGApp.py,
  line 31, in module import Pmw
  ImportError: No module named Pmw
   Detected 4 CPU cores.  Enabled multithreaded rendering.
  OpenGL Warning: No pincher, please call crStateSetCurrentPointers()
  in your SPU
 
 Unfortunately, I don't have the faintest idea as to what is missing.
 Any assistance will be appreciated.  Thanks in advance. 

I would appear that you are just missing the python-pmw package on this
machine, whereas it must have been present on your Wheezy version.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical  Molecular Sciences
Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] PyMOL 1.6 pre-release announcement

[Robert Campbell]

Hello Thomas and David,

Was there any resolution of this?  I've just compiled the latest version
from SVN and I have the same problem opening files created under version
1.5.0.  This is on Debian testing (32-bit).

Cheers,
Rob

 On Fri, 2013-04-26 19:15  EDT,  David Hall li...@cowsandmilk.net
wrote:

 Hi Thomas,
 
 I'm running into issues with color compatibility between 1.6 and
 earlier versions when opening pses
 (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like:
 Setting-Error: type read mismatch (color) 6
 Setting-Error: type read mismatch (color) 663
 Setting-Error: type read mismatch (color) 664
 (b) background color disparity:
 saved in 1.5 with black background; opens in 1.6 with a white background
 saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a red
 background
 
 These are run on openSUSE 12.3 with SVN rev 4028 . On a side note,
 others who would like to beta test can use devel:languages:python repo
 in openSUSE:
 https://build.opensuse.org/package/show?package=pymolproject=devel%3Alanguages%3Apython
 
 -David
 

-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical  Molecular Sciences
Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] PyMOL-users Digest, Vol 82, Issue 1

[Robert Campbell]

Hello Bachar,

On Fri, 2013-05-10 14:29  EDT,  Bachar Cheaib cheaib.bac...@gmail.com
wrote:

  Dear pymol users,
 
 I have wondered whether someone know how to know if a such structure in
 pdb file is multi-mer or mono-mer biologically speaking? Somehow in the
 related publication of structure this information is present in
 occurrence and  in pdb also is not nonintuitive to catch without the
 BIOMT transformations. A monomer could be deposited with multiple copies
 (or chains) of the same protein, but strikingly a biological (in vivo)
 homo-tetrameter (ex.1xiu ) it seems to be represented as a dimeric (two
 chains) and missing the two others in the pdb file
 
 This record REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC
 does not tell us if a structure is really multi or monomeric in the pdb
 file.

This does tell you that the protein is thought to exist as a tetramer.
What is determined by crystallography and therefore what is present in a
PDB file is the structure that exists in the asymmetric unit, in other words
the unique part of the structure.  That could be a portion of the
structure if it has internal symmetry, but it could also be two or more
copies of the biological unit.  If the asymmetric unit is not a tetramer
(as in your case), then you do need to use the BIOMT information to generate
the tetramer. That is why that information is there.  Just in the answers
to a previous question that you included in your message, you could load the
structure with the type=pdb1 option:

  fetch 1xiu, type=pdb1, async=0
  set all_states

which will fetch the biological assembly for that structure.  The extra
monomers that were generated by the crystallographic symmetry will be
visible when you set all_states.  Or you could split the states out into
separate objects.

 I would like just like to know how to conclude multimeric states
 informations from the pdb file without doing transformations ? just this
 information



Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical  Molecular Sciences
Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] PyMOL-users Digest, Vol 82, Issue 1

[Robert Campbell]

Hello Bachar,

On Fri, 2013-05-10 14:29  EDT,  Bachar Cheaib cheaib.bac...@gmail.com
wrote:

  Dear pymol users,
 
 I have wondered whether someone know how to know if a such structure in
 pdb file is multi-mer or mono-mer biologically speaking? Somehow in the
 related publication of structure this information is present in
 occurrence and  in pdb also is not nonintuitive to catch without the
 BIOMT transformations. A monomer could be deposited with multiple copies
 (or chains) of the same protein, but strikingly a biological (in vivo)
 homo-tetrameter (ex.1xiu ) it seems to be represented as a dimeric (two
 chains) and missing the two others in the pdb file
 
 This record REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC
 does not tell us if a structure is really multi or monomeric in the pdb
 file.

This does tell you that the protein is thought to exist as a tetramer.
What is determined by crystallography and therefore what is present in a
PDB file is the structure that exists in the asymmetric unit, in other words
the unique part of the structure.  That could be a portion of the
structure if it has internal symmetry, but it could also be two or more
copies of the biological unit.  If the asymmetric unit is not a tetramer
(as in your case), then you do need to use the BIOMT information to generate
the tetramer. That is why that information is there.  Just in the answers
to a previous question that you included in your message, you could load the
structure with the type=pdb1 option:

  fetch 1xiu, type=pdb1, async=0
  set all_states

which will fetch the biological assembly for that structure.  The extra
monomers that were generated by the crystallographic symmetry will be
visible when you set all_states.  Or you could split the states out into
separate objects.

 I would like just like to know how to conclude multimeric states
 informations from the pdb file without doing transformations ? just this
 information

snip

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical  Molecular Sciences
Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] SS in a trajectory

[Robert Campbell]

Hi,

On Wed, 2013-04-24 10:31  EDT,  Jianghai Zhu j...@idi.harvard.edu wrote:

 Hi,
 
 I have a trajectory file, in which two short helices would merge into one
 long helix.  However, when I play the trajectory in Pymol as cartoon, the
 long helix would still be shown as two helices with a loop in between.
 Is there a way to force Pymol to show a long helix for a specific range
 of frames in a trajectory? Thanks a lot.

When you load the trajectory, use the discrete flag to have PyMOL computer
the secondary structure for each state .

load trajectory.pdb, discrete=1

I'm assuming you are loading a multi-model .PDB file as the trajectory.  If
you are using the load_traj command to load an AMBER trajectory, there is
no similar option.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical  Molecular Sciences
Botterell Hall Rm 644
Queen's University, 
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Tel: 613-533-6821
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Re: [PyMOL] Splitting a PDB file into its constituent chains, and making multiple (smaller) PDB files

[Robert Campbell]

Hello Anasuya,

On Thu, 2013-04-04 15:49  EDT,  Anasuya Dighe anas...@mbu.iisc.ernet.in
wrote:

 Hello,
 
 I wanted to know if its possible in PyMOL to split a PDB file with
 multiple chains,into its component chains and make smaller PDB files
 corresponding to each chain.
 
 For eg: I have a pdb file, 1a55.pdb, having chains P,Q and R. How do I
 make split it to separate components like 1a55_P.pdb, 1a55_Q.pdb,
 1a55_R.pdb
 
 Also, in case I have a large number of multiple chain PDB files, how
 could I go about splitting each of them?

In addition to the other (manual) answers, there is a script on the PyMOL
wiki that does exactly this.  See:

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

Cheers,
Rob

-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical  Molecular Sciences
Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
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Re: [PyMOL] About draw_links.py by Dr. Robert Campbell

[Robert Campbell]

Hi Anasuya,

On Thu, 21 Feb 2013 17:10:40 +0530
Anasuya Dighe anas...@mbu.iisc.ernet.in wrote:

 
 Hi,
 
 I have been trying to use the script draw_links.py at 
 http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ to view links
 between each pair of c-alpha atoms present in an atom selection.
 Once I load a PDB (1q16.pdb) and make an atom selection, lets say :
 PyMOLselect pk1, name CA in resi 5+10+15+12+16 and chain C , on the
 PyMOLcommand-line in pymol, I
 do : PyMOLrun draw_links.py
 
 I wanted to visualise links between all pairs of calpha atoms present in
 the atom selection, pk1.
 However I am unable to do that using draw_links.py
 I am doing: PyMOL draw_links pk1
 
 How can I do this using draw_links.py?
 Where am I going wrong?

Perhaps the instructions are not clear enough, but the script is not
designed to automatically draw links between all pairs of C-alphas in a
selection. It expects two different selections and it will draw links
between the first residue of each selection and then the second and so on.
It doesn't therefore make sense to give it the same selection for both
because, in your example, it draws a zero-length link between residue 5 and
residue 5, and another between residue 10 and residue 10 and so on.

You will have to run the script multiple times to get the links you want:

draw_links name CA  resi 5 and chain C, name CA  resi 10 and chain C
draw_links name CA  resi 5 and chain C, name CA  resi 15 and chain C
draw_links name CA  resi 5 and chain C, name CA  resi 12 and chain C

Sorry that it doesn't quite do what you were expecting!  I designed it for
the situation where I have two structures that exhibit a conformational
change and I wanted to show how the C-alphas were moving so then it made
sense to have the two selections be the same atoms, but in different
molecules.

Cheers,
Rob
-- 
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Senior Research Associate/Adjunct Assistant Professor 
Dept. of Biomedical  Molecular Sciences, Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
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Re: [PyMOL] drawing a bond between the same Calpha atom in different states

[Robert Campbell]

Hi Jon,

On Thu, 2012-12-13 16:09  EST,  Jonathan Grimes jonat...@strubi.ox.ac.uk
wrote:

   Hi All,
 
I have 2 different states of the same molecule..different
 conformations generated from MD, so the same number of Calpha atoms, with
 a direct 1:1 mapping between Calphas with the same residue numbering.
 
I would like to draw a bond between equivalent C-alpha atoms, and I
 will then ramp colour along the bond, say blue-white-red.
 
Could I get advice how to draw a bond between 2 Calpha atoms (same
 resi) from different states

I have a script for drawing a cylinder (you can specify the radius and the
beginning and ending colors) between two atoms.  The script is at:

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/draw_cylinder_cgo.py

First run the script via the File menu or via the command line:

run draw_cylinder_cgo.py

You will then have two new functions defined draw_cylinder and
draw_cylinder_cgo.  The former allows you to pick two atoms to draw the
cylinder between:

draw_cylinder name, atom1, atom2, radius, start_color, end_color

where each atom is a standard PyMOL selection (defaults to pk1 and pk2)
and color is a 3-element RGB tuple defining the color
of the cylinder (where each value of R, G and B is between 0 and 1
inclusive).  The colors default to (1,1,0).


Alternatively, draw_cylinder_cgo takes as arguments the start and end
coordinates of the vector in place of atom1 and atom2.

Hope that helps.

Cheers,
Rob

-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical  Molecular Sciences
Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] drawing a bond between the same Calpha atom in different states

[Robert Campbell]

Hi,

(replying to my own message)

On Thu, 2012-12-13 15:52  EST,  Robert Campbell
robert.campb...@queensu.ca wrote:

 Hi Jon,
 
 On Thu, 2012-12-13 16:09  EST,  Jonathan Grimes jonat...@strubi.ox.ac.uk
 wrote:
 
Hi All,
  
 I have 2 different states of the same molecule..different
  conformations generated from MD, so the same number of Calpha atoms,
  with a direct 1:1 mapping between Calphas with the same residue
  numbering.
  
 I would like to draw a bond between equivalent C-alpha atoms, and I
  will then ramp colour along the bond, say blue-white-red.
  
 Could I get advice how to draw a bond between 2 Calpha atoms (same
  resi) from different states
 
 I have a script for drawing a cylinder (you can specify the radius and the
 beginning and ending colors) between two atoms.  The script is at:
 
 http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/draw_cylinder_cgo.py
 
 First run the script via the File menu or via the command line:
 
 run draw_cylinder_cgo.py
 
 You will then have two new functions defined draw_cylinder and
 draw_cylinder_cgo.  The former allows you to pick two atoms to draw the
 cylinder between:
 
 draw_cylinder name, atom1, atom2, radius, start_color, end_color
 
 where each atom is a standard PyMOL selection (defaults to pk1 and
 pk2) and color is a 3-element RGB tuple defining the color
 of the cylinder (where each value of R, G and B is between 0 and 1
 inclusive).  The colors default to (1,1,0).
 
 
 Alternatively, draw_cylinder_cgo takes as arguments the start and end
 coordinates of the vector in place of atom1 and atom2.

