[PyMOL] spectrum
Hi all, I have a question regarding the spectrum command and b-factors. How are the color-ranges calculated by spectrum? I.e. i would like to know the values for the different shades like in the color_b.py-script, which gives you not only a total range, but also the bins. I would like to put a color-gradient-bar below a picture which shows numbers as well, and for that I need to know the ranges of blue, green, yellow, etc. Or is it possible to do this from within Pymol automatically (like for iso-surfaces)? Thanks in advance. -- Bye, Marc Saric
[PyMOL] installation problem
Hi, Our system administrator of a linux cluster have trouble upgrading from 0.93 to 0.95: [mfitz...@man local]$ sudo rpm -U --test pymol-0.95-1.rh73.py22.i386.rpm [mfitz...@man local]$ sudo rpm -U pymol-0.95-1.rh73.py22.i386.rpm warning: user warren does not exist - using root warning: user warren does not exist - using root warning: user warren does not exist - using root warning: user warren does not exist - using root warning: user warren does not exist - using root warning: user warren does not exist - using root warning: user warren does not exist - using root [mfitz...@man local]$ sudo rpm -V pymol-0.95-1 package pymol-0.95-1 is not installed Any ideas? Thanks! shuhsien -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Marc Saric Sent: Thursday, April 15, 2004 8:15 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] spectrum Hi all, I have a question regarding the spectrum command and b-factors. How are the color-ranges calculated by spectrum? I.e. i would like to know the values for the different shades like in the color_b.py-script, which gives you not only a total range, but also the bins. I would like to put a color-gradient-bar below a picture which shows numbers as well, and for that I need to know the ranges of blue, green, yellow, etc. Or is it possible to do this from within Pymol automatically (like for iso-surfaces)? Thanks in advance. -- Bye, Marc Saric --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470alloc_id=3638op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] installation problem
The warning is ok, just ignore. And to check the rpm package, use pymol as package name, not with version numbers. like 'rpm -q pymol' Chen On Thu, 15 Apr 2004, Shu-Hsien Sheu wrote: Hi, Our system administrator of a linux cluster have trouble upgrading from 0.93 to 0.95: [mfitz...@man local]$ sudo rpm -U --test pymol-0.95-1.rh73.py22.i386.rpm [mfitz...@man local]$ sudo rpm -U pymol-0.95-1.rh73.py22.i386.rpm warning: user warren does not exist - using root warning: user warren does not exist - using root warning: user warren does not exist - using root warning: user warren does not exist - using root warning: user warren does not exist - using root warning: user warren does not exist - using root warning: user warren does not exist - using root [mfitz...@man local]$ sudo rpm -V pymol-0.95-1 package pymol-0.95-1 is not installed Any ideas? Thanks! shuhsien -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Marc Saric Sent: Thursday, April 15, 2004 8:15 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] spectrum Hi all, I have a question regarding the spectrum command and b-factors. How are the color-ranges calculated by spectrum? I.e. i would like to know the values for the different shades like in the color_b.py-script, which gives you not only a total range, but also the bins. I would like to put a color-gradient-bar below a picture which shows numbers as well, and for that I need to know the ranges of blue, green, yellow, etc. Or is it possible to do this from within Pymol automatically (like for iso-surfaces)? Thanks in advance. -- Bye, Marc Saric --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470alloc_id=3638op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470alloc_id=3638op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] installation problem
On Thu, Apr 15, 2004 at 10:27:32AM -0400, Shu-Hsien Sheu wrote: [mfitz...@man local]$ sudo rpm -V pymol-0.95-1 package pymol-0.95-1 is not installed Just a shot in the dark, but are you sure the package is called pymol-0.95-1 and not just pymol? Michael
Re: [PyMOL] Selections
For example, I found a PDB online called 'pope.pdb' (a cool lipid
bilayer; http://moose.bio.ucalgary.ca/Downloads/) and simply wanted to
select all the hydrophobic tails and hydrophilic heads so that I may
apply different attributes to each. If I need to select the tails,
which in the PDB are labeled from C10 (or so) to C50 depending on the
molecule, can I use something like c10-c50 (experience tells me no) or
must I do c10+c11+c12...c50?
I don't know an easy way to do this .. like almost does what you want,
but not quite. You could do something like
select sol, resn sol
select heads, name
N4+C5+C6+O7+O9+O10+O11+C12+C13+O14+C15+O16+C32+O33+C34+O35+P8+H1+H2+H3
select tails, not sol and not heads
Or .. even easier .. drop this in a file called something like
select_names.py
---
#!/usr/bin/env python
from pymol import cmd,stored
def select_names(newSelectionName,selection):
Makes a new selection called newSelectionName comprised of
everything that has the same atom name as something in selection.
stored.selected_names = []
cmd.iterate(selection,'stored.selected_names.append(name)')
cmd.select(newSelectionName,'name %s'%'+'.join(stored.selected_names))
cmd.extend('select_names',select_names)
---
and type run selected_names.py from within PyMOL.
