Re: [PyMOL] set transparency for selected elements of secondary structure
Hi James and Ali, Are you using PyMOL 2.3 yet? "As of PyMOL version 2.3, cartoon transparency is now an atom-level setting." https://pymolwiki.org/index.php/Cartoon_transparency Cheers, Thomas > On Jun 26, 2019, at 10:26 AM, Ali Kusay wrote: > > Hi James, > > I am not sure what the exact cause of your issue is but I think if you make a > selection first then apply the transparency to the selection that should > work, i.e.: > > sele ss H+S > set cartoon_transparency, 0.5, sele > > Something to do with selection based transparency settings not enabling newer > ones to be made > > Cheers, > > Ali > > On 26/6/19, 6:18 pm, "James Starlight" wrote: > >Dear pymol users! > >I am trying to set transparency based on the secondary structure using >pymol selection algebra > ># set transparency to all helix and sheets but not loops >set cartoon_transparency, 0.5, ss H+S > >which produce the following output >PyMOL>set cartoon_transparency, 0.5, ss H+S > Setting: cartoon_transparency set for 144 atoms in object > "0190_before_minim". > >but actually do nothing in terms of visualization. > >Could you suggest me how it would be possible to fix it? > >Thanks in advance! > > >___ >PyMOL-users mailing list >Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] PDB post-processing and TER records
If you want to rename multiple chains at once, make a selection like (chain
A+B+C). This list selection syntax is documented here:
https://pymolwiki.org/index.php/Property_Selectors
cmd.load(pdb)
cmd.alter('chain ' + '+'.join(chains_array), 'chain=""')
cmd.save('output.pdb')
Cheers,
Thomas
> On Jun 25, 2019, at 4:14 PM, James Starlight wrote:
>
> thanks so much Thomas, for this example!
>
> Actually, your python script does exactly what my bash script -
> produces number of pdbs for each of the renamed chain.
> I would like rather to produce at the end ONE pdb with all chains
> renamed to empty chain...
> I guess I need to save the result outside of the loop something like this
>
> hop hey lalaley #
> from pymol import cmd
> pdb = "Ev_complex_model_final.pdb"
> chains_array = ["A", "B"] # add more chains in case of more complex pdb
>
> # loop over chains to rename it
> for chain in chains_array:
>cmd.load(pdb)
>cmd.alter('chain ' + chain, 'chain=""')
>cmd.delete('*')
> ##
>
> # save output as pdb
> # I need to add something in the name of output indicating how much
> chains have been renamed
> # like output_withoutAB.pdb
> cmd.save('output_' + '.pdb')
>
> thanks in advance for help!
--
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PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] PDB post-processing and TER records
> generally if I integrate a pymol silent script inside my
> bash script, I do not need to use cmd.* syntax, right?
Correct. The -d argument takes PyMOL commands, like a .pml script. Python
syntax is optional.
Python syntax (cmd.*) is necessary and most useful if you write a Python script
(.py extension) and run that with PyMOL. You could write your multi-chains loop
as a Python script:
example.py ##
from pymol import cmd
pdb = "my.pdb"
chains_arrays = ["A", "B", "C", "D", "E", "F", "G"]
for chain in chains_array:
cmd.load(pdb)
cmd.alter('chain ' + chain, 'chain=""')
cmd.save('output_' + chain + '.pdb')
cmd.delete('*')
##
Then run it with PyMOL:
pymol -ckqr example.py
See also:
https://pymolwiki.org/index.php/Launching_From_a_Script
https://pymolwiki.org/index.php/Python_Integration
Cheers,
Thomas
> On Jun 25, 2019, at 3:08 PM, James Starlight wrote:
>
> one extra programming question:
>
> imagine now in my pdb I have severals chain which I would like to
> rename to blank chain.
>
> I can do it simply like this
> # a case for 3 chains to be renamed
>
> #!/bin/bash
> pdb="my.pdb"
> output=$(pwd)
> pymol -c -d "
> cmd.load('${pdb}')
> cmd.alter('(chain A)', 'chain=\"\"')
> cmd.alter('(chain B)', 'chain=\"\"')
> cmd.alter('(chain C)', 'chain=\"\"')
> cmd.save('${output}/output.pdb','all')
> "
>
> or for multi-chain protein I can alternatively create external loop,
> thus running pymol 3 times iteratively (which is not good realization)
> providin array info from external shell session
>
> # this example save 7 different pdbs renaming one chain in each of them
> #!/bin/bash
> pdb="my.pdb"
> output=$(pwd)
> chains_arrays=( A B C D E F G )
>
> for i in "$chains_array[@]}"; do
> pymol -c -d "
> cmd.load('${pdb}')
> cmd.alter('(chain $i)', 'chain=\"\"')
> cmd.save('${output}/output_$i.pdb','all')
> "
> done
>
> would it be possible rather to make an array and loop inside the pymol
> to rename all chains into the blank chain during one execution of
> pymol?
>
> Thanks in advance!
>
> вт, 25 июн. 2019 г. в 14:50, James Starlight :
>>
>> I have got the idea!
>> thank you so much Thomas!
>> One question: generally if I integrate a pymol silent script inside my
>> bash script, I do not need to use cmd.* syntax, right? In what cases
>> cmd.* sytax might be usefull?
>>
>> Thank you again!
>>
>> вт, 25 июн. 2019 г. в 12:05, Thomas Holder :
>>>
>>>
>>>> On Jun 25, 2019, at 11:48 AM, James Starlight
>>>> wrote:
>>>>
>>>> so what I need is just to update my pymol, keep using the same command?
>>>
>>> Yes
>>>
>>>> P.S.would the following integration of the code into bash script be
>>>> usefull to remove chains in no gui mode?
>>>>
>>>> pymol -cQkd "
>>>> from pymol import cmd
>>>> fetch $pdb, type=pdb, tmp
>>>> cmd.alter('(chain A)',chain='')
>>>> "
>>>> I am not sure whether I used here cmd.alter in correct way ..
>>>
>>>
>>> With fetch, use "async=0" or use Python syntax. And keyword arguments
>>> (type=) must be after positional arguments (tmp).
>>>
>>> It's easier if you don't use Python syntax for alter, otherwise you'll need
>>> three levels of nested quotes, which gets ugly:
>>>
>>> pymol -cQkd "
>>> fetch $pdb, tmp, type=pdb, async=0
>>> alter (chain A), chain=''
>>> "
>>>
>>> With Python syntax (note the ugly escaping of quotes):
>>>
>>> pymol -cQkd "
>>> cmd.fetch('$pdb', 'tmp', type='pdb')
>>> cmd.alter('(chain A)', 'chain=\"\"')
>>> "
>>>
>>> Cheers,
>>> Thomas
>>>
>>> --
>>> Thomas Holder
>>> PyMOL Principal Developer
>>> Schrödinger, Inc.
>>>
--
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PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] Thermal ellipsoid plot
Hi Koji,
Interesting question, I wasn't aware of the ellipsoid_probability setting.
The probability to radius conversion is done with a lookup table, see:
https://github.com/schrodinger/pymol-open-source/blob/d1359f125d/layer2/RepEllipsoid.cpp#L114
To get sphere scaling equivalent of ellipsoid_probability=0.5, you can do:
set sphere_scale, 1.53820
I calculated this value with the following script:
problevel = [ \
0.4299, 0.5479, 0.6334, 0.7035, 0.7644, \
0.8192, 0.8694, 0.9162, 0.9605, 1.0026, \
1.0430, 1.0821, 1.1200, 1.1570, 1.1932, \
1.2288, 1.2638, 1.2985, 1.3330, 1.3672, \
1.4013, 1.4354, 1.4695, 1.5037, 1.5382, \
1.5729, 1.6080, 1.6436, 1.6797, 1.7164, \
1.7540, 1.7924, 1.8318, 1.8724, 1.9144, \
1.9580, 2.0034, 2.0510, 2.1012, 2.1544, \
2.2114, 2.2730, 2.3404, 2.4153, 2.5003, \
2.5997, 2.7216, 2.8829, 3.1365, 6. ]
iprob = int((cmd.get_setting_float('ellipsoid_probability') + 0.01) * 50 - 1)
pradius = problevel[iprob]
cmd.set('sphere_scale', pradius * cmd.get_setting_float('ellipsoid_scale'))
Hope this helps.
Cheers,
Thomas
> On Jun 24, 2019, at 7:21 AM, koji naka wrote:
>
> Dear all,
>
> The size of isotropic atoms plotted by using "alter all, vdw = sqrt(b/8)/pi"
> and "show sphere" looks small compared with the size of anisotropic atoms
> displayed by "show ellipsoid" in PyMOL default setting with 50% probability.
>
> How can I plot the isotropic atoms with 50% probability?
>
> The data is a pdb file converted from a cif through Mercury software.
>
> Thank you very much for your help.
>
> Best regards,
> Koji
>
>
> ___
> PyMOL-users mailing list
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> Unsubscribe:
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Re: [PyMOL] PDB post-processing and TER records
Hi James, pdb_use_ter_records works in PyMOL 2.3.0, but not in previous versions (was broken and then removed). See https://pymolwiki.org/index.php/pdb_use_ter_records Cheers, Thomas > On Jun 25, 2019, at 10:25 AM, James Starlight wrote: > > Dear Pymol Users! > > I need to process input PDB via pymol (this time no need to do it via > no-gui mode!!) to remove chain id from PDB. > > I am using alter command to do it with the following syntax > #rename chain A to phantom chain :-) > alter (chain A),chain='' > > the problem that in my initial PDBs there are many TER records (e.g. > to separate protein from ligand etc), which should be keeped after > such post-processing in the form of original PDB (with chain A). > > I have tried to do this before saving of the PDB > get pdb_use_ter_records > > however, as the result, all the TER records were removed from the > processed pdb. How I could fix it? > > Many thanks in advance! > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] possible bug mouse coordinates
Hi Arnaud, This should be fixed now, see https://github.com/schrodinger/pymol-open-source/commit/af28e453c6 Cheers, Thomas > On Jun 13, 2019, at 5:46 PM, Thomas Holder > wrote: > > Hi Arnaud, > > I can reproduce both issues, at least with "sticks" representation. > Apparently PyMOL is missing pick color invalidation somewhere. > > As a workaround, click the "Rebuild" button (upper right button box), or type > the "rebuild" command. After that, picking should be correct again. > > Cheers, > Thomas > >> On Jun 13, 2019, at 4:21 PM, Arnaud Basle wrote: >> >> Dear All, >> >> We found that our home compiled version has the problem just even doing: >> >> load a pdb >> >> change the colour >> >> and then the mouse coordinates are wrong... Anyone else? >> >> Cheers, >> >> Arnaud >> >> >> On 13/06/2019 14:33, Arnaud Basle wrote: >>> Dear All, >>> >>> We may have found a bug where pymol does not get the correct mouse location >>> on the screen. >>> >>> We are using Version 2.3.0a0 on linux Mint 19 (~ubuntu). >>> >>> Maybe people can try to reproduce the bug: >>> >>> open a pdb file >>> >>> display sticks >>> >>> try to select residues or recenter and it should work fine. >>> >>> Now, reduce the top part window of pymol with the log output, movie buttons >>> and command line (the mouse pointer will change then click and drag). >>> >>> repeat selecting/centering and it should work. >>> >>> Then use a menu entry, for example Display>Background>White >>> >>> And if not only us now it seems we click on a residue but another one is >>> selected. It looks like there is a bug where pymol cannot determine the >>> correct mouse co-ordinates? >>> >>> Cheers, >>> >>> Arnaud >>> >>> >> -- >> Dr Arnaud Basle X-ray facilities manager >> Newcastle Structural Biology Laboratory >> University of Newcastle >> Medical School >> ICAMB >> Framlington place >> NE2 4HH Newcastle upon tyne >> Phone 0191 208 8931 >> >> >> >> ___ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Advice on plugin creation
Hi Ed, The tutorial doesn't consider that the "dialog" variable must not go out of scope. It needs an additional reference to keep it alive, e.g. a global will work: dialog = None def run_plugin_gui(): from pymol.Qt import QtWidgets global dialog if dialog is None: dialog = QtWidgets.QDialog() # TODO: FILL DIALOG WITH WIDGETS HERE dialog.show() The full example plugin on github doesn't suffer from this problem, it's kept alive by circular references - at least until you run the Python garbage collector (ouch!). Cheers, Thomas On Wed, Jun 12, 2019 at 7:02 PM Edward Lowe wrote: > > Hello, > > I'm trying to create what I think should be a fairly simple plugin to > use pymol to showcase structures for a University Open day - all it > needs to do is load up coordinate files and maps and present a very > simple GUI that visitors can use to move between pre-defined scenes. > > I've constructed a PyQt plugin following the tutorial on pymolwiki > which works up to a point... > If I display the window using dialog.show() as in the tutorial example, > the window disappears immediately on opening. > If I change this to using dialog.exec() my widget opens correctly and > everything works - but since this is now a modal window it is not > possible to return to the main pymol gui and interact with the > structure. This was the point of the exercise an why I'm not just > making a movie! > > Does anyone have any advice on what could be done to fix this > behaviour? It probably goes without saying that I am very much a > novice at this! > > Thanks, > Ed. > -- > Dr. E.D. Lowe edward.l...@bioch.ox.ac.uk > Department of Biochemistry Tel: ++44 (0)1865 (2)75392 > University of Oxford > Oxford UK, OX1 3QU > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] possible bug mouse coordinates
Hi Arnaud, I can reproduce both issues, at least with "sticks" representation. Apparently PyMOL is missing pick color invalidation somewhere. As a workaround, click the "Rebuild" button (upper right button box), or type the "rebuild" command. After that, picking should be correct again. Cheers, Thomas > On Jun 13, 2019, at 4:21 PM, Arnaud Basle wrote: > > Dear All, > > We found that our home compiled version has the problem just even doing: > > load a pdb > > change the colour > > and then the mouse coordinates are wrong... Anyone else? > > Cheers, > > Arnaud > > > On 13/06/2019 14:33, Arnaud Basle wrote: >> Dear All, >> >> We may have found a bug where pymol does not get the correct mouse location >> on the screen. >> >> We are using Version 2.3.0a0 on linux Mint 19 (~ubuntu). >> >> Maybe people can try to reproduce the bug: >> >> open a pdb file >> >> display sticks >> >> try to select residues or recenter and it should work fine. >> >> Now, reduce the top part window of pymol with the log output, movie buttons >> and command line (the mouse pointer will change then click and drag). >> >> repeat selecting/centering and it should work. >> >> Then use a menu entry, for example Display>Background>White >> >> And if not only us now it seems we click on a residue but another one is >> selected. It looks like there is a bug where pymol cannot determine the >> correct mouse co-ordinates? >> >> Cheers, >> >> Arnaud >> >> > -- > Dr Arnaud Basle X-ray facilities manager > Newcastle Structural Biology Laboratory > University of Newcastle > Medical School > ICAMB > Framlington place > NE2 4HH Newcastle upon tyne > Phone 0191 208 8931 > > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Question about Pymol method / ESP rendering