I could add more instructions here.  You can specify the colours by
name and if you have picked the atoms with the mouse you can easily do
something like:

  draw_cylinder dist1, start_color=red, end_color=yellow

and it will default to using atom selections pk1 and pk2 and a radius
of 0.1 A.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical  Molecular Sciences
Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] sequence file extraction

[Robert Campbell]

Hi Thomas,

On Tue, 2012-07-24 12:57  EDT,  Thomas Holder
spel...@users.sourceforge.net wrote:

 Hi Stefano,
 
 this is a known bug and it has not been fixed yet. A workaround is to 
 only save one object at a time to fasta format.
 
 See bug report:
 http://sourceforge.net/tracker/?func=detailaid=3466472group_id=4546atid=104546

Another bug (I guess I should report it via the bug tracker) is that if a
structure has multiple conformations (at least at the CA atom), then the
residue appears twice in the sequence.

Cheers,
Rob


-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Dept. of Biomedical  Molecular Sciences, Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] about super_all.py Plugin installation.

[Robert Campbell]

Dear Pavan,

On Tue, 27 Dec 2011 00:15:38 +0530, PAVAN PAYGHAN pavana...@gmail.com wrote:

 Dear PyMol Users,
 
 I am using PyMol +v0.97 version on Windows XP .I have downloded
 super_all.pyhttp://pldserver1.biochem.queensu.ca/~rlc/work/pymol/super_all.py
 and tried to install the plugin by using install Plugin option menu.
 Then I got the message that the plugin was installed but after
 re-initialization I dont find the Plugin for the same in Plugin list,also
 was unable to run
 super command .So will you please help me to solve this problem.Is there
 any incompatibility issues for OS XP?
 Please help me in solving this problem.Or suggest the proper way of doing
 the same as I am new user .

This is not a plugin that needs installing, but simply a script that you run.

To use it, you just store the super_all.py file somewhere on your computer
(I have a directory/folder dedicated to PyMOL scripts) and you load the
script's function by using the Run function from the File menu.  This has
to be done once each time PyMOL starts.  I load my commonly used scripts
automatically via my .pymolrc file. Once the script loaded, then you can call
the super_all function from the command line within PyMOL. You can see the
options by typing

  super_all ?

and you can get more information by typing

  help super_all

I hope this helps.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Dept. of Biomedical  Molecular Sciences, Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] Forced Linux/Python upgrade, killed PyMol, please help!

[Robert Campbell]

Hi John,

On Wed, 2011-12-21 11:12  EST,  John Ladasky john_lada...@sbcglobal.net
wrote:

 Hello everyone.  It has been a while since I posted here.  Apologies to 
 the admins, I tried to subscribe again, and I forgot that I was already 
 subscribed.
 
 For some non-PyMol work, I was obligated to upgrade my operating system 
 to Ubuntu Linux 11.10.  In fact, the specific reason that I had to 
 upgrade was to get Python 2.7 as the default Python on my computer.
 
 The Ubuntu Linux 11.10 repository listed PyMol 1.4.1, so I downloaded it 
 and installed it.  When I attempted to launch PyMol, nothing happened.  
 So I visited the PyMol web page and found this:
 
 PyMOL v1.4+ do not run on SLED 10.2 due to a bug in Python 2.7 and
 Tcl/Tk.
 
 http://www.pymol.org/support/platforms
 
 Ouch.

I use Debian testing, upon which Ubuntu is based.  I use PyMOL with python
2.7 without any problem.  The only problem I do have is that I have to
compile it with gcc-4.5, rather than the default gcc-4.6 compiler (at least
this was true the last time I checked a few weeks ago).

I compile PyMOL myself after downloading from the SVN sources using the
simple routine of:

CC=gcc-4.5 python setup.py build
python setup.py install --prefix=/software/Linux
python setup2.py install

The --prefix option just allows me to put the software on an NFS mounted
disk, rather than on my own machine, so it is available to all the lab
computers.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Dept. of Biomedical  Molecular Sciences, Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
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Re: [PyMOL] Pymol: Cartoon representation for .pdb file with multible entries

[Robert Campbell]

Hi Alexander,

On Wed, 2011-10-26 12:53  EDT,  Alexander Schulz
sch...@dwi.rwth-aachen.de wrote:

 Hi Thomas,
 
 thank you very much for the answer, I'm beginning to understand the
 actual problem now. 
 
 dss state=1 
 helps, but it changes the problem: I would like to see the secondary
 structure that corresponds to the single snapshot. When I use dss
 state=1, I just see the secondary structure of the first snapshot in all
 snapshots. 
 
 Is there a way to calculate the secondary structure for each individual
 snapshot stored in this single .pdb file?

Yes, simply load the pdb file with the discrete=1 flag:

load md_file.pdb, discrete=1
dss md_file

Setting the discrete flag causes PyMOL to store more information
(B-factors, secondary structure) with each atom of each state -- so it can
also be noticeably slower to load and uses more memory.

Cheers,
Rob

-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Dept. of Biomedical  Molecular Sciences, Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
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Re: [PyMOL] change transparency for only a selection

[Robert Campbell]

Hi Nick,

On Wed, 2011-05-18 11:39  EDT,  Nicolas Bock nicolasb...@gmail.com wrote:

 Hello list,
 
 I would like to change the stick_transparency for a selection but it
 doesn't seem to work. I am using the xyz file from the wiki:
 
 http://www.pymolwiki.org/index.php/Visualizing_a_computed_structure_-_a_commented_example
 
 and the attached script. What am I doing wrong?
 
 Thanks already, nick

Your commands are:

load example.xyz
hide all
show sticks
select sel_01, ID 38 ID 39 ID 42 ID 43 ID 44 ID 45
select rest, all and not sel_01
disable rest

set stick_transparency, 0.8, rest
set stick_transparency, 0.0, sel_01

I think you'll find that the transparency settings only work with whole
objects and not with selections that are subsets of objects.

Cheers,
Rob
-- 
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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
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Re: [PyMOL] slab mode fine-tuning

[Robert Campbell]

Hi,

On Tue, 29 Mar 2011 6:12 AM Nadine Utz [mailto:nad...@mmb.pcb.ub.es]
wrote:

  Dear pymol users,
  
  I am looking for a way to zoom in a molecule, like the slab mode when
  you are rolling the scroll wheel. The reason why rolling the scroll
  wheel does not work in my case is that the resulting change is too
  coarse grained, i.e. either I cannot see all the atoms I want to or
  there are some atoms in front of the part I am interested in. I tried
  as
  well clip slab, x, but then not just atoms in front of the
  interesting
  part are not shown but as well behind it.
  
  So, what I need is a cross-sectional view of my system, in which only
  everything in front of the cut is not shown (but everything behind).
  
  Thank's a lot for any help,
  
On Tue, 29 Mar 2011 07:56:09 -0400 Schubert, Carsten [PRDUS]
cschu...@its.jnj.com wrote:

 Nadine,
 
 Probably the command line is your best friend here. Look into the 'clip
 near,x' and 'clip far,x' command, which allows to move the front and
 back clipping planes in x increments. Positive values move towards you,
 negative values of x away from you.
 If that does not provide enough fine grained control you may want to
 think about making a composite picture to 'fake' clipping planes per
 object.

You can also control the front and rear clipping planes independently by
holding down the Shift key along with the right mouse button (assuming you
are in the standard 3-button viewing mode).  Moving the mouse vertically
changes the front clipping plane and moving it horizontally changes the rear
clipping plane.

Cheers,
Rob



-- 
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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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] Selecting ASP and GLU

[Robert Campbell]

Hi Martin,

On Tue, 01 Mar 2011 13:44:36 +0100 Martin Hediger ma@bluewin.ch wrote:

 Dear all
 What is the selection syntax to select all GLU and ASP residues within 
 an object?
 
 I'm trying it the way its written on the wiki:
 
 remove resn hoh# remove water
 h_add  # add hydrogens
 
 as surface
 color grey90
 
 color slate, resn lys   # lysines in light blue
 color paleyellow, resn cys  # cysteines in light yellow
 *color tv_red, (resn asp or(resn glu))  # aspartic and glutamic acid in light 
 red*

The easier way to write that is:

 color tv_red, resn asp+glu

You can string several sorts of selections together that way, for example:

select actsite, resi 105+262+286

select aliphatic, resn ala+val+leu+ile

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
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Re: [PyMOL] set sphere_scale question

[Robert Campbell]

On Wed, 26 Jan 2011 10:13:25 -0500 Bradley Hintze
bradle...@aggiemail.usu.edu wrote:

 Hi all,
 
 I have a question regarding the changing of sphere size in a PyMOL API. When
 I use the command as presented on the PyMOLwiki, namely:
 
 cmd.set (sphere_scale, size=1, selection='', state=0, updates=1, log=0,
 quiet=1)
 
 I get an error saying
 
 set() got an unexpected keyword argument 'size'
 
 I get the error wether 'size' is a string or an integer. What am I missing?

size is the wrong option,  You want value.  Typing help set at the
PyMOL command prompt shows the following:

   cmd.set(string name, string value, string selection, int state,
   int updates, int quiet)

So you need to change your command to:

cmd.set (sphere_scale, value=1, selection='', state=0, updates=1, log=0,
quiet=1)

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] Loading multiple ligands into a single view

[Robert Campbell]

Hello Tom,

On Fri, 21 Jan 2011 15:28:26 +1100 Tom Dupree t.dup...@unsw.edu.au wrote:

 Hello all,
 
 I have a *.sdf (it can be a *.mol2 if that makes it easier) that contains
 multiple ligands. I'd like to open this one file and see them all at once.
 It currently loads each ligand into its own state. Is there a way to
 over-ride this behaviour?

You don't need to over-ride the loading behaviour.  You can simply set the
all_states variable to 1 (or on):

set all_states, 1

(or use the Settings - Edit all menu item).

Cheers,
Rob

-- 
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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
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Re: [PyMOL] Loading multiple ligands into a single view

[Robert Campbell]

On Fri, 21 Jan 2011 10:10:02 -0500 Robert Campbell
robert.campb...@queensu.ca wrote:

 Hello Tom,
 
 On Fri, 21 Jan 2011 15:28:26 +1100 Tom Dupree t.dup...@unsw.edu.au wrote:
 
  Hello all,
  
  I have a *.sdf (it can be a *.mol2 if that makes it easier) that contains
  multiple ligands. I'd like to open this one file and see them all at once.
  It currently loads each ligand into its own state. Is there a way to
  over-ride this behaviour?
 
 You don't need to over-ride the loading behaviour.  You can simply set the
 all_states variable to 1 (or on):
 
 set all_states, 1
 
 (or use the Settings - Edit all menu item).

I could have added that you can set this variable specifically for one (or
more) objects.  Say you have a set of structures that you want to see all at
once (we'll call it multi), but you have another object with multiple
states, but you only want to see those one at a time and step through them
(we'll call it single), then you can set the above variable to 1 for just
the one object:

set all_states, 1, multi
set all_states, 0, single

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
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Re: [PyMOL] Rendering issues with education version 1.3

[Robert Campbell]

Hi Paul,

On Mon, 17 Jan 2011 19:00:09 -0800 Paul Rigor paul.ri...@uci.edu wrote:

 Hi gang,
 Just wondering if anyone has experienced some weird rendering issues, ie,
 aberrant bonds between atoms. I've attached a sample pdbqt file which
 contains 4 molecules which are outputs of autodock vina. Can someone try
 loading and visualizing it?
 
 I'm currently using the educational version 1.3. I've tried on linux and mac
 os x.  The nvideo cards include both ATI and NVidia.

It isn't really a rendering issue, but a bonding issue (or an atom-ordering
issue -- the structures in this multi-model file do not have the same atoms
in the same order). You need to load the structures in this multi-model file
with the discrete flag turned on. This will force PyMOL to construct a
bonding-table for each model separately.

load top4fix.pdbqt, discrete=1

Cheers,
Rob
-- 
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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
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Re: [PyMOL] Model pdb section support

[Robert Campbell]

Hello Sergey,

On Mon, 10 Jan 2011 16:38:52 +0100 Sergey Ivanov icegood1...@gmail.com
wrote:

 Have pdb file with pseudobeads:
 MODEL 2
 HETATM1   O24.000  46.000  39.000
 HETATM2   O24.000  47.000  39.000

etc.

