Dear List
I'm trying to automate the following sequence of steps in a PyMOL python
script:
1. Start the mutagenesis wizard
2. Mutate a reside according to an input from the script (some integer
to specify the id)
3. "Apply" and close the mutagenesis wizard
4. Start the Sculpt Wizard
5. Fix all co
]?
I would like to illustrate the alignment of the principal axes of a
protein with the coordinate system.
Kind regards and thank you for answers.
Martin Hediger
--
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It's a major breakthrough. An authen
.py
>
> hope it helps,
> hongbo
>
> On 04/08/2011 04:29 PM, Martin Hediger wrote:
>> Dear all
>> I'm sure this question was answered before, but I could not find
>> anything related to it in neither the mail list nor on the Wiki.
>> Is it possible to disp
Dear all
I found that PyMOL offer the cmd.get_extent('protein') function, which
returns the dimensions of the selection.
Is it complicated to make this function available from within an
ordinary Pythonscript?
Thanks for hints.
Martin
---
eds to be tuned if you need only the first MODEL or
> only the first alternate position etc.
>
> cheers,hongbo
>
> On 04/26/2011 01:40 PM, Martin Hediger wrote:
>> Dear all
>>
>> I found that PyMOL offer the cmd.get_extent('protein') function, which
>>
Dear all
I would like to ask how it is possible to download the coordinate file
for the biological assembly of a protein structure from the PDB.
Naturally, this is not a question directly related to PyMOL, but I
thought I'll be reaching at least a couple of
Biochemists/Chrystallographers who kno
;
>> The key is adding 1 to the suffix. Sometimes there is more than one
>> biological unit, in which case, there is a pdb2, pdb3, etc.
>>
>> -David
>>
>> On May 3, 2011, at 4:00 PM, Martin Hediger wrote:
>>
>>> Dear all
>>> I woul
:
> http://www.rcsb.org/pdb/files/1avd.pdb1
>
> The key is adding 1 to the suffix. Sometimes there is more than one
> biological unit, in which case, there is a pdb2, pdb3, etc.
>
> -David
>
> On May 3, 2011, at 4:00 PM, Martin Hediger wrote:
>
>> Dear all
>>
Dear List
I am trying to prepare a figure. I have a protein structure, enclosed by
a rectangular box. Is it possible to copy/translate the enboxed
structure for a given amount of times? This would end up as something as
an illustration of a system with periodic boundaries.
I attached a figure o
Dear List
Is there any other information about the force field of the sculpting
wizard available other than what is on the wiki?
Kind regards
Martin
--
BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA
The must-a
Dear List
I was wondering if there could be a way of having every residue of a
protein structure being saved to a separate file. How could this be done?
I believe the 'iterate' method might be useful in combination with the
'byres' identifier, but I havent figured out how to combine them in the
quot;, "byres _tmp")
> python end
> delete _justca _tmp
>
> Hope that helps.
>
> Cheers,
> Thomas
>
> On 08/15/2011 09:14 AM, Martin Hediger wrote:
>> Dear List
>> I was wondering if there could be a way of having every residue of a
>> protei
Hi Troels
It's indeed possible.
The wizards are available through the cmd module.
# Initialize
load yourProtein
cmd.wizard("mutagenesis")
cmd.do("refresh_wizard")
# To get an overview over the wizard API:
for i in dir(cmd.get_wizard(): print i
# lets mutate residue 104 to GLN
cmd.get_wizard().s
3, 2 RE<http://maps.google.dk/>
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752
2011/8/22 Martin Hediger mailto:ma@bluewin.ch>>
Hi Troels
It's indeed possible.
The wizards are available through the cmd module.
# Initialize
load yourProtein
cmd.wiza
you may want to check out the Popen class from the subprocess module...
hth
Martin
On 23.08.11 10:48, Troels Emtekær Linnet wrote:
Hi.
If one writes a pymol script, and calls an external function, the
pymol script continues its operation before waiting for the "success"
of the external functi
E
shell=False)
propkap.stdout.read()
Martin Hediger
On 28.08.11 19:24, Troels Emtekær Linnet wrote:
Thanks Jason. But still no luck...
So, I changed it to a python script. It was important that the ending
of the file is .py :-)
But, I can see from the list of objects, that P
10-1.
Kind regards.
Martin Hediger
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Dear List
Does anyone have a script to calculate torsion angles lying around?