Hi Taka, Your ESP.cube file doesn't look like an electrostatic potential map, it looks like electron density. You need two map files, one for the density, and one for the ESP. Cheers, Thomas > On Jun 8, 2019, at 12:39 AM, Taka Seri wrote: > > Dear Pymol users, > I am newbie of Pymol. > I have a question of coloring method. I would like to draw isosurface with > ESP and would like to set color with ramp_new function. > Attached files are example. > When I load ESP file and type following command, I could get isosurface. > But I could get only blue colored surface after setting color with ramp_new > function. > > > isosurface esp_surf, ESP, 0.2 > > ramp_new color_map, ESP, [-0.1, 0.1] > > I read following url and it worked well. > https://pymolwiki.org/index.php/Ramp_New > > Is something wrong in my ESP file or approach? Any advice or suggestions will > be greatly appreciated. > > Kind regards, > > Taka > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] [EXTERNAL] Absymal performance when creating large numbers of bonds
Hi Lorenzo, Looks like the cmd.bond() function is indeed very inefficient. I've found a "TO DO: optimize for performance" comment in the code - that speaks for itself. https://github.com/schrodinger/pymol-open-source/blob/master/layer2/ObjectMolecule.cpp#L4492 Parallelization is not the solution. You are probably right that a new API function is needed which allows you to directly add a bond by atom indices instead of atom selections. Cheers, Thomas > On May 25, 2019, at 5:11 PM, Lorenzo Gaifas wrote: > > Hi Blaine, > > Thanks for your help. > I don't think what you suggest is going to solve the problem. The loop itself > is quite fast, and I don't need to perform anything else in the loop other > than adding those bonds. > I already have a list of tuples [(atom1, atom2), (atom3, atom4)] and all I > need to do is create a bond between each pair. The bottleneck is the bond > function, not the loop itself. > > Also, I doubt simply the speed difference between C++ and Python could > explain such a drastic difference (minutes against fractions of a second). > There is clearly a difference in the way the `bond` command is implemented > and the way bonds are generated at startup. > > What I think is needed, is either a way for pymol to perform those actions in > parallel (unlikely) or a way to get my hands on the way bonds are generated > at startup and use those functions or at least the same approach. > > Thank you, > Lorenzo > > Il giorno sab 25 mag 2019 alle ore 16:23 Mooers, Blaine H.M. (HSC) > ha scritto: > Hi Lorenzo, > > You can import numpy and replace your lists of coordinates with NumPy > arrays. > Operations with numpy arrays can be >100 times faster than with lists in for > loops. > See the last example the following blog post for inspiration: > > https://medium.freecodecamp.org/if-you-have-slow-loops-in-python-you-can-fix-it-until-you-cant-3a39e03b6f35. > > Please recall that PyMOL is collection of C and C++ programs wrapped by > Python. > The fast display of bonds inside the viewport is due to C or C++ programs. > > 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: Lorenzo Gaifas [bris...@gmail.com] > Sent: Saturday, May 25, 2019 5:48 AM > To: pymol-users@lists.sourceforge.net > Subject: [EXTERNAL] [PyMOL] Absymal performance when creating large numbers > of bonds > > Dear pymol users, > > I'm working on a script, using the python API, that needs to add a very large > number of bonds to the loaded structure. > > I thought simply using cmd.bond() in a for loop would do the trick, but -even > though it works- it is extremely slow. I figured something was fishy, since > pymol at startup is almost istantaneous and there, too, it has to compute, > draw and even guess equally large numbers of bonds. > > I also tried to parallelise the command, but by now I *think* this can't be > done due to the Global Intepreter Lock. > > I feel like there must be something I'm missing (maybe a way to prevent pymol > from updating the rendering between each cmd.bond call?) or at least an API > function that better exposes the bond generation procedure. Does someone have > suggestions on how to solve this problem? > > Cheers, > Lorenzo > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] STL export in PyMol
Hi Jan, With Incentive PyMOL, just type on the command line: PyMOL> save file.stl We haven't released STL export with Open-Source PyMOL yet (I should update the release notes to make that clear). Other geometry formats that PyMOL can export are COLLADA (.dae) and VRML (.wrl). Cheers, Thomas > On May 22, 2019, at 4:03 PM, Jan Gebauer wrote: > > Dear all, > > I found this in the 2.1 release note: > > Release Date: March 13, 2018 > > Features > >.stl export (requires pycollada) > However, I cannot find any hint how to use ist... > > Thanks for any hints. > > Best, > > Jan > > -- > Dr. Jan Gebauer > AG Prof. Baumann > Institut für Biochemie / Uni-Köln > Zülpicher Str. 47 / 50674 Köln > Fon: +49 (221) 470 3212 > Fax: +49 (221) 470 5066 > > > http://px.uni-koeln.de/ -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] [EXTERNAL] Question about polymer selection criteria
Hi Ryan and Blaine,
In addition to the classification by residue identifiers, PyMOL looks for
nucleic acid backbone atoms by name.
See:
https://github.com/schrodinger/pymol-open-source/blob/master/layer3/Selector.cpp#L1393
--
} else if (found_o3star && found_c3star && found_c4star && found_c5star
&& found_o5star && (found_o3_bond || found_p_bond)) {
mask = cAtomFlag_polymer | cAtomFlag_nucleic;
--
Hope that helps.
Cheers,
Thomas
> On May 18, 2019, at 12:26 AM, Mooers, Blaine H.M. (HSC)
> wrote:
>
> Hi Ryan,
>
> I think that the manual page for polymer will answer your question clearly
>
> https://pymol.org/dokuwiki/doku.php?id=selection:polymer
>
> 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: Kung, Ryan [ryan.k...@uleth.ca]
> Sent: Friday, May 17, 2019 4:46 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [EXTERNAL] [PyMOL] Question about polymer selection criteria
>
> Hello,
>
> I have a question about how the pymol polymer.nucleic selection defines what
> is nucleic? Is there a list of atom names that are required? Does it have to
> actually be part of a polymer for the selection process to identify it? If
> someone can help me understand this, that would be great.
>
> Thank you,
> Ryan Kung
>
> ___
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PyMOL Principal Developer
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Re: [PyMOL] How to make protein blur but keep ligand clear?
Hi Arthur, The origin of rotation will become the focal point. So all you have to do is: PyMOL> origin resn DUD The blur will look better if you increase the sample size, e.g. samples=20. Cheers, Thomas > On May 15, 2019, at 9:50 AM, sunyeping via PyMOL-users > wrote: > > Dear all, > > I have a protein-ligand complex and I wish to make the protein looks blur but > keep the ligand clear and sharp with pymol. I find a "focalblur" script > (https://pymolwiki.org/index.php/FocalBlur) which seems to be able to do > this. However I can get the fancy effect illustrated in the examples of the > wiki for this script. With the follow command: > > FocalBlur aperture=2,samples=10,ray=1,width=1000,height=1000 > > > I just make the ligand rather the the protein become blur (Please see the > image at https://drive.google.com/open?id=1qzXDLzVyxI85sJ8H6Zhv8pd8Cq7rA18U, > and the pse file used to make this image is availabe at > https://drive.google.com/open?id=1Gjrl5ePifadWEK8-AZYVXY7yX07kOLF7). > > Could anyone help with this？ What does the argument "aperture" do? How to > control which part become blur? Is there better way to make the ligand blur? > > Thank you very much! > > Arthur > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] stereo in pymol 2
Hi Gary, Stereo has not been dropped, it should work with PyMOL 2.x on Windows and Linux. Does PyMOL report "quad-buffer stereo 3D detected and enabled" on startup? Does it work if you run "pymol -S" (or "pymolwin +2 -S") from a command prompt? Cheers, Thomas > On May 10, 2019, at 1:55 PM, Gary Hunter wrote: > > try as I might I cannot get quad buffered stereo to work in pymol since > version 2 was released. Tried up to 2.3. > My emitter does not even switch on. > pymol 1.8.6 is still good to go in stereo mode, so whats happened? Has stereo > been dropped in version 2? > > using nvideo control panel and real D emitter with nuvision glasses on > windows 7 and a CRT display - Quadro card with DIN plug. > > Also tried using nvidia 3D vision with a TFT stereo display (USB controlled > emitter). Thats also good with 1.8.6 but not 2.2 or 2.3 > > Any ideas what to try? Or let me know its no longer a feature please. > > > > -- > Prof. Gary J. Hunter > > Laboratory of Biochemistry and Protein Science > > Department of Physiology and Biochemistry > > University of Malta > > Msida MSD 2080 > > Malta > > phone: +356 2340 2917 > > mobile: +356 7931 9138 > > phone: +356 21316655 (departmental secretary) > > Fax: +356 21310577 > > http://www.um.edu.mt/ms/physbiochem > > There may be confidential information within the contents of this email meant > only for the person addressed. This email must not be forwarded to third > parties without the express consent of the sender. If you believe you have > received this email in error please inform the sender and remove it from your > system. > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] [pymol] Wrong Visualization of set Spheres
Hi Julian,
I think the problem is that you format the radius as an integer:
# wrong (%d)
cmd.alter("helix%d" % i, expression="vdw=%d" % vdw_a)
# correct (%f)
cmd.alter("helix%d" % i, expression="vdw=%f" % vdw_a)
# also correct:
cmd.alter("helix%d" % i, "vdw=vdw_a", space={'vdw_a': vdw_a})
Hope that helps.
You didn't break any support-requesting rules, your problem was well described,
just a bit tricky to understand. The only thing you should add next time is
PyMOL version and operating system (wasn't relevant for this problem, but you
never know).
Cheers,
Thomas
On Tue, May 7, 2019 at 3:40 PM Julian Krumm wrote:
>
> Dear Pymol-Team,
>
> very new in this forum i come along with a specific problem.
> I wrote a little pymol-script:
>
>
> load /work/jkrumm/edgelook/0.00M/cter/40-helix-edge/helix-40.pqr
>
> hide lines
> show cartoon
>
> radius = 2.7
> vdw_a = 2.7
>
> for i in range(401,413,1):\
> print(i)\
> vdw_a = vdw_a + 2.7\
> print(vdw_a)\
> cmd.create("helix%d" % i, "/helix-40///PRT`%d/PRT" % i)\
> cmd.alter("helix%d" % i, expression="vdw=%d" % vdw_a)
> rebuild
>
> disable all
>
>
> for i in range(401,413,1):\
> cmd.set(name="sphere_transparency", value=0.0, selection="helix%d" % i)\
> cmd.show(representation="sphere", selection="helix%d" % i)\
> cmd.enable(name="helix%d" % i)
>
> enable helix-40
>
> set_view (\
> 0.246392056, -0.601405144,0.760001123,\
>-0.951444209, -0.299392790,0.071540825,\
> 0.184513614, -0.740724683, -0.645971537,\
> 0.0,0.0, -270.700958252,\
> 0.528925896,8.660091400, -2.648437977,\
> 100.995597839, 440.40625, -20.0 )
>
> bg_color white
> set reflect, 0
> png ./test.png, width=2400, height=1200, dpi=300, ray=0
>
>
> It is reading the PRT-entrys out of the input file to new objects and then
> adjusts the proper radius.
> The radius of the protein spheres is incremented by 2.7 Å. Moreover the
> sphere center is shifted away from the C-terminus towards the N-terminus
> by a distance equal to its radius (not done by pymol).
> This should lead to the situation, that the surfaces of all
> protein-spheres cut succinctly in one point at the C-Terminus, which they
> do not.
> It comes to slightly deviations when the spheres are getting visualized.
>
> I already checked the sphere-centers. They are placed right. Also the
> radii are set right. After i showed this to my advisor he is the same
> opinion that the problem has to be pymol-based. I can't explain and i hope
> You are able to help me with this problem.
>
> Attached to this mail You will find the pymol-session and the input PQR.
>
> Sincerely,
> JuK
>
>
> P.S. If i broke any rule of support-requesting or if any information is
> missing please let me know.___
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> Unsubscribe:
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PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] Minimum mesh spacing
Hi Vatsal, The "min_mesh_spacing" setting only affects the "mesh" representation of molecules (molecular surface). To increase the mesh density of an isomesh, you need to upsample the map with the "map_double" command. https://pymolwiki.org/index.php/Map_Double Hope that helps. Cheers, Thomas > On Apr 26, 2019, at 12:42 AM, Vatsal Purohit > wrote: > > Hello, > > I've been trying to use the minimum mesh spacing feature on pymol to make my > meshes more defined and it doesn't seem to do anything. > > I use .map.ccp4 files that I generated on ccp4 using .mtz files I generated > on phenix. Any suggestions on what I might be doing wrong and what I could do > to fix this would be really appreciated! > > Regards, > Vatsal > > -- > Vatsal Purohit > > PhD Candidate, Stauffacher Lab, Dept. of Biology, Purdue University > PULSe-Biophysics and Structural Biology training group > vpur...@purdue.edu | 346-719-9409 > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Electron density map color
Hi Vatsal, This is how you show positive and negative contour: fetch 1ubq, diffmap, type=fofc, async=0 isomesh diffmesh, diffmap, 3.0 color green, diffmesh set mesh_negative_color, red set mesh_negative_visible Example copied from: https://pymolwiki.org/index.php/mesh_negative_visible Cheers, Thomas > On Apr 26, 2019, at 12:37 AM, Vatsal Purohit > wrote: > > Hello, > > I've been trying to color my Fo-Fc electron density maps in pymol with the > positive Fo-Fc maps showing as green and negative Fo-Fc maps showing as red > and having no luck with it. They either show up as red or green. > > I generate my maps by converting .mtz from phenix to .ccp4 files on ccp4. Any > suggestions about how I can try to color them individually this would be > greatly appreciated! > > Regards, > Vatsal > > -- > Vatsal Purohit > > PhD Candidate, Stauffacher Lab, Dept. of Biology, Purdue University > PULSe-Biophysics and Structural Biology training group > vpur...@purdue.edu | 346-719-9409 > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] monitor same protein conformational change with multiple trajectory files
Hi Yu and David,
I like to throw in one of the many ways to do this inside PyMOL :-)
from pymol import cmd
# load 3000 files into the "multi" object
for i in range(3000): cmd.load('file_{}.pdb'.format(i + 1), 'multi')
# if you want, fit to the first state
cmd.intra_fit('multi')
Morphing between each state is possible, but will take some time, and with the
defaults you'll end up with 9 states, which might be more than PyMOL can
handle (also you'll have a 50 minute movie).