I displayed this file using Nathan's suggestion to set all_states to 1.  That
appeared to work just fine.  But then I noticed that your second model is
simply a box.  If that is what you always have in the second model, you could
replace that with a CRYST1 line used to represent the unit cell of a
crystal structure.  Hence, your file could look like this:

CRYST1   50.0050.000   50.000  90.00  90.00  90.00 P 1
HETATM1   O24.000  46.000  39.000
HETATM2   O24.000  47.000  39.000
HETATM3   O24.000  47.000  38.000
HETATM4   O25.000  47.000  38.000
HETATM5   O25.000  47.000  39.000
HETATM6   O25.000  46.000  39.000
HETATM7   O25.000  45.000  39.000
HETATM8   O25.000  45.000  40.000
HETATM9   O26.000  45.000  40.000
HETATM   10   O26.000  45.000  39.000
HETATM   11   O26.000  45.000  38.000
HETATM   12   O25.000  45.000  38.000
HETATM   13   N11.000  43.000   8.000
HETATM   14   C12.000  43.000   8.000
HETATM   15   C13.000  43.000   8.000
HETATM   16   C13.000  44.000   8.000
HETATM   17   N 0.000   5.000  29.000
HETATM   18   C49.000   5.000  29.000
HETATM   19   C48.000   5.000  29.000
HETATM   20   C47.000   5.000  29.000
HETATM   21   N23.000  30.000  17.000
HETATM   22   C22.000  30.000  17.000
HETATM   23   C21.000  30.000  17.000
HETATM   24   C20.000  30.000  17.000
END

Then you can turn on the display of the box by showing the cell
representation for the object (under the S menu or by typing show cell).

Cheers,
Rob
-- 
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Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
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Re: [PyMOL] Pseudoatom for Benzene Centre

[Robert Campbell]

Hello Imtiaz,

On Fri, 10 Dec 2010 08:41:14 + imtiaz biobr...@gmail.com wrote:

 I want to create a Pseudoatom in the center of a benzene ring for a ligand.
 
 I can easily create a Pseudoatom in the center of aromatic ring of
 amino acids in a protein by following the instructions give at
 
 http://www.pymolwiki.org/index.php/Pseudoatom
 
 i.e
 load $TUT/1hpv.pdb
 pseudoatom pi_cent,b/53/cg+cz
 
 
 However I am not sure how I can do similar thing for the lignad. The
 lignad I have is an indole derivative and I want to create a
 pseudoatom in the center of the 6 member ring of the indole.

If you simple select to of the atoms on opposite sides of the ring (i.e. so
they are called pk1 and pk2, then you can do something like this:

pseudoatom indole_centre, pk1|pk2

Cheers,
Rob

-- 
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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
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Re: [PyMOL] small molecule geometry gets whacked in creating multi-state object

[Robert Campbell]

Hi Seth and Jason,

I just tried out Jason's commands and while that works for this case I can't
verify that it fails in Seth's case.  While checking the command line options
for create, I did notice that, like the load command, the create command also
has a discrete flag.  It is not described in the help (i.e. when typing help
create), but it is listed in the PYMOL API syntax and it is clearly listed
when you type: create ?.

So I would suggest that you should try your usual script but add a
discrete=1 flag to it.

Cheers,
Rob


 On Tue, 16 Nov 2010 21:46:17 -0500 Jason Vertrees
jason.vertr...@schrodinger.com wrote:

 Hi Seth,
 
 When using the create command, you need to specify target and source
 states.  Here's an example.  Let's assume 1oky and 1t46 are the same
 protein (they're really close, so good for this example).  They both
 have ligands, 1t46 has STI and 1oky has STU.  I can (1) load each
 structure. using fetch:
 
 # fetch the proteins from the PDB, or local file system
 fetch 1t46 1oky, async=0
 
 # align the two proteins (you may not need this step for your application)
 align 1t46, 1oky
 
 and then (2) extract their small molecules, into a new multi-state
 object, called 'ligands using the 'create' command:
 
 # create the object called 'ligands' and put 'resn STI' from state 1
 into state 1
 create ligands, 1t46 and resn STI, 1, 1
 
 # create the object called 'ligands,' which in PyMOL re-creating an
 object that already exists
 # will add another state, and put 'resn STU' from state 1 into state 2
 create ligands, 1oky and resn STU, 1, 2
 
 Hide the first two objects and then use the arrow keys to switch from
 state 1 to state 2.
 
 Cheers,
 
 -- Jason
 
 
 
 On Tue, Nov 16, 2010 at 12:51 PM, Seth Harris set...@gmail.com wrote:
  Hi Jason,
  The end result I am trying to get is a single multi-state object that has
  a different small molecule stored in each state, so that you can use the
  cursor keys and flip through the various ligands (i.e. states) all aligned
  at a given binding site. So what Robert described generates such an
  object, but does so at the point of loading the ligand from an external
  file. I was just trying to see if there was a way to get there from
  objects already loaded in pymol. For instance, I'd have a protein:small
  molecule structure loaded and aligned, and I want to bring just the
  aligned small molecule into one of the states of the multi-state object.
  When I use the create command all kinds of extra bonds were being drawn
  within a given ligand, along with atom colors changing unpredictably. I
  assumed that different small molecules have matching atom names across
  the various states and likely that was causing the trouble. But when
  loaded with the discrete flag it avoids this. Essentially, I was
  imagining something like the 'create' command along with the discrete
  flag. I was searching for some pdb's to share and further explore this
  with. I think it would happen with most any small molecule structure from
  the PDB. Anyway, the workaround seemed to be that once I had loaded the
  protein:small molecule, aligned it, I could save out the aligned small
  molecule only in a temp file, and load it back in to the multi state
  object with the discrete=1 and carry on through all the objects I wanted
  and at the end delete the temp file. The part I thought was a bit clunky
  was having to save the file back out to the file system in order to bring
  it back in with the load command just to be able to get access to the
  'discrete' flag. That's where I thought I might be missing something if I
  explained the case further. Thanks,
  Seth

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Botterell Hall Rm 644
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Re: [PyMOL] Access viewport size

[Robert Campbell]

Hi,

On Wed, 22 Sep 2010 23:29:14 -0400 Jason Vertrees
jason.vertr...@schrodinger.com wrote:

 Hi Mark,
 
 We used to be able to call this to get the viewport size.  But,
 somewhere along the line Warren removed this.  I'll see if I can add
 it back in, or find out why he removed it.

As mentioned in this email:

http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05888.html

this works for me:

width,height = cmd.get_session()['main'][0:2]

I note that a more recent e-mail:
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07563.html

suggests that it doesn't work.  In the latter case, printing
cmd.get_session().keys() showed the absence of the 'main' key.  I couldn't
say why it was absent then and present now (I build PyMOL for Linux from the
SVN sources).

Cheers,
Rob


-- 
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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
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Re: [PyMOL] coloring labels

[Robert Campbell]

Hi Craig,

On Tue, 31 Aug 2010 09:29:44 -0500 Craig Smith boiler...@mac.com wrote:

 Hello,
 
 Thanks for the prompt responses I received so far.  That really helped.
 But, set_color black changes the color globally.  Can I do this locally?
 For example, I'm highlighting two polypeptide chains one blue and one
 yellow.  The yellow labels are hard to see and I want to change them to
 black but the keep the blue chain labels blue.

Yes you can to this locally (at least by object). Simply add the object name
to the command. Say you have two objects called object1 and object2 and
you want to label all of the C-alpha carbons with the residue name and
number, you could do:

label name ca, %s %s % (resn,resi)

set label_color, black, object1
set label_color, blue, object2

Cheers,
Rob
-- 
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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
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Re: [PyMOL] PyMol Connectivity Data

[Robert Campbell]

Dear Martin,

On Thu, 05 Aug 2010 10:44:45 +0200 Martin Hediger ma@bluewin.ch wrote:

 I am confused about the requirement of providing connectivity data in a 
 pdb file to properly render a protein with PyMol.
 Right now, I am displaying a pdb file not containing any connectivity 
 data but still the protein seems perfectly valid.
 
 My question is: how does PyMol know how to properly display structures 
 when no connectivity is provided (i understand this usually is at the 
 end of the file in the 'CONECT...' section. Can it determine 
 connectivity from the atom-labels, like the residue and the 
 atom-descriptor (e.g ATOM   5   CB  VAL A 1 ...)?
 Related to this: I'm not a specialist in protein dynamics, but i 
 understand, every reasonable force field (AMBER, CHARMM, ...) will 
 require me to provide connectivity, correct? The point is, i see the 
 protein displayed correctly in PyMol, but there is no connectivity in 
 the PDB file. Does this mean the force field computation will also work?

PyMOL simply draws bonds where atoms are close enough (defined by the sum of
their vdw radii) or where there are explicit CONECT records.  CONECT records
are only needed where bond lengths are longer than expected.

Molecular dynamics programs require explicit topology (bond lengths, angles,
dihedral angles, chirality), because they are doing much more than simply
making pretty pictures.  So no, a force field computation will not work
simply because PyMOL can draw the bonds you expect to see.

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
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Re: [PyMOL] No module Error in running pymol

[Robert Campbell]

Hi Rituraj,

On Mon, 12 Jul 2010 17:43:02 +0530 rituraj purohit riturajpuro...@gmail.com
wrote:

 Dear friends
 
 I am having Ubuntu 10.04 and want to use pymol.
 There is no error in installation but it is giving following error
 during running pymol
 
 r...@ritu-laptop:~$ pymol
 Traceback (most recent call last):
   File string, line 1, in module
 ImportError: No module named pymol
 /usr/local/bin/python2.6: No module named pymol

You seem to be running a python from the /usr/local/bin directory which is
probably not what you want.  The ubuntu 10.04 python is also python version
2.6, so you have no need to install another version in /usr/local/bin. Did you
install PyMOL from the Ubuntu software repository (as opposed to getting from
the PyMOL web site?  It should work fine with the python in /usr/bin.

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
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Re: [PyMOL] Ray Trace Triangles

[Robert Campbell]

Hi Sean,

On Fri, 09 Jul 2010 11:05:09 -0400 Sean Law magic...@hotmail.com wrote:

 I have been tackling this problem (on and off) for quite some time now but
 without any luck.  I have been trying to create CGO triangles using the
 following simple sample script:
 
 
 ###
 
 from pymol.cgo import *
 from math import *
 from pymol import cmd
 
 def triangle ():
 name=test;
 obj=[ BEGIN, TRIANGLES ]
 obj.extend([COLOR,1.0,0.0,0.0,VERTEX,0.0,0.0,0.0])
 obj.extend([COLOR,1.0,0.0,0.0,VERTEX,2.0,0.0,0.0])
 obj.extend([COLOR,1.0,0.0,0.0,VERTEX,0.0,2.0,0.0])
 obj.extend([END])
 cmd.delete(test)
 cmd.load_cgo(obj,test)
 
 return
 cmd.extend(triangle,triangle)
 
 ###
 
 
 This creates a nice red triangle for me in the viewing window.  However,
 when I move it around and then ray trace the image, I end up getting either
 a triangle with the original bright red color, a black triangle, or a dark
 red triangle.  What I'm looking for is to be able to get the same bright
 red triangle no matter how I manipulate the object.  I've tried playing
 around with the NORMAL value but, if I recall correctly, ray tracing
 produced a blank image.
 
 Any help or suggestion would be greatly appreciated.  Thanks!

I can't find any way to have a CGO object that is not lit in the normal
sense especially when ray traced.  When you leave out the NORMAL vector, then
your triangle is fully lit no matter it's orientation, until you ray trace it.

If you do include a normal vector then its brightness will vary with
orientation both in normal viewing and when ray traced.  You can at least
avoid the problem of having one side completely black when ray traced by
turning on two-sided lighting (in the Display menu).

I guess this doesn't really answer your question, though!