Ideally, i would like to be able to enter x1, x2, x3, x4 and get the
(smaller) angle between the two normals of the planes defined by x1, x2,
x3 and x2, x3, x4, respectively. For some odd reason the measurment
wizard i
ne of the tools from the Richardson Lab which allows quick
> output of various bond length, angle, torsion and plane measurements.
>
> -bob
>
> On Fri, Sep 2, 2011 at 5:48 AM, Martin Hediger wrote:
>> Dear List
>> Does anyone have a script to calculate torsion angles lying a
Dear List
When I try to save an object as a PDB (after editing it slightly with
the PyMOL edit mode, i.e. adjusting a dihedral angle),
the "Save Molecule" dialog asks to save "all", "global" or "objects
current" state. When saving with the last two, I get no coordinates in
the generated file onl
Dear List
I have the below model of three charged atoms (as a PQR file).
ATOM 1C ASP A 0.0 0.010.0 -2.0 4.0
ATOM 2C ASP A 0.0 0.0 0.0 -2.0 4.0
ATOM 3C ASP A 0.0 0.0 -10.02.0 4.0
The last two numbe
Dear List.
When aligning two structures using the PyMOL align command, one gets a
final RMS value indicating some kind of "convergence" i would say. Can I
somehow access the function for calculating this value directly from the
pymol prompt without aligning?
Thanks for hints
Martin
---
Dear PyMOL List
It comes up once in a while, is it possible to use PyMOL features from
outside of PyMOL? An example, the below is a script (inspired by Thomas
Holder) which saves down to disk all amino acids of a protein structure
into separate PDB files.
# *
This would imply that you cannot use MacPyMOL like in the
>> "Launching_From_a_Script" examples. Maybe someone of the MacPyMOL users
>> knows more?
>>
>> Cheers,
>>Thomas
>>
>> Martin Hediger wrote, On 11/22/11 13:14:
>>> Thanks
If you are in the PyMOL Viewer and in Edit mode, you can hit
+<{a,g,d,e,...}> to build up a linear polypeptide, where the single
letters correspond to the amino acide identifiers.
Is this useful to you?
Am 23.11.11 11:43, schrieb James Starlight:
Dear PyMol Users!
I wounder to know ab
In this example below (from Thomas), the method 'iterate' is used. The
function saves every amino acid of a structure to a separate file. First
of all, I'm not sure of how to understand the docs:
" "iterate" iterates over an expression within a temporary namespace for
each atom."
What does tem
27;foo', 'bar', transform=0)
> print 'RMSD:', x[0]
>
> About the "some kind of refinement": There are arguments "cutoff" and
> "cycles" that control this behaviour.
>
> Cheers,
> Thomas
>
> On 11/11/2011 02:46 PM,
Dear List
How can I compute the numbers of residues in a model?
Martin
--
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threat
t;
> x = cmd.align('foo', 'bar', transform=0)
> print 'RMSD:', x[0]
>
> About the "some kind of refinement": There are arguments "cutoff" and
> "cycles" that control this behaviour.
>
> Cheers,
> Thomas
>
>
Dear PyMOL List
I'm frequently using the PyMOL mutagenesis wizard. Consider the mutation
of tryptophan to phenylalanin. If the sidechain is mutated from W to F,
its reasonable to assume that the plane of the phenyl moiety of F
would/should/could/might lie in the same plane as the indol part of t
Dear List
I'm frequently loading a number of objects into PyMOL which formally
have the same name, but are different in structure. Sometimes it can
become a bit difficult to keep track of which object is what.
Is there a way to display technical information about a loaded object?
Say, the file p
do more recording of properties you choose
>
># ask PyMOL to now load the file
>
>cmd.load(fileName,objName)
>
> Then you could just query obj_info based on object name:
>
> for obj in cmd.get_names():
>print obj_info[obj]
>
> Cheers,
>
> -- Jason
&g
Dear PyMOL List
What is the segi-identifier?
Thanks for your answer.
Martin
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Dear List
In a crystal structure, there are usually a number of relevant crystal
waters, as well as water molecules on the surface. In our approach, we
model the protein structure within a dielectric continuum, so surface
water molecules are not required (to save computer time). However,
waters
ks,
Martin
On 13.12.10 16:52, Jason Vertrees wrote:
> Hi Martin,
>
> As you've found, the mutagenesis wizard destroys the ordering in some
> cases. I'll look into it.