Now use the mouse to select one of the heads (I use shift+lb to put things
into the selection (lb).
Now type select_names heads, lb and you'll have a selection called
heads that has all of the heads.
Maybe someone who knows more about selections will know a better way,
though.
So, it comes down to: do you prefer the macro method or standard; and,
do you have any hints or tips for more accurate or powerful selections?
If you're going to be using PyMOL a lot, it's definately worth your time
to learn how to write Python scripts. I'd also recommend looking through
the PyMOL source itself. I don't have anything much to say about
selections, though .. I've always been quite happy with simple PyMOL
selections.
-michael
As an example, how could I select just the tails or just the heads in
the aforementioned pope.pdb file?
Thanks.
--
Jason Vertrees
BSCB Graduate Student @ UTMB, Galveston
javer...@utmb.edu :: http://www.bscb.utmb.edu
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Re: [PyMOL] Selections
Hi Jason, * Jason Vertrees javer...@utmb.edu [2004-04-14 22:55] wrote: Master Users, I'm a bit new to PyMol and still trying to master selections. I've read the documentation and played with quite a few macromolecules now and still have some problems with selections. For example, I found a PDB online called 'pope.pdb' (a cool lipid bilayer; http://moose.bio.ucalgary.ca/Downloads/) and simply wanted to select all the hydrophobic tails and hydrophilic heads so that I may apply different attributes to each. If I need to select the tails, which in the PDB are labeled from C10 (or so) to C50 depending on the molecule, can I use something like c10-c50 (experience tells me no) or must I do c10+c11+c12...c50? The latter is correct, unfortunately. You can certainly do a selection like: select tails1, r. pop n. c17+c18+c19+c20+c21+c22+c23+c24+c25+c26+c27+c28+c29+c30+c31+ca1+ca2+c36 +c37+c38+c39+c40+c41+c42+c43+c44+c45+c46+c47+c48+c49+c50 (where I've wrapped the line) or you could do the shorter selection first: select heads, r. pop n. c5+c6+c12+c13+c15+c32+c34+n4+o7+o9+o10+o11+o14+o16+o33+o35+p8+h1+h2+h3 and then do: select tails2, r. pop ! heads If you don't want to go to the trouble of picking every atom to see its name, just select one atom in the residue (ctrl-middle-click) and show the atom name labels for the residue (use the pkresi selection in the right menu and labels are under L) So, it comes down to: do you prefer the macro method or standard; and, do you have any hints or tips for more accurate or powerful selections? As an example, how could I select just the tails or just the heads in the aforementioned pope.pdb file? I found clicking on each atom to add them to the lb selection as Michael suggests less simple, but then I type quickly! Cheers, Rob -- Robert L. Campbell, Ph.D. r...@post.queensu.ca Senior Research Associatephone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
RE: [PyMOL] Selections
must I do c10+c11+c12...c50? Yes, unfortunately. However, this long selection: select tails1, r. pop n. c17+c18+c19+c20+c21+c22+c23+c24+c25+c26+c27+c28+c29+c30+c31+ca 1+ca2+c36 +c37+c38+c39+c40+c41+c42+c43+c44+c45+c46+c47+c48+c49+c50 Can be replaced with some Python code in your script: my_list = map( lambda x: c%2d%x, range(10,51) ) my_str = string.join( my_list, '+' ) cmd.select( tails1, resn pop name + my_str ) show lines, tails1 Which allows you to adjust the range manually by changing the values in the range call. FYI: print my_str gives c10+c11+c12+c13+c14+c15+c16+c17+c18+c19+c20+c21+c22+c23+c24+c25+c26+c27+c28+ c29+c30+c31+c32+c33+c34+c35+c36+c37+c38+c39+c40+c41+c42+c43+c44+c45+c46+c47+ c48+c49+c50 Cheers, warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Robert Campbell Sent: Thursday, April 15, 2004 8:39 AM To: PyMol Users List Subject: Re: [PyMOL] Selections Hi Jason, * Jason Vertrees javer...