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
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Re: [PyMOL] crankshaft flip

[Robert Campbell]

Dear Jakob,

On Mon, 28 Jun 2010 15:32:59 +0200 Jakob Nielsen jtoudahl.niel...@gmail.com
wrote:

 I would like to modify a protein pdb file with a crankshaft flip, which
 is the anti-correlated double change: psi(i-1) += delta and phi(i) -= delta.
 Such a change should leave the protein coordinates unchanged effecting only
 atoms in residues i-1 and i. However implementation in pymol (see below)
 changes the coordinates of _all_ residues from i-1 to the C-terminal. Can
 you help me? Can I somehow do the two changes simultanious?...
 
 set_dihedral 21/n, 21/ca, 21/c, 22/n,  148.435 #was 168.4
 set_dihedral 21/c, 22/n, 22/ca, 22/c, -83.704  #was -103.7

I don't see how this change can leave the other coordinates unchanged.  Even
if the psi(i-1) and phi(i) bonds are exactly parallel (meaning that the
angles CA-C-N and C-N-CA are exactly the same, which they are not
necessarily), rotation of the psi(i-1) bond will move the N(i) and
CA(i) atoms, so therefore while a rotation in the opposite direction of the
phi(i) bond will tend to keep the rest of the change travelling in the
direction it was before those two counter-rotations, the backbone itself will
be shifted.  One textbook I consulted lists the angles at the C(i-1) and N(i)
atoms as 116 and 122, respectively, so the psi(i-1) and phi(i) bonds are not
even theoretically going to be parallel.  In practice, with real
structures, they certainly are not usually going to be parallel.

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
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Re: [PyMOL] msms_pymol.py

[Robert Campbell]

Hi Sujuan,

On Tue, 18 May 2010 15:58:59 +0800 sujuan wang wsjpy...@gmail.com wrote:

 thank you for you reply and modification of the script. now Ican calculate
 the surface area. but when I calculate the surface of part protein, it seem
 that the surface area including the surface adjacent with other residues,
 means the sum of two fragments is much larger than whole protein surface, is
 there any method to calculate the surface only exposure to solvent?

I'm not sure I understand your problem.  Are you trying to calculate an
interface surface, such as between two proteins or between two chains of one
protein?  Normally the msms program will only calculate the surface that is
exposed to solvent.  The script reports two values for area, the solvent
excluded surface (otherwise known as the molecular surface -- similar to what
is displayed by PyMOL when you show the surface) and the solvent accessible
surface.  The latter is the surface traced out by the centre of a water-sized
probe as it rolls over the van der Waals surface of the protein.  It is
therefore larger than the solvent excluded surface.

Perhaps you could send me at least the output from the calc_msms_area command
to show me what you mean.

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
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Re: [PyMOL] Helices as cylinder and ribbon - both in a single representation

[Robert Campbell]

Hello Abhi,

On Fri, 14 May 2010 12:19:34 +0200 Abhinav Verma abhinav1...@gmail.com
wrote:

  I wish to show one chain in cylindrical helices, while the other one in
 ribbon representation. How can I achieve this with pymol.

If the two chains are in one object, then you need to split them into two
objects.  So if I'm working with the PDB file 1dvi, something like:

create cha, 1dvi  chain a
create chb, 1dvi  chain b

Then I can type:

set cartoon_cylindrical_helices, 1, chb

To make the chain B object have cylindrical helices, while chain A will
remain with the ribbon-style.

Cheers,
Rob
-- 
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Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
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Re: [PyMOL] msms_pymol.py

[Robert Campbell]

Hi Hongbo,

On Wed, 12 May 2010 15:59:36 +0200 Hongbo Zhu
hongbo@biotec.tu-dresden.de wrote:

 You can solve it by adding the following line in the msms_pymol.py you 
 downloaded from Robert's page to line 133, right before msms_cmd is defined.
 
  if msms_path.startswith('C:/'): msms_path = '\%s\' % (msms_path,)
 
 Basically, your problem was caused by the whitespace in the path to the 
 MSMS executable file in Windows systems. By adding quotes to the full 
 path solves the problem.

Thanks for that fix. In fact this problem could exist on other systems if
someone happens to use spaces in their directory names, so I've added escaped
quotes to the msms_path in all cases (not just if it starts with 'C:/'.  Also
if one used the debug=1 flag, it will print out the MSMS command used to help
identify problems. The new version is on my website.  

Cheers,
Rob

-- 
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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
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Re: [PyMOL] How draw the line in images

[Robert Campbell]

Hi Peter,

On Wed, 12 May 2010 10:42:36 -0400 Jason Vertrees
jason.vertr...@schrodinger.com wrote:

 Peter,
 
 If you knew the positions of the end points of the lines you could
 make CGO lines, or you could just use a distance measure between two
 pseudoatoms and modify some label/dash settings:

As Jason says, if you have some end-points you can make CGO lines (or
cylinders).  I have a script to do that called draw_links.py on my
website.  If you have two atoms to define the end-points you can just pick
them (so that they are called pk1 and pk2) and then run the command

draw_links

It has options to control the colour and diameter of the cylinder, and you
can name the atoms rather than picking them.  E.g.

draw_links prot1  c. a  i. 105  n. n, prot2  c. b  i. 311 
n. od1, radius=.2, color=blue

The color can also be specified as a tuple of numbers between 0 and 1 for the
r,g,b components and a second colour can be added if you want the colour of
the cylinder to fade from one end to the other.

draw_cylinder color=(.5,.2,.5), color2=pink, object_name=faded_links

(where pk1 and pk2 are the endpoints and faded_links will be the name of
the object created).

You can also use this to draw a bunch of CGO cylinders between pairs of
atoms.  E.g. you want to show the domain motion after aligning parts of two
structures:

draw_links 1kfu  c. l  i. 105+262+286+288, 1kxr  c. a   i. 
115+272+296+298,color1=red,color2=blue

If more than one atom is specified in each selection, then it will draw a
cylinder between each of the 4 pairs of C-alpha atoms specified in the two
selections.  In this case the colour of the cylinder fades from red to blue,
but if you do not specify color2 then it will be a single colour.

Cheers,
Rob
-- 
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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
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Re: [PyMOL] PyMOL Plugin Architecture

[Robert Campbell]

Hi Maia,

Just to add to what Jason said:

On Thu, 22 Apr 2010 17:16:41 -0400, Jason Vertrees
jason.vertr...@schrodinger.com wrote:

  2. Which plugin allows me to move one structure relative to another. (I
  want to do manual docking of one structure into another).
 
 You don't need a plugin to move objects.  Just use SHIFT-middle-mouse
 button drag, while in editing mode.  If you're starting from one
 object (eg. protein and ligand come from one file) then split them up:

In case it isn't obvious to you, you can switch between viewing mode and
editing mode simply by left clicking in the bottom-right region of the main
PyMOL window where the mouse button functions are described.

Cheers,
Rob

-- 
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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
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Re: [PyMOL] please help-how to generate dimer file from monomer file in pymol

[Robert Campbell]

Hello Jenna,

On Tue, 06 Apr 2010 00:36:38 -0400 JiangJiang Liu jli...@uwo.ca wrote:

  When I open the  pdb file 1B8E (a homodimer protein) through
 pymol I can only see a monomer shown in the screen. Now I know the
 biological dimer is produced through crystallographic symmetry operations
 in pymol. To generate the dimer, I think I need to convert these remark
 comands (list below) to be a readable commands by the pymol program. Does
 anyone know how to do this conversion? Or what's the commands for crystal
 symmetry operation? Thank you very much! Sincerely Jenna Liu
 
 PS: 
 REMARK 350 BIOMOLECULE:
 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT:
 DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS:
 A REMARK 350   BIOMT1   1  1.00  0.00  0.00
 0.0 REMARK 350   BIOMT2   1  0.00  1.00  0.00
 0.0 REMARK 350   BIOMT3   1  0.00  0.00  1.00
 0.0 REMARK 350   BIOMT1   2 -1.00  0.00  0.00
 0.0 REMARK 350   BIOMT2   2  0.00  1.00  0.00
 0.0 REMARK 350   BIOMT3   2  0.00  0.00 -1.00
 33.43000 

Since the file has the crystallographic information in it, you simply have to
tell PyMOL to build the symmetry-related neighbours.  You do this with the
symexp command:

symexp prefix, object, selection, cutoff

So if you have an object called 1b8e, you might do:

symexp s_, 1b8e, 1b8e, 3

This will create new objects whose name begins with s_ and is followed by a
label that identifies the symmetry operation.  You can then turn them on and
off until you find the one that is the mate of the original object.  Given
the BIOMT matrix above, this will be the object that is related by a 2-fold
rotation around the crystallographic b-axis (which in this case is parallel
to the Y-axis) followed by a translation of 1/2 of the c-axis.  This is the
object called s_03-1 in this case.

Or as Jason has just written, fetch the biological unit directly and then
split out the states.

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
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Re: [PyMOL] coordinates

[Robert Campbell]

Hi Jed,

On Mon, 22 Mar 2010 10:23:34 -0400 Jed Goldstone jgoldst...@whoi.edu wrote:

 Of course, you could just use the .pdb file as a text file:
 
 grep CA .pdb | cut -f 2,4,7,8,9
 
 will get you the amino acid number, the amino acid identity, and x,y,z 
 coordinates for the CA.

Often this will work, but unfortunately it is not fool proof.  If there is
no chain ID, if the residue numbers are greater than 999 or if there are
alternate position characters present on the atom names, then your field
counts in your cut command will be off. The PDB file is very strict about
which character columns contain which information and there is no requirement
for spaces between those data columns.

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
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Re: [PyMOL] frustrating rms command

[Robert Campbell]

Hello Alan,

On Tue, 16 Mar 2010 11:33:41 + Alan alanwil...@gmail.com wrote:

 Hello there,
 
 I am very frustrated with a very simple command, let me show:
 
 PyMOLrms (out and not hydrogen), (018.none_neutral.pdb_NEW and not
 hydrogen)
 ExecutiveRMS-Error: No atoms selected.
 PyMOLsele r, (018.none_neutral.pdb_NEW and not hydrogen)
  Selector: selection r defined with 20 atoms.
 PyMOLselect o, (out and not hydrogen)
  Selector: selection o defined with 20 atoms.
 PyMOLrms o, r
 ExecutiveRMS-Error: No atoms selected.
 
 As you can see, I can select properly but no way of using 'rms' command.
 
 Or help rms is missing something?

Yes, the help for rms is missing something. What is missing is the
description in the help for rms (as well as for rms_cur and fit) that the two
selections that rms is comparing must contain the same atom descriptions
(chain ID, residue name, residue number, atom name and segment ID). Are your
molecules out and 018.none_neutral.pdb_NEW identical?

Cheers,
Rob
-- 
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Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
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Re: [PyMOL] frustrating rms command

[Robert Campbell]

Hi,

On Tue, 16 Mar 2010 09:23:50 -0400 David Hall li...@cowsandmilk.net wrote:

 See http://www.pymolwiki.org/index.php/Intra_Rms#USER_EXAMPLES.2FCOMMENTS
 comments that start with Fit, Rms, Rms_Cur are finicky and only
 work... as that likely explains your problem and a possible solution.
 
 But I agree that pymol's behavior with this command can be extremely
 annoying.

I should have added to my previous e-mail that I wrote a script to take care
of this problem.  It will calculate the RMS for a pair of selections by
converting one to match the other (residue names, numbers, atom names etc. --
obviously only matching the backbone atoms).  It creates a new object in
order to do this.  The script is called fitting.py and can be found at my
pymol scripts site:

  http://pldserver1.biochem.queensu.ca/~rlc/work/pymol

and a description of the problems of fitting and an example of the use of
the fitting.py script can be found here:

   
http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol/alignment/

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
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Re: [PyMOL] B-factor replacing problem

[Robert Campbell]

Hi Thomas,

On Tue, 09 Mar 2010 10:29:17 +0100 Thomas Holder
spel...@users.sourceforge.net wrote:

 Hi Simon and Robert,
 
  It sounds like the file as it is read by the script is completely on one
  line. I wonder if this is the old UNIX vs MSDOS line ending problem.
 
 yes, sounds like a linefeed problem. But actually python has universal
 newline support. I made some changes to the script (quite a lot
 changes, sorry ;-)) and now can read any of mac/unix/dos text files
 using MacPyMol.

I wasn't convinced that the linefeed was the problem, but it was the only
thing I could think of and was prompted from a recent teaching experience in
which a group of students using Windows were having some problems with
scripts that they wrote in Wordpad or Notepad. 