As a proof of concept, here is how you make a linear (faster than rigimol)
morph with 3 interpolated states between each consecutive input state, for the
first 100 of your files (yields 495 states):
from pymol import cmd
for i in range(100): cmd.load('file_{}.pdb'.format(i + 1), 'multi')
cmd.intra_fit('multi')
cmd.morph('morph', 'multi', state1=0, state2=0, refinement=0, steps=5,
method='linear')
Hope that helps.
Cheers,
Thomas
> On May 1, 2019, at 3:36 PM, David Gae wrote:
>
> Dear Yu,
>
> Try this bash script and then run "pymol all.pdb” in your PDB directory.
> this might help you view your files as a trajectory.
>
>
> for i in {1..3000}
> do
> # change frame_$i.pdb to your file name. for example mine is frame_1.pdb
> [ -f "frame_$i.pdb" ]
> z=frame_$i.pdb
> sed 's/END/ENDMDL/g' $z > $z.r
> { echo 'MODEL'; cat $z.r; } >$z.new
>
> rm $z.r
> done
>
> cat *.new > all.pdb
> rm *.new
> -
>
> I am sure there are many ways to do this inside pymol as well. you might want
> to look up https://pymolwiki.org/index.php/Main_Page
>
> hope this helps,
> David
>
>> On Apr 30, 2019, at 5:57 PM, Yu Qi wrote:
>>
>> Some background: I'm an undergraduate student and am doing research with my
>> professor about modeling protein conformational changes. I am new to this
>> field and and am actively learning how to use command lines, python and
>> other relative tools. I have simulated how the protein will walk with
>> CAMPARI and have gotten back 3000 trajectory (pdb) files, my question is:
>> how do I use PyMOL to make a movie by using those trajectory files?
>> Basically, I want to know how to visualize how the protein moved from the
>> first pdb file to the second, then to the third, etc.
>>
>> I tried morphing two pdb files with one step from file_1.pdb to file_2.pdb,
>> I aligned them first, then morphed them. I'm not sure how to go from there
>> because I had a result file with 2 states and 2 frames, then when I tried to
>> morph the result file with file_3.pdb, it did not work as I expected.
>>
>> please let me know if you have questions, and I really appreciate the help.
>>
>> Thank you for the help,
>> Yu
>>
>> ___
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>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
> ___
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Re: [PyMOL] Performing backend calculations within PyMOL
Hi Ali,
I would typically use a temporary object for that, which is loaded into the
work space but never rendered:
def intra_rms_tempobj(filename):
from pymol import cmd
tmpname = cmd.get_unused_name('_tmpobj')
cmd.load(filename, tmpname, zoom=0)
try:
return cmd.intra_rms(tmpname)
finally:
cmd.delete(tmpname)
It's also possible to create a new instance of the PyMOL backend, this is
probably closer to what you were looking for:
def intra_rms_tempinstance(filename):
import pymol2
with pymol2.PyMOL() as p:
p.cmd.load(filename)
return p.cmd.intra_rms('*')
See also:
https://pymolwiki.org/index.php/Launching_From_a_Script#Independent_PyMOL_Instances_.28Context_Manager.29
Cheers,
Thomas
> On May 3, 2019, at 2:24 AM, Ali Kusay wrote:
>
> I have noticed that PyMOL can be used to perform fast calculations by using
> it in command line or through something like Jupyter notebook since it
> doesn’t have to worry about the graphical geometries. I am curious if this
> can be performed within the PyMOL program itself. For example, loading the
> python interpreter in PyMOL and using it load a multistate object and
> calculate RMSD through intra_fit without actually loading the object in the
> work space. I would appreciate your help, this would be immensely time saving
> for larger proteins while providing the convince of not having to leave the
> program.
>
> Kin regards,
>
> Ali Kusay
> PhD student
> ___
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Re: [PyMOL] Pymol Activation
Hi Julia, As a student, you can register for a free educational license: https://pymol.org/edu/ Cheers, Thomas > On Apr 4, 2019, at 8:54 PM, Julia Garcia wrote: > > Hello, > > I am currently a student and I am using pymol in one of my classes. I was > able to download the software, but I am confused on whether I need to > activate it or skip the activation (image attached below). I was told that > this software was free to use as a student, but in order to activate it I > have to pay for a subscription. If you could help clarify how to properly set > up pymol on my computer that would be greatly appreciated. > > Thank you, > > Julia Garcia -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] How to best create a sliding window (a selection of specific residues) and compare specific residue names+numbers in pymol/python?
Hi Anne,
This is not at all an obvious question, it's quite advanced! Impressive code
snippet for a newbie :-)
For the sliding window question, I suggest to have a look at the implementation
of "local_rms" from the psico package:
https://github.com/speleo3/pymol-psico/blob/master/psico/fitting.py
Example usage:
import psico.fitting
fetch 1akeA, async=0
fetch 4akeA, async=0
local_rms 1akeA, 4akeA, window=5
It calculates the RMSD of the entire sliding window, not only one residue. And
it only considers the C-alpha atoms (remove the "and guide" selector which is
passed to Matchmaker to include all atoms).
My question would be: What does the RMSD of a single residue really tell you?
The number will reflect something in between the fit of the sliding window and
the sidechain conformation of the center residue. Are you interested in both?
Or only one of them?
Cheers,
Thomas
> On Feb 22, 2019, at 6:28 PM, Anne Nierobisch
> wrote:
>
> Hi,
>
> I need to calculate the RMSD for the same residue, e.g. 131Thr, from 2 pdb
> files for the same target. As I need a local alignment, I use a sliding
> window of 5 residues (the residue of interest is in the middle.)
> I have adapted the script from https://pymolwiki.org/index.php/RmsdByResidue
> (also see below my code below) by adding a sliding window, but I need advice
> on the following:
>
> - I would need to check whether I am actually comparing the intended
> residues, e.g. 131Thr, 131Thr, or whether the same residues (e.g. His, Asp,
> His), with specific residue names and numbers are in the selection I have
> chosen from both pdb files for my sliding window.
> The reason:
> I have coded up the script below, but often it skips and doesn't compare two
> residues, because the atom count is different between the residue from
> protein A and protein B.
> (It is exactly double the number, I have already checked and excluded
> problems like occupancy and different conformations as potential causes.)
>
> - I constructed a sliding window by selecting two residues before the residue
> of interest and two residues which follow said residue. (I know that residues
> can be missing, I am working on this.)
> Is there a better way for constructing a sliding window? I have not found
> such a method in pymol.
>
> For anyone interested, I have attached a code snipplet below.
> I am sorry, if these seem like obvious questions, but I tried various
> approaches and I feel that I need a push in the right direction. I have the
> feeling that I am missing something fundamental.
>
> Many thanks for any suggestion!
> Anne (Newbie in Pymol)
>
> ##
>
> Code snipplet (Python/Pymol interface):
> referenceProteinChain = cmd.fetch(pbdstructure1)
> targetProteinChain = cmd.fetch(pdbstructure2)
> sel = referenceProteinChain
> list_atoms = [[133, 133]] # example list, I want to calculate the rmsd
> between residue 133 and residue 133 of two pdb structures
>
> for j in list_atoms:
># I formulate my sliding window of 5 residues, my residue of interest is
> in the middle
> ref_begin = int(j[0])-2
> ref_end = int(j[0])+2
> target_begin = int(j[1])-2
> target_end = int(j[1])+2
>
> # I create a selection for the reference protein and the target protein
> cmd.create("ref_gzt", referenceProteinChain+" and polymer and not alt B
> and not Alt C and not alt D and resi %s-%s"
> cmd.alter("ref_gzt", "chain='A'")
> cmd.alter("ref_gzt", "segi=''")
> cmd.create("target_gzt", targetProteinChain+" and polymer and not alt B
> and not Alt C and not alt D and resi %s-%s" %(target_begin,target_end) )
> cmd.alter("target_gzt", "chain='A'")
> cmd.alter("target_gzt", "segi=''")
>
> # I align my selected 5 residues for a local alignment window
> cmd.align("target_gzt","ref_gzt",object="align", cycles =5)
>
>
># select alpha carbon of in reference structure to loop over
> calpha=cmd.get_model(sel+" and name CA and not alt B and not Alt C and
> not alt D and resi %s-%s" %(ref_begin,ref_end) )
>
>## here I loop over all residues in the sliding window and calculte the
> rmsd for my residues of interest.
> for g in calpha.atom : I loop over the slinding window
> if g.resi == str(j[0]): ## we select only our residue of interest
> within the sliding window
> if cmd.count_atoms("ref_gzt and polymer and resi
> "+g.resi)==cmd.count_atoms("target_gzt and polymer and resi "+g.resi):
>
>
Re: [PyMOL] cmd.get_model
Hi Jeong, cmd.get_model() has not been replaced or removed. What error do you get? This code should work: from pymol import cmd print(cmd.get_model()) Cheers, Thomas > On Mar 22, 2019, at 3:16 AM, 정보성 wrote: > > Hi All, > > My Pymol version is 2.1.1 and I can not find the cmd.get_model in my version. > but there is document of 'get_model' in pymol wiki > (https://pymolwiki.org/index.php/Get_Model) > is it replaced some other cmd? > I want to use 'cmd.get_model', if anyone can give the python code of > 'get_model'? > > Thanks > > Jeong. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] fix cartoon backbone
Hi Adam, The atom naming is nonstandard. If you fix that, the cartoon will be complete. alter name P01, name="P" alter name O01, name="O5'" alter name O02, name="OP1" alter name O03, name="OP2" unbond name OP1, name O3'+O5' unbond name OP2, name O3'+O5' PyMOL doesn't yet write bonds to mmCIF (it's on our TODO list, unfortunately the mmCIF spec doesn't make this straight forward). You could save to MMTF instead, it stores all bonds. Cheers, Thomas > On Mar 22, 2019, at 5:42 PM, h. adam steinberg > wrote: > > Thank you, that certainly brought the chains together, but sill no completed > cartoon even after a rebuild. > > Attached is chain F, can you see anything wrong with this file that won’t let > it display a complete chain? It must be with how I joined the missing atoms? > > I also notice that every time I open this object in PyMOL I get odd bonding > happening. Even when I unbond those odd connections and resave the file, it > puts them right back in when I reopen the file. > > I could simply fake the connection using photoshop, but I’m trying to learn > to do it correctly! :) I appreciate your help! > > > >> On Mar 22, 2019, at 11:31 AM, Jared Sampson >> wrote: >> >> Hi Adam - >> >> The characters between the object names and the chain IDs are the segment >> IDs. You can remove them by setting them to the empty string using `alter`: >> >> alter all, segi="" >> >> Hope that helps. >> >> Cheers, >> Jared >> >> >> On March 22, 2019 at 12:14:46 PM, h. adam steinberg >> (h.adam.steinb...@gmail.com) wrote: >> >>> >>> >>>> On Mar 21, 2019, at 1:41 AM, Kevin Jude wrote: >>>> >>>> The DNA in 1CGP is made up of two annealed half sites, so there are four >>>> chain assignments for the two strands. If you want to display it as intact >>>> DNA, after adding the linking phosphate you can use the alter command to >>>> make the chains continuous. HTH. >>>> >>>> -- >>>> Kevin Jude, PhD >>>> Structural Biology Research Specialist, Garcia Lab >>>> Howard Hughes Medical Institute >>>> Stanford University School of Medicine >>>> Beckman B177, 279 Campus Drive, Stanford CA 94305 >>>> Phone: (650) 723-6431 >>>> >>>> On Wed, Mar 20, 2019 at 12:18 PM h. adam steinberg >>>> wrote: >>>> Hi All, >>>> >>>> I opened 1cgp and the DNA has two breaks in the nucleic acid backbone. >>>> After I fixed those two breaks (add in the correct atoms and join them) >>>> how do I get the cartoon of the DNA to be complete? PyMOL still creates >>>> the cartoon with the breaks. >>>> >>>> Thanks! >>>> >>>> Adam -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Compiling open source pymol 2.4
Hi Markus,
I recommend to use Python 3. The PyMOLWiki has updated versions of those two
failing scripts:
https://pymolwiki.org/index.php/Pairwise_distances
https://pymolwiki.org/index.php/Polarpairs
I don't know why there would be no menu bar with Python 2.7. But if Python 3
works for you, I think there is no need to figure that out.
Cheers,
Thomas
> On Mar 12, 2019, at 7:34 PM, Markus Heller wrote:
>
> Hi all,
>
> I'm having trouble compiling open source Pymol 2.4.
>
> If I compile with python 2.7, the compilation finishes without errors or
> warnings, but when I start Pymol, I don't see the menu bar at the top of the
> window, and I don't see any errors.
>
> If, on the other hand, I compile with python 3, Pymol starts and I see the
> menu bar, but I get warnings in the Pymol console that are related to a
> version conflict of python 3 used for compilation and python 2 used in some
> scripts, e.g. the ones shown below.
>
> What's the python version to use for compiling, and how do I best proceed?