@utmb.edu [2004-04-14 22:55] wrote: Master Users, I'm a bit new to PyMol and still trying to master selections. I've read the documentation and played with quite a few macromolecules now and still have some problems with selections. For example, I found a PDB online called 'pope.pdb' (a cool lipid bilayer; http://moose.bio.ucalgary.ca/Downloads/) and simply wanted to select all the hydrophobic tails and hydrophilic heads so that I may apply different attributes to each. If I need to select the tails, which in the PDB are labeled from C10 (or so) to C50 depending on the molecule, can I use something like c10-c50 (experience tells me no) or must I do c10+c11+c12...c50? The latter is correct, unfortunately. You can certainly do a selection like: select tails1, r. pop n. c17+c18+c19+c20+c21+c22+c23+c24+c25+c26+c27+c28+c29+c30+c31+ca 1+ca2+c36 +c37+c38+c39+c40+c41+c42+c43+c44+c45+c46+c47+c48+c49+c50 (where I've wrapped the line) or you could do the shorter selection first: select heads, r. pop n. c5+c6+c12+c13+c15+c32+c34+n4+o7+o9+o10+o11+o14+o16+o33+o35+p8+h1+h2+h3 and then do: select tails2, r. pop ! heads If you don't want to go to the trouble of picking every atom to see its name, just select one atom in the residue (ctrl-middle-click) and show the atom name labels for the residue (use the pkresi selection in the right menu and labels are under L) So, it comes down to: do you prefer the macro method or standard; and, do you have any hints or tips for more accurate or powerful selections? As an example, how could I select just the tails or just the heads in the aforementioned pope.pdb file? I found clicking on each atom to add them to the lb selection as Michael suggests less simple, but then I type quickly! Cheers, Rob -- Robert L. Campbell, Ph.D. r...@post.queensu.ca Senior Research Associatephone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2 --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470alloc_id=3638op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Re: give unique chain identifiers
Dan,
First, get down to 26 or fewer objects, then issue the following commands:
objs = cmd.get_names('objects')
pairs = map(None, objs, range(65, 65+len(objs))
for pair in pairs: \
cmd.alter(pair[0], chain='%s'%chr(pair[1]))
NOTE: That last comment will take a little while...
Cheers,
Warren
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Dr. Daniel James White PhD
Sent: Wednesday, April 14, 2004 7:47 AM
To: Warren DeLano
Cc: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Re: give unique chain identifiers
Hi Warren,
OK, that works just as you say it does.
however, what I really need is each chain to have a unique
chain identifier in the pdb file written out.
I see there might be a problem here as there are 60
molecules, and only
24 letters in the alphabet
I actually only want to have 15 of them in my model, so we
could get round it that way, by deleting the ones I dont want
but then how to give them unique pdb chain identifiers?
I want to load the 15 molecule model in Bodil to do my actual
modelling.
cheers
Dan
On 6 Apr 2004, at 21:36, Warren DeLano wrote:
Dan,
That's the not expected result, but indeed you have a
problem -- each
of those subunits will have identical atoms. To resolve
this, assign
a unique segment identifier to each subunit:
load 1c8e.pdb1, 1c8e
split_states 1c8e
delete 1c8e
alter all, segi = model[-4:]
rewind
save test.pdb, all
dele all
load test.pdb
The reason why you were getting a PDB file with just END is
that you
didn't return the viewer ro frame/state 1 after moving all
of the data
to state 1.
After the above, you'll now be able to address each subunit
indepently
as:
hide
show ribbon
color red, segi 0001
zoom segi 0001
http://delsci.com/img/1c8e-subunit.jpg
Cheers,
Warren
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Dr.
Daniel James White PhD
Sent: Tuesday, April 06, 2004 6:22 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] save all not working for multiple objects from
split_states?
Hi all,
I opened a biological unit pdb file of a viral capsid protein
containing the 60 states or models making up the whole viral
capsid structure.
I did
split_states
to get all 60 molecules as individual objects
sweet!
then I deleted the ones I didnt want, leaving 15 molecules
around one
of the 5 fold symmetry axes.
now I want to save these molecules to a pdb file.
so I did
save 5fold.pdb, all
this gave no errors, but the pdb file written only contains
END
what am I doing wrong? I expect it is my simple mistake?
cheers
Dan
Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of
biological and environmental science PO Box 35 University of
Jyväskylä Jyväskylä FIN 40014 Finland
+358 14 260 4183 (work)
+358 468102840 (new mobile)
NEW PHONE NUMBER!!!
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Dr. Daniel James White BSc. (Hons.) PhD
Cell Biology
Department of biological and environmental science PO Box 35
University of Jyväskylä Jyväskylä FIN 40014 Finland
+358 14 260 4183 (work)
+358 468102840 (new mobile)
NEW PHONE NUMBER!!!
http://www.chalkie.org.uk
d...@chalkie.org.uk
wh...@cc.jyu.fi
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