Thanks for sending along your version of this script. I've learned something
from it!  I didn't know about the dictionary .setdefault function -- that
looks very useful, although a little harder (at least for me) to comprehend
for the dictionary of dictionaries in this script.  It certainly makes the
code look cleaner.

Cheers,
Rob

-- 
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Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
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Re: [PyMOL] B-factor replacing problem

[Robert Campbell]

Hi Simon,

On Mon, 08 Mar 2010 18:09:31 +0100 Simon Lindhoud simon.lindh...@wur.nl
wrote:

 Dear all,
 
 Unfortunately I'm not really familiar with programming in Python (yet) but
 I've encountered a problem with MacPyMol in running the script that can be
 found here: 
 http://cavanagh-lab.bch.ncsu.edu/bobay/intranet/pymol/data2bfactor.py

That is a slightly older version of my script, although I don't believe that
is the problem.

 I've tried a couple of things to get the script running, and in the end I
 managed to narrow the problem down to the fact that the file that contains
 the data for the new b-factors is not imported correctly. I have made a text
 file, containing four columns that I've copied from excel; the Chain, the
 residue number, the residue name, and the b-factor. These columns are
 separated by tabs. In the script this code is used to determine the number
 of columns in my file:
 
 words = line.split()
 
 # check number of columns of data
   if len(words) == 4:
 etc
 
 Apparently, this is where it goes wrong because if I print the words
 variable. I get the total number 'words' in my input file instead of the
 number of columns...
 Does anybody know the solution to this problem?

It sounds like the file as it is read by the script is completely on one
line. I wonder if this is the old UNIX vs MSDOS line ending problem.  Did the
data file happen to come from a Windows computer?

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
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Re: [PyMOL] Whitespacing?

[Robert Campbell]

Hi,

On Tue, 26 Jan 2010 10:48:58 -0600 Michael Zimmermann micha...@iastate.edu
wrote:

 If you have a lot of files to do this to, I would suggest learning at
 least a little bit of perl.  It might not be as nice an option as a
 python tab manager (depending on your point of view), though.

Or even better, try sed (the following is in a bash-type shell)!

for file in *.py; sed 's/   /  /g'  $file ${file}.notab

In order to type the tab key in the command line, type the key combination
CTRL-V followed by the Tab key.

I use vim as my editor and I have it set to always use spaces and not tabs
using the expandtab setting, so when I hit the Tab key, it just inserts
two spaces for me.

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
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Re: [PyMOL] difficulties with pymol’s fuse command .

[Robert Campbell]

Hi,

I posted an answer on the blog, but I'll copy it here.  Someone can correct
me if I'm wrong!

On Tue, 08 Dec 2009 10:02:59 -0600 Michael Zimmermann micha...@iastate.edu
wrote:

 I have no experience with fuse, but my guess would be Mariana might
 want to just use 'bond' and translate one termini as needed.  If she
 doesn't want to manually translate, there is always energy
 minimization to correct bond lengths.
 Take Care.

 On Tue, Dec 8, 2009 at 12:59 AM, Nir London n...@rosettadesigngroup.com
 wrote:
  Hi PyMOL list,
 
  Can anyone help Mariana with her question ?
  http://rosettadesigngroup.com/blog/10/pymol-scripts/#comment-9695

Given that Marianna describes the sequence display as if the 2 original
sequences have been interjected into one another, then I think the problem is
that the two original objects have the same chain IDs and their residue
numbers overlap. Perhaps if they had different chain IDs or if the second
molecule is renumbered to have residue numbers that start after the first
molecule it would work correctly.  PyMOL can get confused when there are
multiple residues with the same chain ID and residue number.

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
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Re: [PyMOL] Show hydrogen bonds in current object only

[Robert Campbell]

Hi Jason,

On Sun, 29 Nov 2009 12:29:08 -0500, Jason Vertrees jason.vertr...@gmail.com
wrote:

 You can automate the task.  Load your 100 proteins.  Use a wildcard
 from the command line or a script like loadDir
 (http://pymolwiki.org/index.php/LoadDir).  Align them.  Then, run:
 
 python
 for n in cmd.get_names(objects):
   selName = s + n
   cmd.select(selName, n)
   cmd.distance(dist+n, selName, selName +  and (organic and  + n + ), 
 3.2, mode=2)
 python end

I'm just curious, but why do you go to the trouble to create a selection that
is just the whole object? Especially if Chimed has 100s of objects, he
doesn't need to add a named selection for each. Why not do the following?

python
for n in cmd.get_names(objects):
  cmd.distance(dist+n,n,n +  and organic,3.2, mode=2)
python end

The latter worked for me.  If you wanted to eliminate waters from
the selection for the protein, you could change it to:

python
for n in cmd.get_names(objects):
  cmd.distance(dist+n,n +  and not solvent,n +  and organic,3.2,mode=2) 
python end

Or to make it more readable:

python
for n in cmd.get_names(objects):
  protein_sele = n +  and not solvent
  organic_sele = n +  and organic
  cmd.distance(dist+n, protein_sele, organic_sele, 3.2, mode=2)
python end

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
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Re: [PyMOL] spectrum

[Robert Campbell]

Hi Mark and Sean,

On Sat, 07 Nov 2009 10:05:59 -0500 Sean Law magic...@hotmail.com wrote:

 Sorry for the earlier confusion.  I think I found a hackish way of getting
 a gray spectrum:

snip Sean's extensive explanation

I know I'm biased, since I wrote the color_b.py script, but I fail to see what
is difficult about typing:

color_b  selectionname, gradient=user, user_rgb=[.2,.2,.2,.5,.5,.5,.8,.8,.8]

In order to colour selectionname in a gray spectrum that goes from 20%
gray, has a midpoint of 50% gray and ends at 80% gray (where 20% gray is the
same as the colour called gray20, i.e. close to black and 80% gray is almost
white). 


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
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Re: [PyMOL] Spectrum

[Robert Campbell]

Hi Sean,

On Mon, 09 Nov 2009 10:58:53 -0500 Sean Law magic...@hotmail.com wrote:

 
 Robert,
 
 I would have to agree with you.  I've used many of your scripts and have
 also learned a lot from them and think that the color B script is pretty
 robust and helpful.

Thanks.
 
 I could be wrong but I remember the original poster commenting about using
 the min  max settings from the spectrum command and I wonder if that is
 used to control the min/max of B-factor values to color (so that any values
 outside of the range of min and max will be colored the extreme min/max
 color values).  Of course, I'm sure it's just as easy to add a couple of
 lines of extra code into your script to account for that (if it isn't
 already there).

The color_b.py script has options called minimum and maximum just
like the spectrum command.  These are used to select the range of
B-values to colour. So (using PDB code 1dvi as an example) if your actual
B-values are between 2 and 55.98 and you set the minimum to 10 and
maximum to 50, then use 8 bins (just to get nice numbers here!), by typing:

color_b minimum=10, maximum=50, nbins=8

You'll see the following output from the color_b.py script:

Minimum and Maximum B-values:  2.0 55.975422
Color select:  n. ca and (b15 or b =   15)
Color select:  n. ca and b15
Color select:  n. ca and b20
Color select:  n. ca and b25
Color select:  n. ca and b30
Color select:  n. ca and b35
Color select:  n. ca and b40
Color select:  n. ca and b45

So yes, anything within the lowest range and below will be in colour 1 and
anything within the highest range and above will be in colour 8.

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
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Re: [PyMOL] Alignment Objects

[Robert Campbell]

Hi David
On Thu, 10 Sep 2009 14:47:43 -0700 (PDT) David Hall dwash59_2...@yahoo.com
wrote:

 Is there any documentation on getting information out of alignment objects
 into scripts?  I tried looking around the wiki, but I didn't see anything.
 
 I'm just wondering things like if I have a residue in one object, finding
 the residue in another object that has been aligned.  

If you create an alignment object when you do the alignment:

  align proteinA, proteinB, object=A_on_B

then you can save a clustal formatted alignment file by typing:

  save A_aligned_with_B.aln, A_on_B

(same applies if you use the super command instead of align).

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] Measure surface area

[Robert Campbell]

Hi Mirek,

On Mon, 10 Aug 2009 11:21:39 -0700 Warren DeLano war...@delsci.com wrote:

 PyMOL isn't the optimal tool for measuring surface area -- perhaps
 others on the list can suggest good alternatives.  

I like MSMS for this.  I have a script that will calculate the area (both
solvent exposed and solvent accessible) for a particular selection.

See my msms_pymol.py script at:

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol

After loading the script with the run command, you can type help
calc_msms_area to get more information on the options.

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] Pymol build from source

[Robert Campbell]

Dear Joseph,

On Tue, 07 Jul 2009 11:00:10 +0200, Andre Joseph andrejos...@gmail.com
wrote:

 Dear Delano Scientific support
 
 I've been fetching source code from the sourceforge repositories yesterday.
 I've no error or warning during ./configure, make or make install
 steps.
 However, when I launch pymol, I've the following error:
 
 Traceback (most recent call last):
File /home/joseph/software/pymol/modules/launch_pymol.py, line 32, in
  module
  import pymol
File /home/joseph/software/pymol/modules/pymol/__init__.py, line 472,
  in module
  import _cmd
  ImportError: /home/joseph/software/pymol/modules/pymol/_cmd.so: undefined
  symbol: molfile_vaspparchgplugin_init
 
 
 I've found in the archive that it might come from a problem in setup.py
 file but I couldn't figure out what was missing (http://tinyurl.com/ndpafb).
 I've been building PyMOL from source for a year or so and never faced up any
 problem. Could it come from the sources or is a problem of dependancies?

I think the recommended way of building PyMOL is with these commands (see
the INSTALL file):

python setup.py build
python setup.py install
python setup2.py install

Since I install it in a non-standard location (an NFS file server accessible
from many workstations of both i686 and x86_64 versions of Linux), I add a
prefix to the install command:

  python setup.py install --prefix=/software/Linux

or

  python setup.py install --prefix=/software/Linux_x86_64


Then I keep a saved and modified copy of the pymol script created by the
python setup2.py install command and copy that back over the newly created
pymol script instead (because I have a few customizations in it).

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] surface for oligosaccharide chains

[Robert Campbell]

On Fri, 03 Jul 2009 16:18:10 +0200, Raluca Mihaela ANDREI r.and...@sns.it
wrote:

 Hi!
 Can somebody tell me why I can't create surfaces for the 
 oligosaccharide chains?

By default, the surface and mesh commands ignore all atoms in HETATM records
in a PDB file.  You can change that with:

  set surface_mode, 1
  set mesh_mode, 1

That means, though, that *all* hetatm atoms will have a surface drawn.  If you
want to draw a surface for your oligosaccharide chains alone, then you can
copy them to a separate object and set the surface_mode flag just for that
object:

  set surface_mode, 0
  create saccharide, object  selection   
(fill in your residue selection for selection)

  set surface_mode, 1, saccharide


Hope that helps,
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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] POVRAY Usage

[Robert Campbell]

Hi Tom

On Fri, 15 May 2009 14:57:36 -0700, Thomas Stout tst...@exelixis.com wrote:

 What version of PyMOL does this work with?  I've been trying your commands
 with versions 1.1 and 1.2b and while PyMOL reports that the primitives have
 been processed, nothing is written to the file protein.pov other than the
 header info:
 
  camera {orthographic location 0.0 , 0.0 , 134.1048736572
  look_at  0.0 , 0.0 , -1.0 right -74.9812240601*x up 59.9849815369*y}
  #default { finish{phong   -1.000 ambient0.500 diffuse0.450
 phong_size 13 .75}}
  light_source{4000.0001,4000.0001,9865.8951  rgb1.0,1.0,1.0}
  plane{z , -206.0869 
   pigment{color rgb1.,1.,1.}
   finish{phong 0 specular 0 diffuse 0 ambient 1.0}}
  #include povray.inc
 
 and povray.inc contains:
  cmd.get_povray()[1]
 
 If I save a povray file with the GUI menu selection: File Save Image As
 POV-Ray then I get everything written to disk.  This occurs on both linux
 and Windows.
 
 Am I missing something that would be more obvious if I had had more coffee
 today?
 