>
> Cheers,
>
> -- Jason
>
> On Tue, Dec 7, 2010 at 11:34 AM, Martin Hediger wrote:
>&g
Dear PyMOL users
I'm using MOPAC to do quantum chemical calculations of enzymes.
I'm wondering if PyMOL could be used to output a PDB file in MOPAC format.
An example of this format is here:
C( 1 LEU 24) 9.0450 +0 4.9440 +0 19.4560 +0
0.4527
O(
Dear PyMOL users
Does anybody know a script to verify that a file contains valid a valid
PDB formatted structure?
The file extension alone obviously does not provide sufficient validation.
Thanks for any feedback.
Martin
---
Dear Jason
Could you point me out to the Python module where the "reader" is
implemented?
I would be interested in seeing how PyMOL handles this because I
recently had to write something similar.
Thanks
Martin
On 23.07.12 18:19, Jason Vertrees wrote:
> Hi Malai,
>
> Thanks for bringing thi
Dear PyMOL users
Is it possible to somehow assign "page up" or "page down" keys to switch
from one loaded model to the next one in the PyMOL models list?
This would be useful because I often have several similar models listed
and in doing so it would be easier and convenient to identify changes
Sweet:)
I disabled the animate but I can see its applicability in some
situations though (makes it pretty impressive).
Definitly a must-have from now on, in fact how could I even live without
it;)
Martin
On 20.09.12 19:38, Tsjerk Wassenaar wrote:
> Hi :)
>
> You can also add
>
> cmd.disab
Dear PyMOL list
I'm adding hydrogens to a crystal structure. Upon saving, however, I
realize all hydrogens have been added to the beginning of the PDB file.
Can PyMOL be configured such that the hydrogens are placed at the
"intuitively appropriate" place in the PDB file?
Thanks for any hints.
M
Dear PyMOL Users
Is it possible to let the PyMOL model player go back and forward,
instead of jumping from the end to the start, once it reached the last
loaded model of an object?
Thanks for hints.
Martin
--
Don't let
Dear PyMOL Users
I use the following script to prepare small side chain fragment PDB
files of mutants in PyMOL:
http://pastebin.com/nDTZApHP
I use the PyMOL built-in mutagenesis wizard and the sculpting wizard to
locally optimize the side chains within the environment of the protein.
For large am
vant ).
>>
>> How I could to select such surrounded water ( e.g via some cutoff
>> radius relative my protein etc) wich I'd like to remove further ?
>
> On 04/25/2012 05:34 PM, Martin Hediger wrote:
>> In a crystal structure, there are usually a number of relev
Hi Carola
What did you try? Does it work when you use these commands right after
starting up PyMOL and before you do any of the steps you take:
set retain_order, 0
set pdb_retain_ids
Martin
On 31.10.12 14:03, Carola Sophie Hengstenberg wrote:
> Dear all,
>
> I recently upgraded to Ubuntu
ng the pymol version 1.5 now. Here
> the problem did not appear anymore, but the real cause of the problem I
> could not find out...
>
> Carola
>
> Am Mittwoch, den 07.11.2012, 11:24 +0100 schrieb Martin Hediger:
>> Hi Carola
>> What did you try? Does it work when you use
Dear PyMOL users
In a directory are PDB files of combined size equal to around 3MB. When
I load all files into PyMOL, I observe that the required RAM of PyMOL
(MacOS X 10.6) increases by roughly this amount.
When I delete all objects, the RAM requirement remains the same and when
I then reload a
Hi Jason,
I'm using PyMOL 1.3.
Best regards
Martin
On 20.12.12 15:53, Jason Vertrees wrote:
> Hi Martin,
>
> Which version of PyMOL are you using?
>
> Cheers,
>
> -- Jason
>
> On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger wrote:
>> Dear PyMOL us
iterating over structures and deleting
> them when done? You sure you're not missing a cleanup step somewhere?
> (Any chance we can see the script or a stub of it?)
>
> Cheers,
>
> -- Jason
>
> On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger wrote:
>> Hi Jason,
>
hybrid (I can reach
>> 10GB of ram memory with relatively small sessions). I'm on MAC OS 10.7.5 and
>> pymol version 1.5.0.3.
>> I had to renounce working with Hybrid unless I really need some plug-in.
>>
>> Gianluigi
>>
>>
>> Da: Jason Vertree
Hi PyMOL users
I wonder, what is a most meaningful way of programmatically determining
that a line of text in an arbitrary file contains atomic coordinates?