>
> Thanks
> Markus
>
> This is part of the output shown in the Pymol console on startup:
>
> PyMOL>run /home/mheller/.pymol/show_bumps.py
> PyMOL>run /home/mheller/.pymol/pairwisedistances.py
> Traceback (most recent call last):
> File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 483, in run
>run_(path, ns_pymol, ns_pymol)
> File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 532, in
> run_file
>execfile(file,global_ns,local_ns)
> File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 526, in
> execfile
>co = compile(pi.file_read(filename), filename, 'exec')
> File "/home/mheller/.pymol/pairwisedistances.py", line 13
>print ""
> ^
> SyntaxError: Missing parentheses in call to 'print'. Did you mean print("")?
> PyMOL>run /home/mheller/.pymol/supercell.py
> PyMOL>run /home/mheller/.pymol/get_raw_distances.py
> PyMOL>run /home/mheller/.pymol/polarpairs.py
> Traceback (most recent call last):
> File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 483, in run
>run_(path, ns_pymol, ns_pymol)
> File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 532, in
> run_file
>execfile(file,global_ns,local_ns)
> File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 526, in
> execfile
>co = compile(pi.file_read(filename), filename, 'exec')
> File "/home/mheller/.pymol/polarpairs.py", line 39
>print 'Settings: cutoff=%.1fangstrom angle=%.1fdegree' % (cutoff, angle)
> ^
> SyntaxError: invalid syntax
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PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] command to append a log file?
Hi Michael,
Use mode="a" to append to the log file:
cmd.log_open('/tmp/log.pml', 'a')
Cheers,
Thomas
> On Mar 6, 2019, at 5:47 AM, Michael Morgan wrote:
>
> Dear all,
>
> I hope my log file can keep recording operations.
>
> I put “log_open” in the pymolrc.pml file. However, it seems it creates a new
> file. All operations from last time are wiped out.
>
> “Append…” from “File -> Log File” menu seems work. But how can I make it
> automatically for every time pymol is open? It seems there is no “log_append”
> command.
>
> Thanks.
>
> Michael
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Re: [PyMOL] About legal/copyright issue with developing PyMOL plugin
Hi William, You can use any version of PyMOL, the plugin API is the same in all of them (Open-Source, Incentive with edu/academic/commercial license). Your own code, if open-sourced, needs a GPL-compatible license. You're in the same situation as the person asking "can I release my SW under the MIT license in situation 3?" (answer: Yes) here: https://riverbankcomputing.com/pipermail/pyqt/2016-September/038129.html Only if you are going to sell your plugin, you need to purchase a commercial PyQt license. See https://riverbankcomputing.com/commercial/license-faq Hope that helps. Cheers, Thomas > On Mar 4, 2019, at 7:03 PM, William Tao wrote: > > Hi PyMOL community, > > I am planning to develop a PyMOL plugin based on PyMOL 2.x versions with > PyQt. > > However, I am not quite clear about the legal implications and copyright > issues if I would like to make my plugin open-source in future. > > First, PyMOL has incentive version and open-source version. I have an > educational license for incentive version and open-source version. If I am > going to describe my plugin in a scientific article or website, which version > of PyMOL version am I allowed to use? > > Second, the PyQt requires the code based on it must also be open-source > according to GPL. > > These two factors make me confused about the possibility of publishing a > plugin for PyMOL in future. > > If anybody has experience in this aspect, please feel free to advise. > > Many thanks. > > William -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] UnicodeDecodeError
Hi Seán, This issue is fixed in PyMOL 2.3.0, please download the new version from https://pymol.org/#download Cheers, Thomas > On Mar 2, 2019, at 8:45 PM, sean downey wrote: > > Hi, > > I'm having an issue with a UnicodeDecodeError. I have an academic licence for > the proprietary version of Pymol, however, when I go to install the licence > file, I get the below error message. > I'm very new to Pymol and I don't really have any coding experience (I'm from > a biology background). I'm just looking for a quick fix for this problem. Is > there some way to change the codec, which is what I see suggested online, but > I don't honestly understand them. > > Thanks in advance, > > Seán > > > PyMOL(TM) 2.2.3 - Incentive Product > Copyright (C) Schrodinger, LLC > > This Executable Build integrates and extends Open-Source PyMOL. > Detected OpenGL version 4.5. Shaders available. > Detected GLSL version 4.50. > OpenGL graphics engine: > GL_VENDOR: Intel > GL_RENDERER: Intel(R) HD Graphics 515 > GL_VERSION: 4.5.0 - Build 24.20.100.6286 > Setting: precomputed_lighting set to on. > Detected 4 CPU cores. Enabled multithreaded rendering. > > > Traceback (most recent call last): > File "C:\ProgramData\PyMOL\lib\site-packages\pmg_qt\lic_dialog.py", line > 38, in browse > licensing.install_license_file(fname) > File "C:\ProgramData\PyMOL\lib\site-packages\pymol\licensing.py", line 128, > in install_license_file > return install_license_key(open(filename, 'rb').read()) > File "C:\ProgramData\PyMOL\lib\site-packages\pymol\licensing.py", line 92, > in install_license_key > licfile = get_license_filename_user() > File "C:\ProgramData\PyMOL\lib\site-packages\pymol\licensing.py", line 75, > in get_license_filename_user > filename = os.path.expanduser(filename) > File "C:\ProgramData\PyMOL\lib\ntpath.py", line 311, in expanduser > return userhome + path[i:] > : 'utf8' codec can't decode byte 0xe1 in position 11: invalid continuation > byte -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Display running commands
Hi Pedro,
There is a command logging option:
From the menu: File > Log File > Open...
Or use the "log_open" command:
https://pymol.org/d/command:log_open
Decorating cmd.create like you suggested also works, but you need to update the
command language as well:
cmd.keyword['create'][0] = cmd.create
Cheers,
Thomas
> On Feb 22, 2019, at 12:27 AM, Pedro Lacerda wrote:
>
> Hi,
>
> I want to show executed commands when right before they run, so I can track
> my script execution.
>
> Something like the following for all the commands:
>
> orig_create = cmd.create
> def create(*args, **kwargs):
> print('create', repr(args), repr(kwargs))
> orig_create(*args, **kwargs)
> cmd.create = create
>
>
> I also want it to figure out what commands some GUI actions really do. Like
> those in presets and so on.
>
> There is some verbose option that does it?
>
> Thank you,
> Pedro Lacerda
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PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] How to catch PyMOL command exception within a Python script
Hi Thomas,
In general, the PyMOL API should raise pymol.CmdException if things go wrong.
But in case of cmd.pair_fit() this wasn't happening (see my fix that I pushed
few minutes ago:
https://github.com/schrodinger/pymol-open-source/commit/b26d91c40d20344fef511ea9d6bb664a93f1bb4a
)
cmd.select() correctly raises an exception, so if you want to make a script
more robust against selection failures, you could always create a named
selection first to check if it's valid.
tmpsele1 = cmd.get_unused_name('_sele1')
try:
cmd.select(tmpsele1, someexpression, 0)
except pymol.CmdException:
print('invalid selection')
finally:
cmd.delete(tmpsele1)
Cheers,
Thomas
> On Feb 22, 2019, at 12:11 PM, Thomas Evangelidis wrote:
>
> Hi Thomas,
>
> This is great! I can even include more atom types in the selection.
> Just for the record, is it possible to catch PyMOL exceptions like
> "Selector-Error" from within a Python script? Is there any general strategy
> to select which exception type to look for? In the past, I was catching
> exceptions from 'tmalign' with "except AssertionError:" which doesn't work
> for "Selector-Error".
>
> Best,
> Thomas
>
>
> --
> ==
> Dr Thomas Evangelidis
> Research Scientist
> IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
> of Sciences
> Prague, Czech Republic
> &
> CEITEC - Central European Institute of Technology
> Brno, Czech Republic
>
> email: teva...@gmail.com
> website: https://sites.google.com/site/thomasevangelidishomepage/
--
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PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] How to catch PyMOL command exception within a Python script
Hi Thomas,
Getting rid of the string length limitations would need some major refactoring.
There is currently no good workaround, other than avoiding such long selections.
In this particular case, the script could use cmd.select_list() instead of
concatenating the index list to a string:
cmd.select_list('sel1', obj1, [int(i) for i in id1], mode='index')
cmd.select_list('sel2', obj2, [int(i) for i in id2], mode='index')
cmd.pair_fit("sel1 and aln", "sel2 and aln")
cmd.delete('sel1')
cmd.delete('sel2')
Hope that helps.
Cheers,
Thomas
> On Feb 22, 2019, at 9:32 AM, Thomas Evangelidis wrote:
>
> Greetings,
>
> I am trying to run focus_alignment command
> (https://pymolwiki.org/index.php/Focus_alignment) from within a Python script
> with my own custom selection (I include CA+CB atoms instead of only CA as in
> the default). Sometimes the selection is very large and PyMOL cannot hand it:
>
> Selector-Error: Word too long. Truncated:
> Selector-Error:
> 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+115Selector-Error:
> Invalid selection name "730".
> poly and 4kz6A and aln and index
> 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+1158+1175+1178+1183+1421+1424+1428+1431+1647+1650+1655+1658+
> 730<--
> Selector-Error: Word too long. Truncated:
> Selector-Error:
> 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+121Selector-Error:
> Invalid selection name "868".
> poly and 2r9wA and aln and index
> 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+1212+1229+1232+1237+1491+1494+1498+1501+1747+1750+1755+1758+
> 868<--
> ExecutiveRMS-Error: No atoms selected.
> Selector-Error: Word too long. Truncated:
> Selector-Error:
> 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+115Selector-Error:
> Word too long. Truncated:
> Selector-Error:
> 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+121Selector-Error:
> Invalid selection name "730".
> ( ( poly and 4kz6A and aln and index
> 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+1158+1175+1178+1183+1421+1424+1428+1431+1647+1650+1655+1658+
> 730 ) in ( poly and 2r9wA and aln and index
> 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+1212+1229+1232+1237+1491+1494+1498+1501+1747+1750+1755+1758+
> 868 ) )<--
>
> Is there a way to ask PyMOL to accept longer selection strings?
> Alternatively, is it possible to catch this exception from within the script
> using "try: ... except :" statement?
>
> Thanks in advance.
> Thomas
>
> --
> ==
> Dr Thomas Evangelidis
> Research Scientist
> IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
> of Sciences
> Prague, Czech Republic
> &
> CEITEC - Central European Institute of Technology
> Brno, Czech Republic
>
> email: teva...@gmail.com
> website: https://sites.google.com/site/thomasevangelidishomepage/
--
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PyMOL Principal Developer
Schrödinger, Inc.
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[PyMOL] Making scripts/plugins Python 3 compatible
Hi all, If you have Python scripts or plugins which aren't Python 3 compatible yet, you might find this guide useful: https://pymolwiki.org/index.php/2to3 Cheers, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Problem with Pymol 2.3.0 with 'undefined symbol: MMTF_unpack_from_string'
Hi Heng-Keat, A "clean" build will probably fix this. It looks like you partially recompiled with --use-msgpackc=no? To do a clean build: Remove the "build" directory and try again. Cheers, Thomas > On Feb 14, 2019, at 8:00 PM, t...@em.uni-frankfurt.de wrote: > > Dear all, > > I installed the pymol on my machine with Ubuntu 18.04.1 LTS. When I launch > pymol and error appears: > > Traceback (most recent call last): > File > "/home/mauricetam/Documents/software/pymol-2.3.0//lib/python2.7/site-packages/pymol/__init__.py", > line 64, in >import pymol > File > "/home/mauricetam/Documents/software/pymol-2.3.0/lib/python2.7/site-packages/pymol/__init__.py", > line 580, in >import pymol._cmd > ImportError: > /home/mauricetam/Documents/software/pymol-2.3.0/lib/python2.7/site-packages/pymol/_cmd.so: > undefined symbol: MMTF_unpack_from_string > > Any idea what is going wrong? > > Thank you for your help. > > Best > Heng-Keat -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Problem with Open source Pymol 2.3.0 (missing external GUI)
Hi Heng-Keat, Getting CCTBX to work with PyMOL is quite a journey. Please read: https://pymolwiki.org/index.php/CCTBX#Open-Source_PyMOL Cheers, Thomas > On Feb 14, 2019, at 11:27 AM, t...@em.uni-frankfurt.de wrote: > > Dear all, > > After I reinstalled the pmw, it ran through and now it said 'no modules named > _tkinter' as shown below: > > Warning: GL_DRAW_BUFFER0=0 -> using GL_BACK > Detected OpenGL version 3.0. Shaders available. > Geometry shaders not available > Detected GLSL version 1.30. > OpenGL graphics engine: > GL_VENDOR: Intel Open Source Technology Center > GL_RENDERER: Mesa DRI Intel(R) Haswell Mobile > GL_VERSION: 3.0 Mesa 18.2.8 > Traceback (most recent call last): > File > "/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/__init__.py", > line 27, in run >from .PMGApp import PMGApp > File > "/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/PMGApp.py", > line 22, in >import Pmw > File > "/home/mauricetam/software/cctbx/cctbx_plus_build/base/lib/python2.7/site-packages/Pmw.py", > line 8, in > Detected 4 CPU cores. Enabled multithreaded rendering. >import Tkinter as tkinter > File > "/home/mauricetam/software/cctbx/cctbx_plus_build/base/lib/python2.7/lib-tk/Tkinter.py", > line 39, in >import _tkinter # If this fails your Python may not be configured for Tk > ImportError: No module named _tkinter > > Thanks for the help. > > Best > HK > > Quoting t...@em.uni-frankfurt.de: > >> To whom it may concern, >> >> I installed the pymol on my machine with Ubuntu 18.04.1 LTS >> >> I have a problem with 'Qt not available, using GLUT/Tk interface' when >> install pymol with: >> >> python setup.py install --prefix=/home/mauricetam/software/pymol-2.3.0/ >> --use-msgpackc=no >> >> After I installed it with: >> >> python setup.py install --prefix=/home/mauricetam/software/pymol-2.3.0/ >> --use-msgpackc=no --glut >> >> Now, the problem is I don't see the external GUI and there is an error as >> shown below: >> >> Warning: GL_DRAW_BUFFER0=0 -> using GL_BACK >> Detected OpenGL version 3.0. Shaders available. >> Geometry shaders not available >> Detected GLSL version 1.30. >> OpenGL graphics engine: >> GL_VENDOR: Intel Open Source Technology Center >> GL_RENDERER: Mesa DRI Intel(R) Haswell Mobile >> GL_VERSION: 3.0 Mesa 18.2.2 >> Traceback (most recent call last): >> File >> "/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/__init__.py", >> line 27, in run >> from .PMGApp import PMGApp >> File >> "/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/PMGApp.py", >> line 22, in >>import Pmw >> ImportError: No module named Pmw >> Detected 4 CPU cores. Enabled multithreaded rendering. >> >> Any idea what is going wrong on my machine? >> >> Thank you for the help. >> >> Best >> Heng-Keat -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] PyMOL 2.3.0/CentOS-7: Qt not available, using GLUT/Tk interface ?