 Thanks!
 -Tom
 
 PS - There was a missing quotation mark:
 open(povray.inc,w).write(cmd.get_povray()[1]) --
 open(povray.inc,w).write(cmd.get_povray()[1])

I think this is the real key!  There was an extra quote.  Try:

open(povray.inc,w).write(cmd.get_povray()[1])

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

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Re: [PyMOL] problem in showing the electron density map

[Robert Campbell]

Hi Peter,

On Fri, 03 Apr 2009 02:38:03 +0530, peter hudson
peter.hudson.pe...@gmail.com wrote:

 Hello all
 
 I am trying to upload the ED map on pymol. but, it is not visible on the
 screen. Although i checked at pymol wiki and i did as it is given on the
 wiki.
 For example.
 
 I took ccp4 format map and coverted it into xplor format with
 mapman.(beacuse i tried with ccp4 format map with test_file.map as well as
 test_file.ccp4 maps, but pymol showed this kind of error. I begin like this-

Warren answered the later problem regarding the site selection or object.
You should be able to load a ccp4 map either directly as a .ccp4 file, or to
force it to load as a ccp4 format with:

load test_file.ccp4, map, format=ccp4

Does PyMOL complain that it doesn't know the format with an error like:

  PyMOLload test_ccp4.map
  Error: .map is ambiguous.  Please add format or use another extension:
  Error: For example, load fofc.map, format=ccp4 or load 2fofc.xplor.

or was the error that you couldn't display the map on the molecule (as in the
error that Warren commented on about using site as a selection when site
has not been defined?

Also be aware that PyMOL needs to have a map that is calculated to cover the
molecule that you are showing since it does not automatically extend the map
using symmetry.

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] fitting problem

[Robert Campbell]

Hi Sébastien,

On Mon, 02 Mar 2009 18:21:15 +0100, sconill...@chimie.u-strasbg.fr wrote:

 Hi all (for the second time today ...),
 
 I have a problem using the fit function. When I try to do this :
 
  fit (fittest1 and resn P and !h.), (2VT4 and resn P and !h.)
 
 I have this message error :
 
 ExecutiveRMS-Error: No atoms selected.
 
 which seems very strange to me because doing something like :
 
  select d1, (fittest1 and resn P and !h.)
 or
  select d2, (2VT4 and resn P and !h.)
 returns
 Selector: selection d1 (or d2) defined with 21 atoms.
 
 Any idea ?

Do (fittest1 and resn P and !h) and (2VT4 and resn P and !h.) have the same
list of atoms with the same residue number, chain and atom names?  If not,
then you will get that sort of message.

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] trouble with symexp command

[Robert Campbell]

Hi Dave,

On Tue, 03 Feb 2009 16:33:28 -0500, David Garboczi
dgarbo...@niaid.nih.gov wrote:

 I am examining packing in several space groups by issuing the command
 
 symexp foo, foo.pdb, sele, 10
 
 If I select the whole reference molecule, I think that I should get 
 all the symmates within 10 A displayed.  But for one of the crystals 
 that I am dealing with,
 CRYST1   29.24   44.19  107.67  90.0  90.0  90.0 P 21 21 218
 
 only four molecules are generated, the molecules are on top of one 
 another, and also are so far from each other that the packing can't 
 be real.  The cell has 22% solvent. In Coot, however, this same 
 molecule and the Cell  Symmetry command gives rise to symmates 
 that look right and don't clash with each other.
 
 Help in figuring this out?  I am using MacPyMol 1.1r1 on a ppc 10.4.11

Since you say that you are examining packing in several space groups (and so
I'm guessing that maybe you have the same molecule in different space groups),
I'm led to ask if you happened to move the molecule foo by aligning it to
another molecule? This would cause the clash that you're seeing because PyMOL
would be applying the symmetry operators to foo in the wrong position.

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] Showing conserved residues

[Robert Campbell]

Hi Abhinav,

On Thu, 29 Jan 2009 13:10:25 -0800, Abhinav Kumar
abhin...@slac.stanford.edu wrote:

 Is there someway to select and show conserved residues when a bunch of 
 superimposed structures are loaded into Pymol?
 And if so, can identical and similar residues be selected separately?

I don't believe that there is a direct way to do it from the
superimposition, but I commonly apply external data to the B-factor
column of a PDB file for colouring purposes. For example, you could
calculate the degree of sequence conservation at each residue and colour
on that. I use the following scripts:

http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/variability.py
http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/seq_convert.py
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/data2bfactor.py

See the pages:

http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/
  and
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol

for more information.

When you align the structures, if you use the object= keyword (or do
it using the align menu) it will create an alignment object that you
can save as a Clustal format file. This file can then be used to calculate the
sequence variability. 

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] I want to represent a domain of my molecule as a low resolution solid shape

[Robert Campbell]

Dear Pietro,

On Thu, 11 Sep 2008 13:18:20 +0100, Pietro Roversi
pietro.rove...@path.ox.ac.uk wrote:

 Dear everyone,
 I want to represent a domain of my molecule as a low
 resolution solid shape. 
 
 I have chosen surface representation but the surface is clipped,
 exposing the inner part, which makes the domain appear hollow. The
 rendering of the inner surface appears greyish and different from the
 outer part. 
 
 Can I make the clipped surface filled so that this greyish inner part is
 not there anymore? It should look solid inside.  
 
 Alternatively, do you think I should switch to spheres representation?
 But I still would need to blur the spheres to achieve the low-resolution
 look of the domain. 

I am presuming that by low resolution you mean that you have increased the
solvent radius from the default of 1.4 to something larger, like 6
Angstroms.  I see that this can result in gaps in the surface.  I wouldn't
call it clipped, though.  If you draw a solvent accessible surface instead of
a molecular surface (by setting the variable surface_solvent to 1 instead of
0) then the gaps will disappear, but the surface will now be 6 Angstroms out
from the van der Waals surface.  It doesn't appear to have gaps now.

Alternatively, you can draw the surface using the MSMS program.  It does not
have the same artifacts as the built-in PyMOL surface generation routine for
large probe radii.

I have a script for running that from within PyMOL:

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/msms_pymol.py

Unfortunately I have not written any colouring schemes to the script other
than specifying a single solid colour for the whole surface (or two colours
if you specify a selection, e.g. if looking at an interface surface).

Hope this helps,
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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] coloring based on sequence identity

[Robert Campbell]

Dear Morri,

On Fri, 22 Aug 2008 13:35:32 -0700, Morri Feldman
morrifeld...@gmail.com wrote:

 Dear Rob,
 
 I'm interested in using your variability script with a substitution matrix.
 Would you please send me an example of a substitution matrix file?  Thanks
 for writing such a useful script.

Sure.  Attached are a couple of matrices.  One is a blosum80 matrix and
one is a hydrophobicity matrix.  I think I found them at:

http://www.techfak.uni-bielefeld.de/bcd/Curric/PrwAli/nodeD.html
http://www.techfak.uni-bielefeld.de/bcd/Curric/PrwAli/nodeE.html

You should be able to easily create your own following those examples.

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc


blosum80.mat
Description: Binary data


hydrophobicity.mat
Description: Binary data

Re: [PyMOL] How to view electron densities from the PDB

[Robert Campbell]

Hi,

On Fri, 27 Jun 2008 13:25:02 -0400, Michael Lerner mgler...@gmail.com
wrote:

 This is probably a fairly basic question, but I'm stumped. I want to
 visualize electron densities along with my PDB file. So, say I'm interested
 in 2DJX. I go to the PDB and download 2DJX.pdb and 2djx-sf.cif. PyMOL
 doesn't seem to read the CIF file (?), so I downloaded and installed the
 PDB's tool sf-convert (http://sw-tools.pdb.org/apps/SF-CONVERT/index.html).
 I tried
 
 sf-convert -i CIF -o Xplor -sf 2djx-sf.cif
 
 but got some errors about the input format.
 
 sf-convert -i mmCIF -o Xplor -sf 2djx-sf.cif
 
 seemed to work (it produced a .Xplor file with what looks like data to me).
 However, PyMOL gives me errors when I try to load the resulting .xplor file.

The sf file that you have is not electron density but structure factors.
You need to calculate electron density from the data in that file and phases,
which you would have to calculate from the structure.  Fortunately someone
else is already doing that for you.  Try the Electron Density Server
(http://eds.bmc.uu.se/eds/).

Simply enter the PDB code and you'll find ... oh dear ... that 2djx is not
entered yet. :(

I see that it is a fairly new structure (released yesterday) and EDS is
updated weekly.  So either wait a week or so, or find a crystallographer to
run the coordinates and structure factors through a single refmac cycle to
calculate a map for you.

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] Spheres for metal ions

[Robert Campbell]

Hi Gary,

On Tue, 20 May 2008 12:12:43 +0200, Gary Hunter
gary.hun...@um.edu.mt wrote:

 I am displaying pdb files of metalloenzymes, and like to show the metal ions
 as spheres.
 I select the metal and use showspheres
 Fine
 Somehow recently I must have done something to reset the vdw radius of
 manganese (MN in the pdb), as Mn atoms now display as small spheres (a
 little larger than solvent as nb_spheres).
 They were fine originally (!) and other metal atoms display at correct sizes
 (much bigger than my Mn).
 What could I have done?
 
 A global edit of sphere_scale etc. simply changes all.
 I reset the settingedit_all using the dialog as a check too.
 I can use:
 Alter name MN, vdw=vdw*2
 Rebuild
 
 Or whatever, but I have to do it for each pdb file I read in now (if it has
 a Mn atom).
 Could I have messed with the vdw value in some way?
 
 Is there a way to actually check the values being used for vdw radii?

You can get the vdw radii for any items (say you have a selection called
metals) with:

  iterate metals, print chain, resn,resi,vdw

which will print the chain ID, residue name, residue number and van der Waals
radius for each.  Of course, this only applies to the vdw radius that is
assigned after you read in the PDB file.

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] getting a list of main-chain hydrogen bonds

[Robert Campbell]

Hi Tomoko,

On Mon, 05 May 2008 18:26:17 +0900, Tomoko Niwa tmk.n...@gmail.com
wrote:

 Thanks for kind advices.
 
 Whatif and PISA worked excellently, but I want to get the list within Pymol.
 
 
 By parsing the pymol modules, I found
 
 hb = cmd.find_pairs(((byres +sss1+) and n;n),
   ((byres +sss1+) and n;o),mode=1,
   cutoff=3.7,angle=55,
   state1=state,state2=state)
 
 in util.py. Is it possible to get a list of main-chain hydrogen bonds with
 this function?

Yes it is.  I thought this was a useful idea, so I've just scribbled together
a script to do just that and it is attached.

You can load it the usual way (run print_hb_list.py) and then run it
with:

   print_hb selection

Warning, if you have waters in your selection it will mess it up, so try:

  print_hb 1nzl ! resn hoh

I haven't fixed that part yet.  You may wish to alter the formatting of the
output, but I copied the example in your first e-mail:

 /GLY`56/N  /ASN`181/O  2.86
 /TYR`26/N  /VAL`182/O  2.92
 /ASN`54/N  /THR`183/O  2.95
 /ASN`52/N  /TRP`185/O  2.92
 
In my case the PDB file had no chain identifier.

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc
from pymol import cmd

def print_hb(selection):
  hb = cmd.find_pairs(((byres +selection+) and n;n),((byres +selection+) and n;o),mode=1,cutoff=3.7,angle=55)

  pair1_list = []
  pair2_list = []
  dist_list = []
  for pairs in hb:
cmd.iterate(%s and ID %s % (pairs[0][0],pairs[0][1]), 'print %s/%3s`%s/%s  % (chain,resn,resi,name),')
cmd.iterate(%s and ID %s % (pairs[1][0],pairs[1][1]), 'print %s/%3s`%s/%s  % (chain,resn,resi,name),')
print %.2f % cmd.dist(%s and ID %s % (pairs[0][0],pairs[0][1]),%s and ID %s % (pairs[1][0],pairs[1][1]))

cmd.extend(print_hb,print_hb)

Re: [PyMOL] merging many frames to one

[Robert Campbell]

Hi again, Dimitry,

On Tue, 12 Feb 2008 09:10:23 -0500, Robert Campbell
robert.campb...@queensu.ca wrote:

 Hello Dimitry,
 
 On Tue, 12 Feb 2008 16:43:28 +0300, DimitryASuplatov
 gene...@gmail.com wrote:
 
  Hello,
  I have a .pdb1 file with biological unit. It consists of two frames
  representing two chains (one per frame) together forming biologicaly
  significant molecule. I could apply crystallographic symmetry, instead I
  want to make use of file that I already have.  What is the command to
  merge this two frames to a single one?
 