The context of this question is that I plan to write a program that
reads two files containing coordinates and has to perform operations on
Hi Abida
Is it possible that you have multiple states in your PDB file? Try
clicking the ">" arrow in the bottom right corner of PyMOL and see if
you can display the other protein. If so, you probably need to delete
the "MODEL" and "END" from your PDB file. Then all should appear at once.
Mar
Hi PyMOL users
Can PyMOL write a vector based picture of a session? Does not require to
be very "fancy", but vector based would be cool. Something like in the
old days with molscript.
Best regards
Martin
--
Master Visua
r EPS?
>
> Cheers,
>
> -- Jason
>
> On Sat, Jan 12, 2013 at 6:31 AM, Martin Hediger wrote:
>> Hi PyMOL users
>> Can PyMOL write a vector based picture of a session? Does not require to
>> be very "fancy", but vector based would be cool. Something like
Hi PyMOL users
If I display these coordinates
HETATM 38 C LIG 2 1.535 2.288 -4.156 1.00 0.00 C
HETATM 39 C LIG 2 2.284 1.535 -3.066 1.00 0.00 C
HETATM 40 O LIG 2 3.406 2.362 -2.714 1.00 0.00 O
HETATM 41 C
Dear PyMOL Users
If you load these coordinates in PyMOL
HETATM1 W LIG 1 -1.357 -0.079 0.052 1.00 0.00 W
HETATM2 C LIG 1 -0.713 -1.686 1.008 1.00 0.00 C
HETATM3 C LIG 1 -0.323 -1.855 -0.270 1.00 0.00 C
HETA
Dear PyMOL users
Assume I have two objects loaded in a PyMOL session and in each I'm
interested in a specific distance. So in both objects I measure this
distance and see it displayed in the viewer. Can I somehow configure the
measurement such that when I disable the object, also the correspond
I describe this in a blog post. Maybe it helps you.
http://qmviews.blogspot.ch/2012/01/pymol-005-optimizing-only-part-of.html
On 24.04.13 19:21, Osvaldo Martin wrote:
Where I can find documentation about the exact meaning of all the
settings related to the sculpt function? In particular wh
Dear PyMOL users
Sometimes PyMOL draws bonds between atoms which are not supposed to be
connected. I know it is possible to unbond them using "unbond atom1,
atom2", however this requires to always select the atoms and rename the
selections to "atom1" and "atom2", respectively. It would be great
It's been a problem for a while, check the thread
"[PyMOL] Memory not released after load and delete of structure" froom 2012.
Martin
On 04.04.14 21:54, Thomas Holder wrote:
> Hi Osvaldo,
>
> you are right, I can reproduce this. We'll look into it and let you know when
> it has been fixed.
>
Hi guys
I wonder if you could help, I'm rendering this image:
http://qmviews.blogspot.ch/2014/05/illustrating-protein-structures.html
and I wonder if and how I could increase the thickness of the black
outlines?
Thanks for help
Martin
--
Hi all
I wonder if it's possible to have something like ray_trace_mode, 2 (i.e.
black and white with outlines) but in the interactive view. Also, is it
possible to have part of the structure in color (say some active site
amino acids) and the rest in black and white?
Thanks for help
Martin
--
, 2014, at 5:10 PM, Martin Hediger mailto:ma@bluewin.ch>> wrote:
Hi all
I wonder if it's possible to have something like ray_trace_mode, 2 (i.e.
black and white with outlines) but in the interactive view. Also, is it
possible to have part of the structure in color (say some active
Hi all
I tried to adjust the 'fetch_path' property such that downloaded PDB
files would be saved in
os.path.abspath(os.path.join(os.path.curdir, "pdbfiles"))
where 'curdir' is $HOME and 'pdbfiles' is within $HOME.
However, I get 'fetch-error'.
What am I doing wrong?
Thanks for help.
---
Hi all,
My problem is:
I have two structures, A and B. Both are part of a protein and contain
residues from the active site. A is a subset of B in a sense that B is
contains residues even further from the active site (generated by the
expand command).
I ran a QM calculation on the active site in
Dear all
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 pr
Hallo
Thanks for the answer. So could PyMol generate the connectivity it sees?
So this could be used for a subsequent force field computation?
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That would be really interesting to know.
If there is no connectivity data provided, then my only guess is that it
has some really precise bond length data to compare to.
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I was thinking about this as well, I saw an older post on this topic
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg06211.html
but it seems that the script mentioned there starts to see 'hydrogen
bonds' between non-polar hydrogens and atoms up to 15 angstrom away.