Don't split "build" and "install" (or pass --glut to both calls): python setup.py --glut build install --prefix=... Cheers, Thomas > On Feb 13, 2019, at 5:44 PM, Tru Huynh wrote: > > On Wed, Feb 13, 2019 at 05:21:09PM +0100, Tru Huynh wrote: > ... >> >> Trying to install PyQt4_gpl_x11-4.12. on CentOS-7 is another issue :) >> ... >> > > I went the easy route and pip3 install PyQt5-sip PyQt5, > and rebuild ... > > the Python-3.5.2 version now works fine, but not the Python-3.6.6 > which still fails! > > [tru@sillage ~]$ module add pymol/release/2.3.0-Python-3.5.2 > [tru@sillage ~]$ pymol > PyMOL(TM) Molecular Graphics System, Version 2.3.0. > Copyright (c) Schrodinger, LLC. > All Rights Reserved. > >Created by Warren L. DeLano, Ph.D. > >PyMOL is user-supported open-source software. Although some versions >are freely available, PyMOL is not in the public domain. > >If PyMOL is helpful in your work or study, then please volunteer >support for our ongoing efforts to create open and affordable scientific >software by purchasing a PyMOL Maintenance and/or Support subscription. > >More information can be found at "http://www.pymol.org;. > >Enter "help" for a list of commands. >Enter "help " for information on a specific command. > > Hit ESC anytime to toggle between text and graphics. > > Detected OpenGL version 4.6. Shaders available. > Detected GLSL version 4.60. > OpenGL graphics engine: > GL_VENDOR: NVIDIA Corporation > GL_RENDERER: GeForce GT 1030/PCIe/SSE2 > GL_VERSION: 4.6.0 NVIDIA 410.93 > Detected 6 CPU cores. Enabled multithreaded rendering. > > > [tru@sillage ~]$ module add pymol/release/2.3.0-Python-3.6.6 > [tru@sillage ~]$ pymol > Traceback (most recent call last): > File > "/c7/shared/pymol/release/2.3.0-Python-3.6.6/lib/python3.6/site-packages/pymol/__init__.py", > line 64, in >import pymol > File > "/c7/shared/pymol/release/2.3.0-Python-3.6.6/lib/python3.6/site-packages/pymol/__init__.py", > line 580, in >import pymol._cmd > ImportError: > /c7/shared/pymol/release/2.3.0-Python-3.6.6/lib/python3.6/site-packages/pymol/_cmd.cpython-36m-x86_64-linux-gnu.so: > undefined symbol: glutSwapBuffers > > Cheers > > Tru > -- > Dr Tru Huynh | mailto:t...@pasteur.fr | tel +33 1 45 68 87 37 > https://research.pasteur.fr/en/team/structural-bioinformatics/ > Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] PyMOL 2.3.0/CentOS-7: Qt not available, using GLUT/Tk interface ?
Hi Tru,
There is one thing we changed: The legacy GLUT support is not enabled by
default anymore. If that's the issue here, you have two options:
1) install PyQt (recommended)
2) or compile PyMOL with --glut
Cheers,
Thomas
> On Feb 13, 2019, at 3:44 PM, Tru Huynh wrote:
>
> Hi,
>
> I have some issue with the latest released version (2.3.0) and
> manually build Python 2.7.15, 3.5.2 and 3.6.6 on our CentOS-7 machines.
>
> [tru@sillage ~]$ module add pymol/release/2.3.0-Python-3.6.6
> [tru@sillage ~]$ module li
> Currently Loaded Modulefiles:
> 1) Python/3.6.6 3) pymol/release/2.3.0-Python-3.6.6
> 2) msgpack/2.1.5
> [tru@sillage ~]$ pymol
> Qt not available, using GLUT/Tk interface
> [tru@sillage ~]$ echo $?
> 0
>
> The different Python versions are isolated through the environment
> modules and the issue has only appeared with 2.3.0 and all the python
> versions except the version using the system provided python version.
>
> these fails:
> pymol/release/2.3.0-Python-2.7.15 pymol/release/2.3.0-Python-3.6.6
> pymol/release/2.3.0-Python-3.5.2
>
> this works:
> pymol/release/2.3.0-Python-centos7
>
> [tru@sillage ~]$ module add pymol/release/2.3.0-Python-centos7
> [tru@sillage ~]$ pymol
> PyMOL(TM) Molecular Graphics System, Version 2.3.0.
> Copyright (c) Schrodinger, LLC.
> All Rights Reserved.
>
>Created by Warren L. DeLano, Ph.D.
>
>PyMOL is user-supported open-source software. Although some versions
>are freely available, PyMOL is not in the public domain.
>
>If PyMOL is helpful in your work or study, then please volunteer
>support for our ongoing efforts to create open and affordable scientific
>software by purchasing a PyMOL Maintenance and/or Support subscription.
>
>More information can be found at "http://www.pymol.org;.
>
>Enter "help" for a list of commands.
>Enter "help " for information on a specific command.
>
> Hit ESC anytime to toggle between text and graphics.
>
> Detected OpenGL version 4.6. Shaders available.
> Detected GLSL version 4.60.
> OpenGL graphics engine:
> GL_VENDOR: NVIDIA Corporation
> GL_RENDERER: GeForce GT 1030/PCIe/SSE2
> GL_VERSION: 4.6.0 NVIDIA 410.93
> Detected 6 CPU cores. Enabled multithreaded rendering.
>
> and all the previous versions of pymol are perfectly fine...
>
> pymol/release/1.8.7-Python-2.7.12 pymol/release/2.1.0-Python-3.6.6
> pymol/release/1.8.7-Python-2.7.15 pymol/release/2.1.0-Python-centos7
> pymol/release/1.8.7-Python-3.5.2 pymol/release/2.2.0-Python-2.7.15
> pymol/release/1.8.7-Python-3.6.3 pymol/release/2.2.0-Python-3.5.2
> pymol/release/1.8.7-Python-3.6.6 pymol/release/2.2.0-Python-3.6.6
> pymol/release/1.8.7-Python-centos7 pymol/release/2.2.0-Python-centos7
> pymol/release/2.1.0-Python-2.7.12
> pymol/release/2.1.0-Python-2.7.15
> pymol/release/2.1.0-Python-3.5.2
> pymol/release/2.1.0-Python-3.6.3
>
> Any idea where I can start looking at?
>
> python3 build process details:
> module purge && module add Python/${PYTHON_V}
> python3 setup.py build
> python3 setup.py install --prefix=/
>
> for python2, I just resplaced python3 by python in the lines above.
>
> Any idea what could be causing this behaviour?
>
> Cheers
>
> Tru
>
> --
> Dr Tru Huynh | mailto:t...@pasteur.fr | tel +33 1 45 68 87 37
> https://research.pasteur.fr/en/team/structural-bioinformatics/
> Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] dark structure
Hi Cyprian and Sunting, Better solutions: - put "set precomputed_lighting" in your pymolrc - or just upgrade to PyMOL 2.3 (has precomputed_lighting on by default) See also: https://github.com/schrodinger/pymol-open-source/issues/15 https://sourceforge.net/p/pymol/mailman/message/36455017/ Cheers, Thomas > On Feb 12, 2019, at 9:54 AM, Cyprian Cukier > wrote: > > Hi Sunting, > > Just need to turn off shaders -> ‘set use_shaders, off’. Do not know how to > switch off the default on. > > Best, > Cyprian > > From: sunting > Sent: Monday, February 11, 2019 7:20 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] dark structure > > Hi, > > Is there any one who knows why the structure look so dark in pymol (see > attached)? I have tried re-install the software but doesn’t work. > Thanks > > Sunting -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] NameError: name 'util' is not defined
Hi Soren, Very interesting script, thanks for sharing! It looks like pymol2.PyMOL() doesn't work with the util module. It would need to wrap all util functions and pass the "_self" argument with every function call, just like pymol2.cmd2.Cmd does. It works for me if I use pymol2.SingletonPyMOL() instead. That's what we use with the PyQt interface. This "singleton" version uses the global pymol.cmd and pymol.util modules as the API. You can only have one instance of the singleton. If you want multiple instances with pymol2.PyMOL(), you'll need to do the wrapping. For example like this: class SelfProxy: def __init__(self, proxied, _self): self._self = _self self.proxied = proxied def __getattr__(self, key): v = getattr(self.proxied, key) def wrapper(*a, **k): k['_self'] = self._self return v(*a, **k) return wrapper # and after "self._pymol.start()": import pymol.util self._pymol.util = SelfProxy(pymol.util, self._pymol.cmd) I've tested this and it works with the color menu. Cheers, Thomas > On Feb 12, 2019, at 8:26 AM, Søren Nielsen > wrote: > > > Hi, > > I am using pymol with a wxpython interface and everything seems to work, > except when I try to change the color of an object using the internal gui, I > get a NameError: name 'util' is not defined error... can you see what is the > problem here? > > Best, > Soren -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Reference point shifts when display screen is changed
Hi Gyan, I think this issue has been fixed (in PyMOL 2.2.2). Can you please upgrade to the latest version? Cheers, Thomas > On Feb 9, 2019, at 11:35 PM, Gyanendra Kumar wrote: > > Hi there, > > I am facing this problem of the reference point moving to a corner of the > display window when I unplug the external monitor and the display moves to > the MacBook screen, or when I connect another display e.g. a TV screen. > Reset command or re-centering on an atom does not fix the problem and I end > up closing pymol and having to restart the program. > > Has anybody faced this problem and found a solution? > > I am running pymol on MacOS Sierra Version 10.12.6. MacBook Pro 2017. > > Thanks, > Gyan -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] PyMOL 2.3 released
Greetings, We are happy to announce the release of PyMOL 2.3. Download ready-to-use bundles from https://pymol.org/ or update your installation with "conda install -c schrodinger pymol". New features include: - Atom-level cartoon transparency - Fast MMTF export - Sequence viewer gaps display This is the first time that we provide PyMOL bundles with Python 3. If you use custom or third-party Python 2 scripts, they might stop working until you convert them (e.g. using a converter tool like 2to3). Find the complete release notes at: https://pymol.org/d/media:new23 We welcome any feedback and bug reports. Cheers, - The PyMOL Team at Schrödinger -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] pymol movie help
Hi Clarisa, You can pass "width" and "height" arguments to the "mpng" command, like this: mpng fileprefix, width=720, height=480 See also https://pymolwiki.org/index.php/mpng Hope that helps. Cheers, Thomas > On Jan 29, 2019, at 5:47 PM, Clarisa Alvarez > wrote: > > Could anyone help me how i could change resolution of my png images make to > perform a video, that changes resolution when i open with movie maer. > Thanks in advance. > Clarisa. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Pandas module in Pymol
Hi Andreas, Looks like a known pandas issue, see: https://github.com/pandas-dev/pandas/issues/16536 According to that issue, upgrading pandas could help. Cheers, Thomas > On Nov 21, 2018, at 5:01 PM, Andreas Tosstorff > wrote: > > Hi all, > > I am trying to use pandas in a script in pymol. > > These are the first lines of the script: > > from pymol import cmd, stored, math > import pandas as pd > > > I get the following error message when running the script: > > 'module 'pandas' has no attribute 'plotting' > > > File > "/home/andt88/anaconda3/lib/python3.6/site-packages/pmg_qt/pymol_qt_gui.py", > line 863, in file_run > self.cmd.run(fname) > File "/home/andt88/anaconda3/lib/python3.6/site-packages/pymol/parsing.py", > line 484, in run > run_(path, ns_pymol, ns_pymol) > File "/home/andt88/anaconda3/lib/python3.6/site-packages/pymol/parsing.py", > line 533, in run_file > execfile(file,global_ns,local_ns) > File "/home/andt88/anaconda3/lib/python3.6/site-packages/pymol/parsing.py", > line 528, in execfile > exec(co, global_ns, local_ns) > File > "/home/andt88/Dropbox/PhD/IFN/Excipient_Screen/IFN_ES_2/NMR/NMR-Data/andreas/nmr/PPI-30 > TEMPOL 250718/loadBfacts.py", line 2, in > import pandas as pd > File > "/home/andt88/anaconda3/lib/python3.6/site-packages/pandas/__init__.py", line > 51, in > plot_params = pandas.plotting._style._Options(deprecated=True) > > I'd really appreciate your help with this! > Kind regards, > Andreas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Linux pymol issues
Hi Evgeny, Is any of the QT_*_SCALE_FACTOR variables set in your environment? Does it help if you set for example QT_SCALE_FACTOR=1? In a bash terminal that would be: bash> export QT_SCALE_FACTOR=1 bash> pymol See also: http://doc.qt.io/qt-5/highdpi.html#high-dpi-support-in-qt Cheers, Thomas > On Nov 27, 2018, at 7:50 PM, Evgeny Osipov wrote: > > Dear Pymol community, > I stumbled upon strange GUI issue with Pymol 2 and Maestro on my linux > laptop ( Xubuntu 18.04 HP Probook 440 G5): it looks like GUI elements have > different scale so it looks rather strange and very inconvenient for work. > Problem appears only at 1920x1080 resolution and everything is fine at lower > resolution. I have uploaded screenshots from pymol 2 at 1920x1080 (highDPI) > and 1680x1050 (lowDPI) here: > https://imgur.com/a/Tlp79Kq > > Do anyone have a clue how to fix this? -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] Announcing 2018/2019 PyMOL Open Source Fellows
Greetings PyMOL users, Please join me in congratulating Mateusz Bieniek, Paul Smith, and Blaine Mooers, who have been awarded the Warren L. DeLano Memorial PyMOL Open Source Fellowship for 2018-2019. Mateusz and Paul will be working as a team on tools for molecular dynamics trajectory handling and analysis. They are graduate students at King’s College in London and use molecular dynamics simulations in their own research. Blaine is a crystallographer and long-time PyMOL user who has introduced hundreds of students to molecular visualization with PyMOL. He will be working on a snippet library of PyMOL scripts with a searchable thumbnail gallery frontend for efficient discoverability of relevant snippets. The Warren L. DeLano Memorial PyMOL Open-Source Fellowship is awarded by Schrӧdinger to supplement the income of an outstanding member of the PyMOL open-source community so that s/he can continue to develop free resources to help scientific progress and the community as a whole. You can read more about the PyMOL Open Source Fellowship Program and the fellows at https://pymol.org/fellowship Cheers, The PyMOL Team at Schrödinger -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] x-forwarding doesn't display bottom panel but displays menu bar and shell output
Hi Sophia, Regarding X forwarding on macOS: It turns out iglx is disabled by default since XQuartz 2.7.10. After enabling it, PyMOL works. I've put this information on the PyMOLWiki: https://pymolwiki.org/index.php/Remote_Desktop Cheers, Thomas > On Nov 19, 2018, at 1:36 PM, Thomas Holder > wrote: > > Hi Sophia, > > This works on my old Mac with macOS 10.9 and XQuartz 2.7.7. However, on a > newer Mac with macOS 10.12 and XQuartz 2.7.11 ssh forwarding of OpenGL apps > doesn't work at all for me. Not even the "glxgears" test program works. > > The good news is: VirtualGL works really well, using macOS 10.12 as the > client and a Linux workstation as the server. > > mac # /opt/VirtualGL/bin/vglconnect linux > linux # vglrun pymol > > See also: > https://virtualgl.org/vgldoc/2_2_1/#hd004003 > > Cheers, > Thomas > >> On Nov 17, 2018, at 4:12 AM, Tan, Sophia wrote: >> >> Hi developers, >> >> I'm using PyMOL (2.2.3) on a Linux remote workstation, and am using X >> forwarding on my Mac by "ssh -Y etc." >> The X forwarding works on other applications, but for PyMOL, only the top >> menu bar with the command line shell output is displayed; the bottom display >> is all white, no matter what I try to load. >> >> How can I get the bottom display to work ? >> >> Thank you, >> Sophia -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] x-forwarding doesn't display bottom panel but displays menu bar and shell output
Hi Sophia, This works on my old Mac with macOS 10.9 and XQuartz 2.7.7. However, on a newer Mac with macOS 10.12 and XQuartz 2.7.11 ssh forwarding of OpenGL apps doesn't work at all for me. Not even the "glxgears" test program works. The good news is: VirtualGL works really well, using macOS 10.12 as the client and a Linux workstation as the server. mac # /opt/VirtualGL/bin/vglconnect linux linux # vglrun pymol See also: https://virtualgl.org/vgldoc/2_2_1/#hd004003 Cheers, Thomas > On Nov 17, 2018, at 4:12 AM, Tan, Sophia wrote: > > Hi developers, > > I'm using PyMOL (2.2.3) on a Linux remote workstation, and am using X > forwarding on my Mac by "ssh -Y etc." > The X forwarding works on other applications, but for PyMOL, only the top > menu bar with the command line shell output is displayed; the bottom display > is all white, no matter what I try to load. > > How can I get the bottom display to work ? > > Thank you, > Sophia > -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] issue with label command as in: label *, name; color red
Hi Xiang-Jun,
Some commands accept the semicolon in their argument list and thus cannot be
followed by other commands on the same line. The "label" command is one of them.