 Type:
 
 set all_states, 1
 
 Or set that in the Setting - Edit All... menu.

Sorry, this method only allows both chains to be viewed, but may not be
ideal for your purposes.  If you really wish an object that shows both
chains as part of one object in one state, then you need to do:

  split_states orig_object

which will create new objects with _0001 and _0002 appended to their names.
You can then merge those objects into a new object with:

  create new_object, orig_object_0001 or orig_object_0002

But before you do that, make sure the new orig_objects have different chain
IDs, or you'll have some problems.  If necessary then, you can do, for
example:

  alter orig_object_0002, chain='B'


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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] MSMS Cavity Visualization in Pymol

[Robert Campbell]

Hi Buz,

On Wed, 30 Jan 2008 14:41:00 -0500, Buz Barstow b...@mac.com wrote:

 Does anyone know of a script that is capable of displaying the  
 surfaces identified by msms in pymol?

I have a script called msms_cgo.py that you can download from:

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

Download it and run it. You can get some usage information by doing:

  PyMOLmsms_cgo ?
  Usage: msms_cgo file_name [, obj_name [, surfcolor ]]

or

  PyMOLhelp msms_cgo
  msms_cgo file_name, [obj_name ] , surfcolor
default surfcolor is white (1.,1.,1.) 
 
So only a file name is required (and you can omit the .face or
.vert).  You can just give it a file name (e.g. your surfaces are in
my_mol.vert and my_mol.face:

  msms_cgo my_mol

It will create an object called my_mol_msms and colour it white.  If you
want a different colour and object name, then do:

  msms_cgo my_mol, my_surf, surfcolor=(.5,.5,.5)

to make it gray.

Unfortunately it can only do one colour at the moment.  I haven't tried to
modify it to colour the surface according to the atom, although that
shouldn't be too hard to do.

Remember that if the cavities are enclosed, interior surfaces, then they
likely have inward pointing normals and the outside of the cavity will not
be lit unless you select Two Sided Lighting from the Display menu.

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] Changing Bfactors

[Robert Campbell]

On Sat, 12 Jan 2008 20:21:37 +0530, rama krishna ram...@gmail.com wrote:

 Dear User,
 I need to color the Molecule based on generalized order parameter
 after running the script data2bfactor
 i used the command data2b_res 'mol','datafile'
 
 after that it shows that
 IOError: [Errno 2] No such file or directory: 'datafile'
 
 i would like to know whether i need to specify path of input file or
 i need to place it in specified folder.
 
 I prepared the input file like this
 
 1  MET  0.2
 .
 
 so on
 
 kindly suggest me where its going wrong

Perhaps the instructions on my web page were misleading.  Don't put quotes
around the name of the mol or datafile.  I.e. if you have a real object
named my_protein and a data file called interesting_info.dat, then the
command would be:

  data2b_res my_protein, interesting_info.dat

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] obtaining coordinates of solvent-surface points

[Robert Campbell]

Hello John,

On Thu, 22 Nov 2007 12:36:32 -0800 (PST), JJ josh8...@yahoo.com
wrote:

 Hello:
 Im new at pymol and would like to obtain the
 coordinates of the dots that make up the
 solvent-accessible surface.  I can obtain the vertices
 using cmd.get_povray()[1], but that will give me a
 list of coordinates of open cylinders with spheres at
 either end.  Perhaps these sphere and cylinders are so
 small that I could use any of them as the coordinates
 for the surface dot. Or, would it be more exact to use
 the midpoint of the cylinder?  Any suggestions?

Rather than use PyMOL's surface, I've used the triangulated surface output
by Michel Sanner's msms program.  I've written a few python scripts that
allow various manipulations.  Just today, in fact, I wrote a script to
calculate surface areas from within PyMOL.  I also have previously
written some python code that does a calculation similar to the CCP4
program sc (surface complementarity).  This allows me to colour the
surface of, for example, an inhibitor according to how complementarity
it is to an enzyme active site.  I hadn't added these to my PyMOL scripts
web page, but I will do so now.  Look for msms_pymol.py at

  http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

Of course, one needs to obtain msms, but that can be simply found at

  http://mgltools.scripps.edu/downloads

The msms_complementarity calculation is done outside pymol and the
resulting vertex and triangle files are read by a separate script to create
a CGO representation of the msms surface.  I'll get those up on the web
site tomorrow, perhaps.

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] moving objects freely

[Robert Campbell]

Hi Tom,

On Thu, 04 Oct 2007 11:20:35 -0700, Tom tl...@optonline.net wrote:

 From time to time, I have a need to manually move objects relative to
 one another.  For example, manual docking of a ligand requires that it the
 translated and rotated relative to its binding pocket.  It there a simple,
 intuitive way to do this?

Put the mouse in editing mode (either through the Mouse menu in the
external GUI or by clicking anywhere in the bottom right region of the
graphics window where the mouse functions are described).  Then while
holding down the Shift button the left and middle mouse buttons can be
used to rotate and translate an object.  Just make sure your mouse is over
the object you want to move when you press the mouse button.

Just be careful that you haven't picked an atom within the moving object,
or that atom will not move.

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] getting lists of resn, resi, and atom ID of a selection.

[Robert Campbell]

Dear Tomoko,

On Tue, 18 Sep 2007 21:40:34 +0900 (JST), Tomoko Niwa
outp...@yahoo.co.jp wrote:

   Dear all

   I am a beginner in Python programming.
   I would like to get lists of resn (residue names), resi (residue
 identifiers) and atom ID of a selection. 
   For example, in case of 1IEP_organic;
   [STI, STI], [201, 202], and [4639, 4640, 4641, …..] for resn, resi, and
 atom ID, respectively. 

You can use the iterate command to get this.  If you have a particular
selection called 1IEP_organic then you can type this at the PyMOL prompt:

iterate 1IEP_organic, print resn, resi, name

If you want to print it in a more nicely formatted manner you could do:

iterate 1IEP_organic, print %4s %4s %4s % (resn,resi,name)

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] aligning multimodel pdb file

[Robert Campbell]

Hi Abhi,

On Thu, 23 Aug 2007 12:51:10 -0700, Abhinav Verma
abhinav1...@gmail.com wrote:

 I want to align different models of a multimodel pdb file.
 
 How can I do that without extracting models as identical pdb.
 
 cheers,
 Abhi

Try the intra_fit command.

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

[PyMOL] my color_b.py script

[Robert Campbell]

To all you colouring aficionados,

I've updated the color_b.py script on my web page to include Mark Wall's
addition of user-defined, 3-colour, gradients.  Now you can type on the
command line something like:

  color_b selection, gradient=user, user_rgb=(0.,.3,1.,.8,.8,.8,1.,.8,0.)

to get colours that range from a light blue (0, .3, 1) , through grey 
(.8, .8, .8) to orange (1, 0.8, 0). Or you can use integer values between 0
and 255 like so:

  color_b selection, gradient=user,
user_rgb=(0.,77,255,204,204,204,255,204,0.)

If any one value is larger than 1, then it is assumed that all values are
between 0 and 255.  

You can find it in: 

  http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] python for loop with pymol command usage

[Robert Campbell]

Hi Louis,

* Clark, Louis louis.cl...@codexis.com [2007-07-04 12:01] wrote:
 Dear user-group,
 
   I'm trying to learn how to use python commands inside pymol .pml
 scripts.  I seem to be missing some understanding about how the
 interface works.  Could somebody tell me how to fix this command below?
 
  
 
 PyMOLfor x in range(10): cmd.label((name ca and resi %d) % x, %s%s 
 
 PyMOL% (resi, resn))
 
 Traceback (most recent call last):
 
   File /usr/local/pymol/modules/pymol/parser.py, line 232, in parse
 
 exec(com2[nest]+\n,pymol_names,pymol_names)
 
   File string, line 1, in ?
 
 NameError: name 'resi' is not defined

You need quotes around the label expression '%s%s % (resi, resn)':

for x in range(10): cmd.label((name ca and resi %d) % x, '%s%s % (resi, 
resn)')

The expression has to be passed to pymol as a string to be interpreted
correctly.

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] spectral coloring

[Robert Campbell]

Hi Martin,

* Martin Höfling martin.hoefl...@physik.uni-muenchen.de [2007-06-26 15:15] 
wrote:
 Hi there,
 
 i am trying to map b factors on a surface representation. 
 
 I am using spectrum b,blue_white_red,mymol and the colors are fine. Is there 
 a 
 way to fine tune the color spectrum, such as with the Midpoint and Offset 
 sliders in vmd?

My color_b.py script has some controls, although I'm not sure it will
do quite what you want. It has a number of different gradients built
in, plus you can adjust the overall saturation or value (brightness).
Like the spectrum command you can set the minimum and maximum values
to use, which can help to adjust the midpoint. It also has two modes,
histogram, in which the spacing of B-values (or other values) is equal
or ramp, in which the number of atoms in each bin is kept constant,
but the widths of the bins vary.

You are welcome to modify it to add new features, of course. You can
find it at:

   http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/color_b.py


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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] How to dislocate independently each structure when you have loaded two structures?

[Robert Campbell]

* Andreas Henschel a...@biotec.tu-dresden.de [2007-06-27 15:49] wrote:
 Hi Julio,
 
 If I understood you right, you can simply use translate, eg.:
 translate [20,0,0], mol_to_dislocate
 
 The important thing is that turn and move modify the camera, while 
 translate and rotate modify the coordinates.
 
 Cheers,
 Andreas
 
 
 Júlio César wrote:
  Hi,
 
  I have loaded two structure and tried to dislocate one independent on the
  other, but I couldn't. Is it possible to do thit?
  I would like to know how to dislocate independently each structure when you
  have loaded two structures?
 

Or you can put the mouse in editing mode (click in the bottom corner of
the main graphics window where the mouse functions are described) and
you'll now see that Shift middle-button is labelled MovO and Shift
left-button is labelled RotO. So you can use Shift middle-button
to translate one object and Shift left-button to rotate one object
relative to the other. You just have to be careful that you pick your
atom carefully if the two objects are superimposed.

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] low-end graphics cards/laptops

[Robert Campbell]

Hi David,

* David A.  Horita dhor...@wfubmc.edu [2007-06-14 11:52] wrote:
 Hi,
 While I've seen a number of examples of good graphics cards to use with
 Pymol, I'd like some feedback on what an acceptable low-end is for a
 Windows laptop computer.  Specifically, is the Intel GMA950 completely
 useless or just not very good.  Likewise, does the X3100 help (this
 seems to be weak on driver support)?  
  
 My current system uses an ATI Mobility Radeon 9200, which is a few years
 old and not a high-end gaming/workstation card, but lets me spin a
 molecular cartoon or surface of a ~300 residue protein without any
 problems (if the 950 or X3100 equal this level, I'll be satisfied).
 Many of the current crop of 5 lb notebooks use integrated graphics for
 price and battery life.  If these units don't provide sufficient
 graphics power for Pymol/VMD/Deepview, the useful market shrinks
 substantially.

I use a Lenovo (IBM) Thinkpad T43 with the ATI X300. I use Linux
(Debian) only on this laptop and with the fglrx ATI driver it certainly
gives acceptable performance. I can spin a 300-residue protein drawn in
surface mode easily enough. It seems to be only a little slower than my
desktop, which has a ATI 9500 Pro.

I don't recall trying it on this laptop before I blew Windows off the
disk, but I'd expect you'd get at least as good performance with Windows
as Linux.

The Thinkpads are nice small laptops.