Can someone con
Dear all
I am looking for the correct syntax to select an atom by its ID. I am
frequently confronted with needing to identify an atom only by its ID,
since at that point I cant tell what position in a residues it takes. Is
this possible with the PyMOL select command?
Any replies are greatly app
Hi all
Given this situation:
Ser-O-H NH-R2
with the 'bond' and 'unbond' commands, I can form and cut a bond so that
I get
Ser-O H--NH-R2
But this seems to have just a visual effect, meaning the coordinates of
the proton do not change.
I would like to know now if there is a smart way of ad
Hi all
Is there a way to have the command "as sticks" show sticks and only
polar hydrogens? Right now it shows all hydrogens and it would be nice
if I could set it to leave out non polar hydrogens.
Thanks for any suggestions.
Martin
---
Dear all
I am using the script of Robert Campell to collect hydrogen bonds and
the essential part looks like this:
[collect pairs in hb by cmd.find_pairs]
for pairs in hb:
cmd.iterate("%s and index %s" % (pairs[0][0], pairs[0][1]),
'print "%1s/%3s`%s/%-4s " % (chain,
Dear All
I'm using Mac OS X and would like to start PyMOL from the command line,
so I can open up .pdb files from a command line argument by issuing $
pymol -c /directory/*pdb (for some reason, within pymol it seems to be
not possible to issue 'PyMOL > *pdb').
When I enter 'pymol' in the Termi
uses the current directory.
>
> Mike
>
>
>
> On Sep 1, 2010, at 9:44 AM, Martin Hediger wrote:
>
>> Dear All
>> I'm using Mac OS X and would like to start PyMOL from the command line,
>> so I can open up .pdb files from a command line argument by i
Dear All
I'm trying to write a littel function that allows for a short cut to
invoke the "wizard measurement". The idea is, that instead of having to
open the GUI menue>Measurement or typing "wizard measurement", I would
like to be able to just type "mes" and have the measurement tool-box
ava
Dear All
I am trying to cut out a subset of a protein structure. I am selecting
an active site atom and expanding by residue with radius 12 Angstrom
around that atom. Is there a way of doing the following:
If the edge of the selection ends with a carbonyl of a peptide bond,
keep it included. I
Hi all
I want to do some scripted mutations on a range of residues. Say I want
to mutate residue 189 to every rotamer of [Asp, His, Glu, Thr, Lys]
available in the PyMOL internal rotamer library. I'm seeing that PyMOL
issues cmd.get_wizard().do_state(i) to select rotamer 'i' for a
mutation. N
Dear all, let me rephrase my question in a less confusing way.
For a given mutant, I need a PDB file for every available rotamer. I
guess thats the simplest way of putting it. How can I achieve that?
Thanks for hints.
Martin
Am 12.09.10 00:08, schrieb Martin Hediger:
>Hi all
>
n also does 20 and 60 in place of 10--three possible lookups
> key = ( stored.r, int(10*round(phi/10)), int(10*round(psi/10)))
>
> if key in rot_lib.keys():
>print "This rotamer has %s possible positions" % len(rot_lib[key])
>
> Lookups in the independent library are easi
#x27;\n')[1]
> # get it's three-letter residue id
> print three_letter[string.split(cmd.get_fastastr("mySelection"),'\n')[1]]
>
> I just posted this on http://www.pymolwiki.org/index.php/Aa_codes.
> (You will need the two dictionaries found there.)
>
>
replacing
>
>> (phi, psi) = cmd.phi_psi("br. first my_res")
> with
>
> (phi, psi) = cmd.phi_psi("br. first my_res").values()[0]
>
>
> Here's what I have now, for the script (I fixed one more bug):
> import pickle
> rot_lib =
> pickle.load(o
that the hydrogen on the carbonyl group remains there?
I hope I could explain my problem and I would be very happy if there was
a solution to this.
Thanks a lot
Martin
Am 15.09.10 00:33, schrieb Martin Hediger:
>I'm beginning to see things.
> When I issue:
>
> for
_wizard().do_select("("+res+")")
>cmd.frame(i)
> cmd.get_wizard().apply()
>cmd.save("state" + str(i) + ".pdb", cpy)
>cmd.delete(cpy)
>cmd.create(cpy,org)
>
> # end the python block
> python end
>
> # quit the wizard
&g
/PMW are very easy to develop with. Good luck!