See this table and the last column with "parsing.LITERAL1":
https://github.com/schrodinger/pymol-open-source/blob/master/modules/pymol/keywords.py#L140
You could work around this by using Python syntax:
cmd.label("*", "name");cmd.color("red")
Cheers,
Thomas
> On Nov 15, 2018, at 12:23 AM, Xiang-Jun Lu <3dna...@gmail.com> wrote:
>
> I am surprised by the PyMOL error message with the following commands:
>
> # this is fine
> color red; label *, name
>
> # reversing the order causes problems
> label *, name; color red
>
> =
> PyMOL>label *, name; color red
> File "", line 1
> name; color red
> ^
> SyntaxError: invalid syntax
> Label-Error: failed to compile expression
> Label: labelled 0 atoms.
> =
>
> Replacing 'name' with 'resi' or 'resn' etc has the same result.
>
> Issuing each command separately works as expected. The error message shows up
> only if "label *, name" is followed by another command, on the same line.
>
> I am using "Version 1.8.7.0 Open-Source" on macOS.
>
> Any ideas?
>
> Thanks,
>
> Xiang-Jun
>
> --
> Xiang-Jun Lu (Ph.D.)
> Email: xiang...@x3dna.org
> Web: http://x3dna.org/
> Forum: http://forum.x3dna.org/
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] PyMol display problem on Windows 10
Hi Yufeng, This is a problem with a recent graphics driver update from Intel on Windows 10. So far it appears that the build series "4.5.0 - Build 24.20.100." is affected. Can you please tell us what PyMOL reports as "OpenGL graphics engine" (3 lines printed in log window on startup)? Luckily, there is a simple workaround, PyMOL has two different implementations of the lighting model and only one is affected. Type this into the PyMOL command line or put it in your pymolrc file: set precomputed_lighting Cheers, Thomas On Tue, Oct 30, 2018 at 11:48 PM Yufeng Tong wrote: > > Hi there, > > I installed PyMol on a new laptop (Windows 10, within Anaconda3) and > run into a display problem, which does not exist on a Windows 7 > laptop. > > Basically, the displayed molecules does not have the 3D visual effect > and the colors are very dark. Only after I apply "ray", it shows > normal color but then of course I cannot rotate the molecules without > loosing the normal view. The same problem occurs to PyMol version 2.3 > or 2.2 from the Schrödinger channel or the Gohlke's unofficial > packages. Tried to change color space, light position, and all options > under Display menu and none seems to change the results. Installed > PyQt and the problem persists. > > I tried the same installation process on an older Windows 7 laptop and > all looks normal. Attached are two screen copy of the display before > and after applying "ray", they can also be viewed from > https://1drv.ms/f/s!Ao4PGr4qLLsZjQiafUTIaUFTyxNn > > I guess it is a problem of the GUI. Any hints are greatly appreciated. > > Yufeng > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Pymol and Ray Tracing
Hi Steve and Shintaro, Shintaro is right, PyMOL's ray tracing is CPU only. It runs parallel on multiple CPU cores. Our graphics development over the last years was focused on getting the real-time OpenGL rendering (which uses the GPU heavily) as close to the ray traced images as possible. Lighting, antialiasing, and pixel-perfect sticks and spheres should be identical with "draw" and "ray". There are still some gaps, the ray tracer has shadows, better multi-layer transparency, and outline modes (https://pymolwiki.org/index.php/Ray#Modes ) that we don't have in real-time yet. For movies, I would certainly consider "draw" rendering a good option, unless you need shadows or better transparency. # write out PNG images mpng prefixdraw, mode=1, width=1280, height=720 mpng prefixray, mode=2, width=1280, height=720 # write out MPEG 4 (requires ffmpeg) movie.produce draw.mp4, mode=draw, width=1280, height=720 movie.produce ray.mp4, mode=ray, width=1280, height=720 Cheers, Thomas On Mon, Oct 29, 2018 at 1:48 PM Shintaro Aibara wrote: > > I am under the impression that ray tracing is an entirely CPU process in > pymol. GPU accelerated ray tracing is not implemented in pymol, beyond the > command "draw" which is not the same anyway. The software developers need to > decide whether ray tracing in real-time is widely enough adopted hardware and > software to decide to implement code that will use these (think about AMD > card users, for example). > > Currently you are probably better off with upgrading the CPU to something > like the 2990WX > > Best wishes > Shintaro > > > > On Mon, Oct 29, 2018 at 2:08 AM Stephen Gravina > wrote: >> >> Just installed a NVIDIA RTX 2080 for the Ray Tracing capabilities in PyMol. >> Just tested a GTX 1080 and the RTX 2080 and no difference. I did install the >> new Win10 patch and drivers. Update Bios. >> >> The GTX 1080 takes an hour to render the 30 frames for a second of a >> ray-traced movie of my protein a C class GPCR. I need 30 seconds, thus 30 >> hours. >> .Only to find out a messed it up! >> >> Any suggestions? >> >> Thanks >> >> Steve Gravina, Ph.D. >> ___ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > > > -- > Yours Sincerely, > Shintaro Aibara > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] distance
Hi Joseph, Thanks for the example, I can reproduce it! Not sure if this should be considered a bug, or just a misleading user interface. "involving side chains" really means "side chains within selection". There are none if you only select the ligand. If I instead click on "to other atoms in object" I'll get the expected result. You might also find one of these command line options useful: distance polar1, (resn GSH), not (resn GSH), mode=2 distance polar2, (resn GSH), (sidechain), mode=2 distance polar3, (resn GSH), not (solvent), mode=2 Cheers, Thomas > On Oct 26, 2018, at 2:34 PM, Joseph Brock wrote: > > Hi again Jarrett, > > I have built the latest version from git (PyMOL 2.3.0a0 Open-Source) on my > system. > > The behaviour is still there, but I realise that this it is now only when the > selection is a ligand. For instance trying to find polar contacts between a > ligand and sourrounding side chains. If I make a selection involving both the > ligand and side chains of interest first however, it works fine. > > It is an easy workaround, but i would be curious to know if you can replicate > it on your system. For instance if you fetch pdb id: 1EEM and make a > selection from resname GSH, then try to find polar contacts involving side > chains from the action menu, you should see what I mean. > > Cheers, > Joseph. > > > Joseph S. Brock | PhD > Researcher > Drew Lab > Department of Biochemistry and Biophysics > Stockholm University > From: Joseph Brock > Sent: Friday, 26 October 2018 8:57:44 AM > To: Jarrett Johnson > Cc: Pymol User list > Subject: Re: [PyMOL] distance > > Thanks Jarrett! I will try that! > > Cheers, > Joseph. > > > Joseph S. Brock | PhD > Researcher > Drew Lab > Department of Biochemistry and Biophysics > Stockholm University > From: Jarrett Johnson > Sent: Friday, 26 October 2018 12:23:46 AM > To: Joseph Brock > Cc: Pymol User list > Subject: Re: [PyMOL] distance > > Built from source (github repo). > > On Thu, Oct 25, 2018 at 5:56 PM Joseph Brock wrote: > Hi Jarret, > > Thanks for the reply! > > Unfortunately so ;( > > Did you build from source or install via apt-get? > https://pymolwiki.org/index.php/Linux_Install > > Cheers, > Joseph. > > > Joseph S. Brock | PhD > Researcher > Drew Lab > Department of Biochemistry and Biophysics > Stockholm University > From: Jarrett Johnson > Sent: Thursday, 25 October 2018 11:34:28 PM > To: Joseph Brock > Cc: Pymol User list > Subject: Re: [PyMOL] distance > > Hi Joseph, > > I'm not able to replicate that on my end using open-source PyMOL 2.2 on > Ubuntu 16.04. Does this behavior also occur for molecules fetched straight > from the PDB? > > Jarrett J. > > On Thu, Oct 25, 2018 at 4:44 PM Joseph Brock wrote: > Hi pymol users, > > I've observed a weird behaviour with the open source pymol (v 1.7.2.1-2.2 > running on ubuntu 16.04). > > When I try to create some distance objects either via the command line of the > actions menu, an object is created but no dashed lines appear. When I "zoom" > this object it is very far in space from the atoms I selected to make the > distances between, and there is still nothing I can do to make the dashed > lines appear. > > If anyone can let me know what I'm doing wrong I would appreciate it! > > Cheers, > Joseph. > > > Joseph S. Brock | PhD > Researcher > Drew Lab > Department of Biochemistry and Biophysics > Stockholm University > > -- > Jarrett Johnson > PyMOL Developer > Schrödinger, Inc. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] One window instead external and internal windows
If you don't want GLUT to be linked in as a fallback, compile with --no-glut (See https://pymolwiki.org/index.php/Linux_Install#Compile_and_install ) Tcl/Tk could be loaded if there is an activated plugin which imports it. PyMOL does some trickery to provide the event loop for Tkinter from the PyQt thread to support old plugins. Cheers, Thomas > On Oct 16, 2018, at 6:59 PM, David Mathog wrote: > > On 16-Oct-2018 00:07, Thomas Holder wrote: >>> On Oct 15, 2018, at 9:38 PM, David Mathog wrote: >>> There must be something about Qt that is a significant improvement over >>> Tk/Tcl - where/what is that? >> It's not only Tk/Tcl, it's also GLUT which got replaced. > > GLUT still seems to be there though, and the link libraries are loaded to > some extent even when Qt starts. > > On Windows 7 ntldd shows _cmd.pyd linked to libfreeglut.dll. > On linux (ubuntu 16.04 LTS) ldd shows _cmd.so linked to libglut.so.3. > > Start the linux pymol, it finds and uses Qt, then: > > lsof | grep glut > python3010root mem REG8,5 236564 > 1978217 /usr/lib/i386-linux-gnu/libglut.so.3.9.0 > QXcbEvent 3010 3012 root mem REG8,5 236564 > 1978217 /usr/lib/i386-linux-gnu/libglut.so.3.9.0 > > lsof also shows > > python3010root mem REG8,5 1475144 > 1975104 /usr/lib/i386-linux-gnu/libtk8.6.so > QXcbEvent 3010 3012 root mem REG8,5 1475144 > 1975104 /usr/lib/i386-linux-gnu/libtk8.6.so > > and it is clearly using Qt, so perhaps some of the libraries lsof/ldd show > are linked but are not called if Qt is used. > >> So on the >> pure "bug-fix list", we have: >> - HiDPI support (we've seen unusable graphics on Intel/Windows) >> - viewport size issues with multiple screens on Windows >> On top of that, we get: >> - trackpad support (pinch zoom) >> - file open with drag-n-drop > > Which of those fixes, if any, require Qt? > > Thanks, > > David Mathog > mat...@caltech.edu > Manager, Sequence Analysis Facility, Biology Division, Caltech -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] One window instead external and internal windows
Hi Itamar, > On Oct 16, 2018, at 7:44 AM, Itamar Kass wrote: > > I have used the one from the ubuntu repositories. Is it preferably to > manually compile it? Preferable is to use Schrödinger-provided bundles from https://pymol.org/ ;-) If the Ubuntu-provided bundle isn't working as you expect, you should file a bug report with Ubuntu. Cheers, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] One window instead external and internal windows
> On Oct 15, 2018, at 9:38 PM, David Mathog wrote: > > There must be something about Qt that is a significant improvement over > Tk/Tcl - where/what is that? It's not only Tk/Tcl, it's also GLUT which got replaced. So on the pure "bug-fix list", we have: - HiDPI support (we've seen unusable graphics on Intel/Windows) - viewport size issues with multiple screens on Windows On top of that, we get: - trackpad support (pinch zoom) - file open with drag-n-drop Cheers, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] One window instead external and internal windows
Hi Itamar, Have you compiled PyMOL yourself? If yes, have you installed PyQt5? See https://pymolwiki.org/index.php/Linux_Install#Requirements Cheers, Thomas > On Oct 10, 2018, at 9:11 AM, Itamar Kass wrote: > > Hi, > > I am using Pymol 2.1.0 on Ubuntu 18.04. When run, it opens two windows - > unlike Pymol on macos. > > Does anyone knows how to make it run in one window? > > Thanks, > > Itamar -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] change surface charge color