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] APBS

[Robert Campbell]

Hi Vaheh,

* Oganesyan, Vaheh oganesy...@medimmune.com [2007-05-30 09:45] wrote:
 I did not get much luck with those recommendations either. I was doing 
 exactly the same. Something is phishy with my pymol and/or APBS installation. 
 I did check for different pdb files, so it is not pdb related. The roor 
 message is below:
 ==
 Running ('/usr/bin/APBS/apbs-0.5.0/bin/apbs', 
 '/home/Vaheh/Work/Fc3M/pymol-generated.in')
 OSError Exception in Tk callback
   Function: function lambda at 0xf608448c (type: type 'function')
   Args: ()
 Traceback (innermost last):
   File 
 /usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py, 
 line 1747, in __call__
 return apply(self.func, args)
   File 
 /usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwDialog.py,
  line 153, in lambda
 command=lambda self=self, name=name: self._doCommand(name))
   File 
 /usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwDialog.py,
  line 132, in _doCommand
 return command(name)
   File /usr/bin/pymol/modules/pmg_tk/startup/apbs_tools.py, line 1101, in 
 execute
 (retval,progout) = 
 run(self.binary.getvalue(),(self.pymol_generated_in_filename.getvalue(),))
   File /usr/bin/pymol/modules/pmg_tk/startup/apbs_tools.py, line 317, in run
 retcode = 
 subprocess.call(args,stdout=output_file.fileno(),stderr=subprocess.STDOUT)
   File /usr/bin/pymol/ext/lib/python2.4/subprocess.py, line 412, in call
 return Popen(*args, **kwargs).wait()
   File /usr/bin/pymol/ext/lib/python2.4/subprocess.py, line 542, in __init__
 errread, errwrite)
   File /usr/bin/pymol/ext/lib/python2.4/subprocess.py, line 975, in 
 _execute_child
 raise child_exception
 OSError: [Errno 8] Exec format error

 ^^

This error would seem to indicate that you are running PyMOL on one kind
of computer but the apbs executable was compiled for a different one.
Are you perhaps mixing i686 and x86_64 Linuxes, for example?

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] Question about electron density map with mtz file

[Robert Campbell]

Hi Adiphol

* adi di adipho...@yahoo.com [2007-05-11 10:26] wrote:
 Dear all,
 
 I am trying to put on the electron density. I only
 have .mtz file but I have a look at the manual and the
 program need XPLOR file. How can I get the XPLOR file
 or do I need to convert the mtz file to this - if so
 how can I do that? Thank you very much

Actually PyMOL can read ccp4 format maps, but they have to be maps, not
the mtz reflection file with the columns h, k, l, FWT, PHWT etc. as
output by refmac and other programs.  If you ask refmac to output a CCP4
format map, then PyMOL can read it:

load filename.map, map_obj, format=ccp4

will load the map and create an object called map_obj.  The latter then
needs to be contoured by PyMOL.  For example:

  isomesh lev1, map_obj, selection=molecule  c. a   resi 100, level=1, 
buffer=8.

would create an object called lev1 with a contour level of 1 in a box of
8Angstroms around residue 100 of chain a of molecule.

Hope that helps,

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
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] simple cgo question

[Robert Campbell]

Hi Richard,

* Richard Gillilan r...@cornell.edu [2007-02-19 10:22] wrote:
 
 I'm probably making a simpler mistake here, or perhaps there is  
 something wrong with my installation or paths.
 I'm trying to load and display the simple cgo example in the manual.  
 I created a file named arrows containing this definition:
 
 from pymol.cgo import *# get constants
 from pymol import cmd
 
 obj = [
 BEGIN, LINES,
 COLOR, 1.0, 1.0, 1.0,
 
 VERTEX, 0.0, 0.0, 0.0,
 VERTEX, 1.0, 0.0, 0.0,
 
 VERTEX, 0.0, 0.0, 0.0,
 VERTEX, 0.0, 2.0, 0.0,
 
 VERTEX, 0.0, 0.0, 0.0,
 VERTEX, 00, 0.0, 3.0,
 
 END
 ]
 
  From the Pymol prompt I then attempt to load it:
 
 PyMOL cmd.load_cgo(obj,'/Volumes/transport/AFABP_structs/Linoleic4/ 
 rf10_TLS/arrows');
 
 I get the following error:
 
 Traceback (most recent call last):
File /Users/delwarl/MacPyMOL060228/build/Deployment/MacPyMOL.app/ 
 pymol/modules/pymol/parser.py, line 370, in parse
File string, line 1, in ?
 NameError: name 'obj' is not defined
 
 Anyone recognize what I am doing wrong here?

The cmd.load_cgo command wants the object and object name as parameters,
so you want to put the load_cgo command within your file and use the run
command to load it (it is a python file):

# -  arrows.py ---
from pymol.cgo import *# get constants
from pymol import cmd

obj = [
BEGIN, LINES,
COLOR, 1.0, 1.0, 1.0,

VERTEX, 0.0, 0.0, 0.0,
VERTEX, 1.0, 0.0, 0.0,

VERTEX, 0.0, 0.0, 0.0,
VERTEX, 0.0, 2.0, 0.0,

VERTEX, 0.0, 0.0, 0.0,
VERTEX, 00, 0.0, 3.0,

END
]

cmd.load_cgo(obj,'arrows')

Load it into PyMOL with:
PyMOL run arrows.py

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
robert.campb...@queensu.ca http://adelie.biochem.queensu.ca/~rlc

Re: [PyMOL] mesure line width

[Robert Campbell]

Hi Andrea,

* andrea carotti and...@chimfarm.unipg.it [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
robert.campb...@queensu.ca http://adelie.biochem.queensu.ca/~rlc

Re: [PyMOL] Paths to loaded objects

[Robert Campbell]

Hi folks,

* Michael Lerner mgler...@gmail.com [2006-08-21 12:26] wrote:
 I think he means for you to have a Load button as part of your
 plugin.  That button would first record the path to the file and then
 call through to cmd.load().

Perhaps what Ron needs to do is not use the cmd.load() function but
use his own file reading procedure.  The lines containing coordinates
could be extracted from the file (by recognizing them with a regexp) and
passed to the cmd.read_pdbstr() function.  The CGO commands could be
read separately.  Then there is no need to worry about where cmd.load()
thinks file is.

 On 8/19/06, Ron Jacak r...@email.unc.edu wrote:

  Peter,
 
   I'm working on a plugin that reads information appended to the
   end of PDB files to draw CGO objects.  Right now, I have the
   user specify the filesystem path to the currently loaded objects
   through the plugin GUI so that I know where to go to find the
   file.  For one object, this isn't so bad.  But if users load
   multiple objects that are in different directories, I will have
   to change the GUI so that the user has to specify the path to
   each object loaded.  This kind of situation would quickly become
   tedious.  Does PyMOL store the paths for objects that are loaded
   somewhere?  I know I can get the current working directory using
   getcwd(), so I'm hoping there's a way to get the path to the
   loaded objects as well.
 
   I don't know of a way to get file information from a pymol object,
   but you could work around this by using a python dictionary (when
   the pdb file is loaded, store the full path to the file in a
   dictionary using the pymol object name as the key).
 
  I'm not sure I fully understand your suggestion.  It sounds to
  me like what you're saying is that I should add code (e.g. a
  dictionary) to the importing.py load() function which saves the
  file information of objects as they're loaded.  But then instead of
  just distributing my plugin, I would have to get users to change
  their PyMOL source, as well (which I'm not willing to do).  Am I
  understanding correctly?
 
  Any other ways around this problem?

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Department of Biochemistry, Queen's University
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821Fax: 613-533-2497
robert.campb...@queensu.ca http://adelie.biochem.queensu.ca/~rlc

Re: [PyMOL] How can I change the surface_quality of an electron density map surface?

[Robert Campbell]

Hi Jonathan,

* Jonathan Stuckey sblood@yahoo.com [2006-08-15 12:03] wrote:
 How can I change the surface_quality of an electron
 density map surface? set surface_quality=-1 does not
 do anything.

The surface_quality parameter affects the quality of molecular surfaces,
not isosurfaces.  To change the smoothness of the latter, you would need
to sample the electron density at a finer interval (i.e. do the FFT with
a finer grid).

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Department of Biochemistry, Queen's University
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821Fax: 613-533-2497
robert.campb...@queensu.ca http://adelie.biochem.queensu.ca/~rlc

Re: [PyMOL] align states

[Robert Campbell]

Hi,

* Joel Tyndall joel.tynd...@otago.ac.nz [2006-07-15 14:29] wrote:
 Hi andrea,
 
 you can easily do this by
 
 split_states my_struct
 dele my_struct
 
 
 for the NMR ensemble, then I would use the action menu, align function 
 and align them  to state_1. This is in effect aligning the separate 
 states as objects, unless I misunderstood you
 
 J
 
 Andrea Spitaleri wrote:
  Hi all,
  in pymol is it possible to align states rather than object. I mean, I
  have loaded a pdb file with n-structures and I'd like to align each of
  them on the first one of the bundle.

If in fact the n-structures contain all the same atoms, then you can use
the intra_fit command instead:

  PyMOL help intra_fit

  intra_fit

  DESCRIPTION

 intra_fit fits all states of an object to an atom selection
 in the specified state.  It returns the rms values to python
 as an array.

  USAGE 

 intra_fit (selection),state

  PYMOL API

 cmd.intra_fit( string selection, int state )

  EXAMPLES

 intra_fit ( name ca )

  PYTHON EXAMPLE

 from pymol import cmd
 rms = cmd.intra_fit((name ca),1)

  SEE ALSO

 fit, rms, rms_cur, intra_rms, intra_rms_cur, pair_fit


Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Department of Biochemistry, Queen's University
Kingston, ON K7L 3N6  Canada
  r...@post.queensu.ca http://adelie.biochem.queensu.ca/~rlc
  phone: 613-533-6821fax: 613-533-2497
  PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

Re: [PyMOL] debian: error in opening pymol

[Robert Campbell]

Hi Arvind,

* Arvind Marathe arv...@mbu.iisc.ernet.in [2006-06-09 00:14] wrote:
 Hi all,
 my system is a newly installed debian-3.1 linux. 'pymol' seems to be part
 of the installed package. But when I try to open pymol, I get the
 following error:
 
 
 $ pymol
 Traceback (most recent call last):
   File /usr/lib/python2.3/site-packages/pymol/__init__.py, line 329, in ?
 import _cmd
 ImportError: libglut.so.3: cannot open shared object file: No such file or
 directory
 
 
 Can somebody please point out the cause and the remedy? I have never used
 pymol before and this was my first try.

You need to install the freeglut3 package:

  apt-get install freeglut3

should take care of it for you.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Department of Biochemistry, Queen's University
Kingston, ON K7L 3N6  Canada
  r...@post.queensu.ca http://adelie.biochem.queensu.ca/~rlc
  phone: 613-533-6821fax: 613-533-2497
  PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

Re: [PyMOL] Problem loading chempy objects to pymol

[Robert Campbell]

Hello Raúl,

* Raúl Mera butil_li...@yahoo.com [2006-06-07 04:32] wrote:
 Hello all,
 
 I'm writing a Pymol plugin which creates many chempy
 objects (of the class Indexed) and displays the
 objects as diferent states of a structure. The atoms
 in the objects are not standar (they are dummy atoms
 to represent a pore in a channel) and they VdW radius
 changes in time (between states). I use the same value
 for the VdW radius and for the b-factor, so i can
 appreciate the radius value in the color and in the
 spheres size. The problem is that, even when I am
 absolutely sure that all atoms in all objects have
 right values, when i load them to pymol using
 something like:
 
 cont=1
 for model in models_list: #models_list is a list of
 models
   cmd.load_model(model,name,cont)
   print cont, counter
   cont=cont+1
 
 Pymol seems to be unable to accept that the VdW
 radius changes between states and asigns the same
 values to all radius and give weird values to the
 b-factors (I think that gives to one model's b-factors

I haven't used the load_model function, but like the load function,
there is a discrete option.  It think you need to say:

cmd.load_model(model,name,cont,discrete=1)

Then each state will maintain its own values for B-factor etc.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Department of Biochemistry, Queen's University
Kingston, ON K7L 3N6  Canada
  r...@post.queensu.ca http://adelie.biochem.queensu.ca/~rlc
  phone: 613-533-6821fax: 613-533-2497
  PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2