>
> Cheers,
>
> -- Jason
>
> On Sat, Sep 18, 2010 at 6:48 PM, Martin Hediger wrote:
>> This is great. Thanks a lot.
>> I am wondering, are there any scripts/ plugins for PyMOL out there that
>> facilitate the g
d.set("sculpting_cycles",100)
>
> # resume the UI
> cmd.set("suspend_updates",0)
>
> # write coords
> cmd.sculpt_iterate("myProtein")
>
> #quit sculpting
> cmd.unset("sculpting")
>
>
> Load a small protein and call it &quo
resume the UI
> cmd.set("suspend_updates",0)
>
> # write coords
> cmd.sculpt_iterate("myProtein")
>
> #quit sculpting
> cmd.unset("sculpting")
>
>
> Load a small protein and call it "myProtein". Then, copy/paste the
> above code
Dear All
I am trying to get behind the way 'iterate' works, since I see it quite
frequently in PyMOL scripts.
The example in the help page is a bit limited in the sense that I cant
explain to myself what actually is happening.
Say, if I were to write the functionality of 'iterate' using a for-lo
Dear All
I'm trying to figure out for myself, what the two labels 'Label > Atom
Identifiers > ID' and 'Label > Atom Identifiers > index' mean, or what
the respective difference between the two is. For sure, the numerical
value is very different when I show the labels in a structure. ID seems
to
Wassenaar wrote:
> Never get used to that only-reply-to-sender policy...
>
>
> -- Forwarded message --
> From: Tsjerk Wassenaar
> Date: Mon, Oct 25, 2010 at 12:30 PM
> Subject: Re: [PyMOL] What is the difference between Atom ID and Index
> To: Martin Hedige
;6-9")
> label *, "%s-%s" % (index,ID)
>
> Cheers,
>
> -- Jason
>
>
>
>
> On Mon, Oct 25, 2010 at 6:49 AM, Tsjerk Wassenaar wrote:
>> Never get used to that only-reply-to-sender policy...
>>
>>
>> -- Forwarded mess
an atom.
Thanks for your help so far.
Martin
On 31.10.10 18:31, Tsjerk Wassenaar wrote:
Hi Martin,
So it seems I was right :D
ID is an atomic property, read from the PDB file, whereas index is an
'internal' identifier. Following Jasons comments, ID is not changed
upon addition
d of indices. "
>
>
> I suppose you should use>>RANK<<, if you like to "find a way to get the
> 'linenumber-dependent' index of an atom".
>
> cheers,
> Hongbo Zhu
>
>
> On 11/01/2010 10:02 AM, Martin Hediger wrote:
>> Hi Tsjerk,
Dear all
It occured to me that PyMOL is resequencing a structure when saving. I
am trying to interpolate between two structures where it is critical to
have identical sequence in both structures. Is it possible submit a
-option to the save command?
Thanks for your help
Martin
-
Dear all
Is it possible to increase the number of digits displayed when measuring
the distance between two atoms?
Thanks
Martin
--
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PROT H
Can this be explained somehow?
Thanks for your answers.
Martin
On 09.11.10 13:26, Jason Vertrees wrote:
> Hi Martin,
>
> set retain_order
> set pdb_retain_ids
>
> Cheers,
>
> -- Jason
>
> On Tue, Nov 9, 2010 at 4:30 AM, Martin Hediger wrote:
>&
Dear all
Let protein P be of C1 symmetry, so no symmetry elements. It can be
approximated by a cube C, where every face of C has its own value, say 1
to 6.
Lets assume, the positive x-direction is coming out of the computer
screen, the plane of the screen is the yz plane, the lower left corner
Dear all
Is it possible to start a PyMOL viewer through a web browser? What I
mean by this is, is it possible to view a protein over the internet
where the viewing features are provided by some "limited" PyMOL server?
The only thing able to do that right now is Jmol, but i think its very
inconv
particularyl helpful.
Anyway, the questions remains, how one could run a PyMOL session through
a web browser. I will be looking at the input from the previous postings.
Am 19.12.10 14:11, schrieb Rich:
> On 19-12-2010 7:37, Martin Hediger wrote:
>> Dear all
>> Is it possible to start
I was thinking of something like a browser plug-in, just as it is
available for PowerPoint.
We'll see, where it goes.
Am 19.12.10 17:06, schrieb Rich:
> On 19-12-2010 10:27, Martin Hediger wrote:
>> Of course, Jmol is very poweful and I am using it as well for many things.
&
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