Hi Abhik, Assuming you're talking about a ramp-colored surface. You can update the ramp from the "C" color menu (e.g.: C > grayscale), or from the command line: PyMOL> ramp_update yourramp, color=grayscale See also: https://pymolwiki.org/index.php/Ramp_New Cheers, Thomas > On Oct 13, 2018, at 1:58 PM, Abhik Ghosh Moulick > wrote: > > I have generated protein contact potential image using pymol. Where red > color is showing color of negative charge and blue is showing color for > positive charge. But want to change both color to black and grey. How it > can be done. Please help. > Thanking you > Regards > Abhik -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] starting pymol2 withTclTk() problem
Hi Benjamin, You found some ancient piece of API and I'm not sure if it ever was functional. Since the Tcl/Tk GUI is deprecated, we'll probably just remove that broken startWithTclTk method. The pymol2 module is a low level interface and doesn't provide a GUI out of the box. It's also little used (and little tested). What is your goal? Writing a PyMOL plugin or extension script? Or writing your own application on top of a low level PyMOL API? For plugins and extensions, just use the "pymol.cmd" API (check out https://github.com/Pymol-Scripts/Pymol-script-repo for a collection of extensions). Cheers, Thomas > On Oct 15, 2018, at 12:57 PM, Benjamin Schroeder wrote: > > Hej everybody, > I would like to start to write an own PyMol modul. > Therefore I thougth it would be interesting to use the pymol2 package. > But here I encounter a problem starting the GUI. > Can you spot what is missing here? > > my code: > import pymol2 > p1 = pymol2.PyMOL() > p1.startWithTclTk() > > Error: > Traceback (most recent call last): > File "/py", line 8, in > p1.startWithTclTk() > File "/.../anaconda3/lib/python3.6/site- > packages/pymol2/__init__.py", line 145, in startWithTclTk > sys.modules[gui].__init__(self,poll,skin) > TypeError: module.__init__() takes at most 2 arguments (3 > given) > > > > All the best, > Benjamin > > P.s.: Hope I'm correct here on this list. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to unsubscribe
If you need to be unsubscribed from this list, please email me directly and I can do it for you. Or, you can visit this page and unsubscribe yourself: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe Thanks, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] PyMOL 2.2.0 Crashing
Hi Ryan, This problem will most likely be solved if you update your graphics driver. As far as I can tell, your driver version is 5 years old, back then Intel drivers have been quite problematic. You can download the latest driver update here: https://downloadcenter.intel.com/download/27441/Graphics-Intel-Graphics-Driver-for-Windows-7-8-1-15-36-?product=81496 Cheers, Thomas > On Sep 14, 2018, at 4:57 PM, Kung, Ryan wrote: > > Hello all, > > I installed Pymol 2.2.0 for Windows 7 yesterday and I have been running into > some problems. Specifically, when I try to open almost any files it almost > always crashes. Those files that it does open crash as soon as I select any > atoms. On startup my PyMOL prints: > > PyMOL(TM) 2.2.0 - Incentive Product > Copyright (C) Schrodinger, LLC > > This Executable Build integrates and extends Open-Source PyMOL. > Detected OpenGL version 4.0. Shaders available. > GLERROR 0x0500: CShaderPrg::reload begin > Geometry shaders not available > Detected GLSL version 4.0. > OpenGL graphics engine: > GL_VENDOR: Intel > GL_RENDERER: Intel(R) HD Graphics 4600 > GL_VERSION: 4.0.0 - Build 9.18.10.3220 > License Expiry date: 26-jan-2021 > Detected 8 CPU cores. Enabled multithreaded rendering. > > To be clear, when I say crashes it has a popup window that says "pythonw.exe > has stopped working". I was hoping that someone else had experienced similar > problems and had a solution. I have tried uninstalling and reinstalling from > both exe installer and zip archive. Neither have fixed the problem. Thanks > for your help. > > Ryan Kung -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] CentOS 7 PyMOL install
Hi Puneet, Incentive PyMOL installation instructions: https://pymol.org/support#installation Open-Source PyMOL installation instructions: https://pymolwiki.org/index.php/Linux_Install Cheers, Thomas > On Sep 14, 2018, at 7:08 AM, puneet garg wrote: > > Hi, > Can anyone send me instructions on how to install PyMOL on CentOS 7 > Thanks > -- > Puneet -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Difference between backbone and heavy atom RMSD and how to calculate them in PYMOL
Hi Santrupti,
In Chemoinformatics "heavy atoms" are all non-hydrogen atoms. In
crystallography, "heavy atoms" could mean the atoms used for experimental
phasing, like selenium.
I hope these examples answer your questions:
# non-hydrogen RMSD
align prot1 & not hydro, prot2 & not hydro, cycles=0
# SE atom RMSD
align prot1 & elem SE, prot2 & elem SE, cycles=0
# backbone RMSD
align prot1 & name N+C+CA+O, prot2 & name N+C+CA+O, cycles=0
# pairwise RMSD for a lot of structures, using Python API
python
import itertools
models = cmd.get_object_list()
for m1, m2 in itertools.combinations(models, 2):
s1 = m1 + " & name N+C+CA+O"
s2 = m2 + " & name N+C+CA+O"
a = cmd.align(s1, s2, cycles=0)
print("Backbone RMSD for {} and {}: {}".format(m1, m2, a[0]))
python end
Please also read https://pymolwiki.org/index.php/Align
Cheers,
Thomas
> On Aug 30, 2018, at 10:42 PM, Santrupti Nerli wrote:
>
> Hi,
>
> I want to calculate pairwise RMSD for heavy atoms and backbone atoms.
>
> I see that for backbone, I can use name n+c+ca+o. But, do the same atoms also
> represent heavy atoms?
>
> What are the differences between backbone and heavy atoms? How to compute
> pairwise RMSD for a lot of structures? Can I use align here?
>
> Thank you very much.
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] Extra-fit
Hi Abhik, extra_fit calls cmd.align() for all objects in the selection, with target=reference. Implementation: https://github.com/schrodinger/pymol-open-source/blob/master/modules/pymol/fitting.py#L139 Documentation: https://pymolwiki.org/index.php/Extra_fit Hope that helps. Cheers, Thomas > On Aug 22, 2018, at 4:55 PM, abhik.gh...@bose.res.in wrote: > > Hello All > I want to know how the "Extra_fit" option works in pymol (Detail algorithm > or procedure). Any idea regarding this. > All suggestions are welcome. > Thank you. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Display metal coordination
Hi Markus and Joel, Would something like this address your needs? # show metal contacts distance metalcoordination, metals, (donors acceptors), 3.5, label=0 # show metals as semi-transparent spheres show spheres, metals set sphere_transparency, .5 # show the metal neighbors as lines show lines, byres (all within 3.5 of metals) The "metals" selector was added in PyMOL 1.6.1. Cheers, Thomas > On Aug 24, 2018, at 1:29 AM, Joel Tyndall wrote: > > Hi Markus, > > I am not aware of this function in pymol but would be interested in one being > developed. > > J > > -Original Message- > From: Markus Heller > Sent: Friday, 24 August 2018 6:28 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Display metal coordination > > Hi all, > > Is there a way to display the coordination of a metal, e.g. Zn2+ or Mg2+, > that doesn't require manual selection of atoms and showing of bonds? > > I wasn't able to find anything online ... > > Thanks > Markus -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Slice
Hi Divya, Try to output a .phi file with delphi, that format should work fine with slices. In your delphi .param file: out(phi,file=phimap.phi,format=0) Cheers, Thomas > On Aug 17, 2018, at 4:28 PM, Divya Kaur Matta > wrote: > > Dear Thomas, > > It’s phimap.cube file. ( .cube is an extension). These cube files are from > Delphi. ( Poisson Boltzmann solver). > > Thank you , > > Best Regards > Divya > > Get Outlook for iOS > From: Thomas Holder > Sent: Friday, August 17, 2018 4:51 AM > To: Divya Kaur Matta > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Slice > > Hi Divya, > > I can confirm that slices don't work properly with some map formats (those > which define a transformation matrix). > > What's the file format (file extension) of your map? > > Cheers, > Thomas > > > On Aug 15, 2018, at 7:38 PM, Divya Kaur Matta > > wrote: > > > > Dear all, > > > > > > I would like to use the "Isomesh" and "Slice" command for the protein I am > > working on to get the electrostatic potential map of that protein. For that > > , it requires map. I have got Delphi map for that. When I use the commands > > below, I got the mesh that aligns with the atoms of the pdb, however for > > slice, it is not aligned with the atoms. I would like to have a slice plane > > for my protein. > > > > > > For isomesh, > > > > isomesh map_n20, phimap, -20.0 ; color red, map_n20 > > > > isomesh map_p20, phimap, 20.0 ; color blue, map_p20 > > > > For slice, > > > > I did actions, show slice(default) > > > > Please find attached images for the slice I got. > > > > > > Thank you! > > > > Best Regards, > > > > Divya K. Matta > > Ph.D. Student in Chemistry -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Serine phosphorylation
Hi Wei, Phosphorylating a serine with the builder works fine for me. 1) click "Builder" button -> opens panel and should automatically switch to "3-Button Editing" mouse mode 2) click on the serine's OG atom -> should create "pk1" selection 3) click "P=O3" button on the Builder panel To change the orientation of the phosphate group, make sure you're in "3-Button Editing" mouse mode, then 1) double click the CB-OG bond with the *right* mouse button -> shows dihedral indicator 2) CTRL-drag any of the phosphate group atoms with the left mouse button Cheers, Thomas > On Jul 31, 2018, at 6:42 PM, Wei Song wrote: > > Hi all, > > I have a peptide structure and would like to phosphorylate one of the serine > residues to test its binding capacity to a ligand. I tried the Build function > with a PyMol 2.0, but only a phosphorous can be added to the serine. Does > anyone have experiences of creating a phosphorylated residue with PyMol or > other tools? > Any suggestions would be appreciated. > > Thanks, > Wei -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Slice
Hi Divya, I can confirm that slices don't work properly with some map formats (those which define a transformation matrix). What's the file format (file extension) of your map? Cheers, Thomas > On Aug 15, 2018, at 7:38 PM, Divya Kaur Matta > wrote: > > Dear all, > > > I would like to use the "Isomesh" and "Slice" command for the protein I am > working on to get the electrostatic potential map of that protein. For that , > it requires map. I have got Delphi map for that. When I use the commands > below, I got the mesh that aligns with the atoms of the pdb, however for > slice, it is not aligned with the atoms. I would like to have a slice plane > for my protein. > > > For isomesh, > > isomesh map_n20, phimap, -20.0 ; color red, map_n20 > > isomesh map_p20, phimap, 20.0 ; color blue, map_p20 > > For slice, > > I did actions, show slice(default) > > Please find attached images for the slice I got. > > > Thank you! > > Best Regards, > > Divya K. Matta > Ph.D. Student in Chemistry -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] alignment of frame
Hi Abhik,
Try this (with PyMOL 2.1 or newer):
load avg.pdb
loadall frame*.pdb
extra_fit (frame*) & guide, avg
multifilesave {name}-aligned.pdb, frame*
https://pymolwiki.org/index.php/load
https://pymolwiki.org/index.php/loadall
https://pymolwiki.org/index.php/extra_fit
https://pymolwiki.org/index.php/multifilesave
Cheers,
Thomas
> On Aug 9, 2018, at 11:32 AM, abhik.gh...@bose.res.in wrote:
>
> Hello all
> I want to align each frame pdb w.r.t a specific frame pdb. Let assume i
> have 10 pdb files.I have another file "avg.pdb". I want to align each pdb
> w.r.t "avg.pdb" file. I can do it manually using align command i.e align
> 1, avg. But is there any code or anything by which i can produce alignment
> files and save them as new pdb.
> Any suggestion is welcome
> Thank you
> Abhik
--
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PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] allign multiple freme in pymol
Hi Abhik and Jared,
There is also "intra_fit" and "multifilesave":
https://pymolwiki.org/index.php/intra_fit
https://pymolwiki.org/index.php/multifilesave
Example:
intra_fit name CA
multifilesave model{state:06}.pdb, state=0
Cheers,
Thomas
> On Jul 30, 2018, at 9:46 PM, Jared Sampson wrote:
>
> Hi ABhik -
>
> You'll want to have a look at the `split_states` command. Something like the
> following should get you going. Note the embedded multiline `python` block.
>
> # Using 1nmr as a sample structure
> fetch 1nmr, async=0
> split_states 1nmr, prefix=model
>
> python
> # starting at state 2, align each model to state 1
> for i in range(2, cmd.count_states('1nmr') + 1):
> this_model = 'model{:04d}'.format(i)
> cmd.super(this_model, 'model0001')
> cmd.save('{}.pdb'.format(this_model), this_model)
> python end
>
> For your 10 structures you'll also need more zero-padding (e.g.
> '{:07d}'). You can save this as super_states.pml and run from PyMOL with the
> command: @super_states.pml
>
> Hope that helps.
>
> Cheers,
> Jared
>
> On July 30, 2018 at 2:16:54 AM, abhik.gh...@bose.res.in
> (abhik.gh...@bose.res.in) wrote:
>
>> Hello All
>> I have a pdb file containing 10 frames . Now I want to align all frame
>> one by one in pymol and then want to save the final coordinate. How it can
>> be done?
>> All suggestions are welcome
>> Thanking you.
>> ABhik
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] Calculate RMSD between ligands from a crystal structure and from a docking
Forget my last reply ;-) Marko is right, I didn't notice first because this is fixed in PyMOL 2.1. Some PDBQT atom types were not imported correctly in previous versions. Cheers, Thomas > On Jul 26, 2018, at 10:21 AM, Marko Hyvonen wrote: > > Hi Baptiste, > > removing the data at the end of the HETATM lines from ca. character 70 > onwards fixed it. Not sure what these are. According to PDB 3.30 format, > 67-76 should be empty. Some of the elements were non-standard also (NA for N, > OA for O), but looks to be the numbers in the "empty" columns that bother > PyMOL (perhaps it should just ignore these?). > > A lot of other things I do not recognise in PDB files in you docked > rifampicin too, but those seem not to bother the analysis. > > See attached. RMSD 0.032 for 51 atoms. Not a bad docking pose! > > cheers, Marko > > On 26/07/2018 08:42, Baptiste Legrand wrote: >> Thanks for your answers. The molecule is the rifampicin. Please find >> attached the pdb from the crystal structure and the pdbqt from autodock >> vina. May be the format of one or both files is not correct. >> >> Best, >> >> Baptiste >> >> >> Le 25/07/2018 à 18:57, Markus Heller a écrit : >>> Not knowing what your molecule looks like, could it be automorphism? >>> >>>> -Original Message- >>>> From: Baptiste Legrand >>>> Sent: Wednesday, July 25, 2018 9:17 AM >>>> To: pymol-users@lists.sourceforge.net >>>> Subject: [PyMOL] Calculate RMSD between ligands from a crystal structure >>>> and >>>> from a docking >>>> >>>> Dear all, >>>> >>>> I tried to calculate a rmsd value between ligands from a crystal structure >>>> and >>>> after docking. The two molecules share similar nomenclatures and are >>>> really >>>> well superimposed. I think that the RMSD should be < 1 A. I used the >>>> following >>>> lines: >>>> >>>> alter all,segi="" >>>> alter all,chain ="" >>>> rms /ligand_crystal*, /ligand_docking* >>>> >>>> It works but I obtained an abnormal high RMSD value of 6.146 A. When I use >>>> the >>>> pair_fit function, pymol completely return one molecule and also write >>>> "ExecutiveRMS: RMS =6.146 (51 to 51 atoms)". I should have missed >>>> something... >>>> >>>> thanks for the help, >>>> All the Best. >>>> >>>> Baptiste > > -- > > Marko Hyvonen > Department of Biochemistry, University of Cambridge > > mh...@cam.ac.uk > > +44 (0)1223 766 044 > @HyvonenGroup > > http://hyvonen.bioc.cam.ac.uk > > -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Calculate RMSD between ligands from a crystal structure and from a docking
Hi Baptiste, These files look good to me, I get: PyMOL>rms Crystal_Rfp, Vina_Rfp Executive: RMSD =0.032 (51 to 51 atoms) Is it possible that you tried with a multi-model (multiple poses) pdbqt file before? If that's the case, specify "mobile_state" and/or "target_state": PyMOL>rms Crystal_Rfp, Vina_Rfp, mobile_state=1, target_state=1 Executive: RMSD =0.032 (51 to 51 atoms) See also "Notes" section here: https://pymolwiki.org/index.php/Align#Notes Cheers, Thomas > On Jul 26, 2018, at 9:42 AM, Baptiste Legrand wrote: > > Thanks for your answers. The molecule is the rifampicin. Please find attached > the pdb from the crystal structure and the pdbqt from autodock vina. May be > the format of one or both files is not correct. > > Best, > > Baptiste > > > Le 25/07/2018 à 18:57, Markus Heller a écrit : >> Not knowing what your molecule looks like, could it be automorphism? >> >>> -Original Message- >>> From: Baptiste Legrand >>> Sent: Wednesday, July 25, 2018 9:17 AM >>> To: pymol-users@lists.sourceforge.net >>> Subject: [PyMOL] Calculate RMSD between ligands from a crystal structure and >>> from a docking >>> >>> Dear all, >>> >>> I tried to calculate a rmsd value between ligands from a crystal structure >>> and >>> after docking. The two molecules share similar nomenclatures and are really >>> well superimposed. I think that the RMSD should be < 1 A. I used the >>> following >>> lines: >>> >>> alter all,segi="" >>> alter all,chain ="" >>> rms /ligand_crystal*, /ligand_docking* >>> >>> It works but I obtained an abnormal high RMSD value of 6.146 A. When I use >>> the >>> pair_fit function, pymol completely return one molecule and also write >>> "ExecutiveRMS: RMS =6.146 (51 to 51 atoms)". I should have missed >>> something... >>> >>> thanks for the help, >>> All the Best. >>> >>> Baptiste -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Atoms forming more bonds than they should have
Hi Wei, Is this an ensemble of docking poses all overlayed in the same PDB file, and not separated by MODEL records? PyMOL does distance based bonding when loading data from PDB files. Which docking program generated this file? Cheers, Thomas > On Jul 9, 2018, at 4:57 PM, Wei Song wrote: > > Hello, > > I got a structure (attached figure) of a lipid after docking it with a > protein. The original structure before the docking is in SDF file, not > regular PDB. I've never seen a docked structure like this with many of the > atoms having more bonds than they actually can have like some carbons (blue) > are having five even six bonds in the display, and the whole molecule looks > like a plate. Is there anyone who also have met this problem before or any > idea to get the structure back normal display. > > Thank you and I appreciate any suggestions and ideas. > > Best, > Wei > -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] How to visualize electrostatic potential map of a viral particle
Hi Chaava, You need to split the multi-state assembly into separate single-state objects. Then run APBS on a selection which includes all these objects. This is a huge system for APBS, you probably need to increase the grid spacing, otherwise it will take forever or might fail (PyMOL automatically retries several times with increased grid spacing if APBS runs out of memory). Here is an example I successfully ran on my MacBook with PyMOL 2.1: # download assembly (multi-state object) set assembly, 1 fetch 3j7l, async=0 # split states into individual objects split_states 3j7l delete 3j7l In the GUI: - Open "Plugin > APBS Electrostatics" - Selection: polymer & 3j7l_* - Calculate Map with APBS > Options >> Grid Spacing: 2.0 (or larger) - Run Took about 20min to compute. Hope that helps. Cheers, Thomas > On Jul 5, 2018, at 1:21 AM, Chaava CA wrote: > > Hello, > > I am very new to pymol and mainly use it for visualizing proteins and surface > properties. I am trying to generate the electrostatic potential map of a > Adeno associated viral particle which has 60 identical subunits. I have the > PDB file for it but it only shows 1 subunit at a time. In addition when I > generate the pqr I only get the potentials for one subunit. How can I > generate the potential for the entire viral particle and visualize it? I do > have the APBS plugin. > > If someone can explain this process in slightly more layman’s terms and > stepwise approach it would be very helpful. > > Any help is much appreciated. > > Thank you! -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] unable to load the Qt platform plugin "xcb"
Hi Mohammad, This error typically indicates that the PyMOL installation interferes with a different Qt installation on your system. I though we have this under control, our launcher script unsets all (known) interfering environment variables. Can you check which Qt environment variables are set on your system? Type this into a terminal: env | grep QT Our libraries should also be unaffected by LD_LIBRARY_PATH, but just in case, can you also check: env | grep LD For your information, libqxcb should be picked up from pymol/plugins/platforms/libqxcb.so, not from /usr/lib/x86_64-linux-gnu/qt5/plugins/platforms/libqxcb.so Cheers, Thomas > On Jul 4, 2018, at 9:39 PM, Mohammad T Mazhab Jafari > wrote: > > Hello, > > I am trying to run pymol on my linux computer (Ubuntu 17.10). > > I downloaded PyMOL-2.1.1_0-Linux-x86_64.tar.bz2 > > then unpacked with > > tar -jxf PyMOL-2.1.1_0-Linux-x86_64.tar.bz2 > > When I try to execute pymol from the pymol folder, I get the following > message. > > This application failed to start because it could not find or load the Qt > platform plugin "xcb" > in "". > Available platform plugins are: eglfs, minimal, minimalegl, offscreen, xcb. > Reinstalling the application may fix this problem. > Abort (core dumped) > > I have libqxcb, > > locate libqxcb > /usr/lib/x86_64-linux-gnu/qt5/plugins/platforms/libqxcb.so > /usr/lib/x86_64-linux-gnu/qt5/plugins/xcbglintegrations/libqxcb-egl-integration.so > /usr/lib/x86_64-linux-gnu/qt5/plugins/xcbglintegrations/libqxcb-glx-integration.so > > > Any idea how to solve this issue? > > Thanks. > M. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Super and Align missing residues
Hi Nathan, Thank you very much for the files and instructions. I can reproduce the problem. I haven't seen this before and don't know yet what's going wrong, we will investigate. Cheers, Thomas > On Jun 28, 2018, at 10:50 AM, nclem...@cs.utexas.edu wrote: > > The alignment in this example is nearly perfect. Even the residues left > out of the fitting have perfect matches at the sequence level (as can be > seen by saving the super object and turning on the sequence alignment and > contact_all). > > PyMOL>load 1AY7_u.pdb, test > CmdLoad: "1AY7_u.pdb" loaded as "test". > PyMOL>load 1AY7_b.pdb, gold > CmdLoad: "1AY7_b.pdb" loaded as "gold". > PyMOL>select contact_rec, gold & chain R & (all within 10 of gold & chain > L) & n. ca > Selector: selection "contact_rec" defined with 33 atoms. > PyMOL>select contact_lig, gold & chain L & (all within 10 of gold & chain > R) & n. ca > Selector: selection "contact_lig" defined with 33 atoms. > PyMOL>select contact_all, contact_rec + contact_lig > Selector: selection "contact_all" defined with 66 atoms. > PyMOL>super gold & contact_all, test, cycles=0 > MatchAlign: aligning residues (66 vs 185)... > MatchAlign: score 143.882 > ExecutiveAlign: 58 atoms aligned. > Executive: RMS =0.524 (58 to 58 atoms) > > <1AY7_u.pdb><1AY7_b.pdb> -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Super and Align missing residues
Hi Nathan, Sounds like you are doing everything correct. Would it be possible to send me the input files? Thanks, Thomas > On Jun 26, 2018, at 10:58 AM, Nathan Clement wrote: > > Hi, > > I'm trying to compute the interface RMSD (iRMSD) between two protein pairs > that are highly similar (might have a few missing residues, but are otherwise > identical). Right now, my code does something like the following for protein > pairs "gold" and "test" (receptor has chains A+B and ligand has chains C): > > PyMOL>select contact_rec, (gold & chain A+B) & all within 10 of (gold & chain > C) & n. ca > PyMOL>select contact_lig, (gold & chain C) & all within 10 of (gold & chain > A+B) & n. ca > PyMOL>align gold & contact_rec + contact_lig, test, cycles=0 > Match: read scoring matrix. > Match: assigning 82 x 445 pairwise scores. > MatchAlign: aligning residues (82 vs 445)... > MatchAlign: score 257.500 > ExecutiveAlign: 67 atoms aligned. > Executive: RMS = 14.161 (67 to 67 atoms) > > This seems to suggest that, even with cycles=0, 82-67=15 atoms were not > included in the alignment. When I look at the alignment (object=aln), it > appears that most of the "missing" residues from this alignment have the same > residue name, are matches in the sequence alignment, and are in a nearby > location. > > Is it possible to force align to give the full RMSD calculation? super has > the same issue, and I'm concerned that using something like rms or fit won't > work because the "gold" and "test" have different residue numbering (and > might be missing residues so it's not always possible to give them an > equivalent numbering). > > Does anybody have any suggestions? > > Thanks in advance, > > Nathan -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Failed to create menu's
Hi Puneet, This is a know issue with the installer, which can have a variety of reasons. https://docs.anaconda.com/anaconda/user-guide/troubleshooting#windows-error-failed-to-create-anaconda-menus-or-failed-to-add-anaconda-to-the-system-path PyMOL might still be properly installed and only missing the start menu entries. As far as I can tell from your screenshot, you can launch C:\pymoll\PyMOLWin.exe Cheers, Thomas > On Jun 25, 2018, at 10:37 PM, puneet garg wrote: > > Dear Sir, > I am installing PyMOL (education version PyMOL-2.1.1_0-Windows-x86_64) on my > new windows 7 computer. I am getting an error "Failed to create menu's" while > installing. If I ignore it the installation fails. Please advice me on this > issue. I have attached a picture of same. > Thanks > > > -- > Puneet > Structural Biology Lab > Biotechnology Dept. > IIT Madras > Chennai-600036 > -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Migrating Open-Source PyMOL to github
Hi everyone, We've migrated the PyMOL open-source SVN repository to github: https://github.com/schrodinger/pymol-open-source The SourceForge project will be phased out. We will no longer update the SVN repository. Bugs should be reported on the new github page. We will continue to use the pymol-users mailing list provided by SourceForge. Cheers, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Orient every sidechain and make a movie
Hi Murpholino,
This should be the correct selection expression:
sele = '(sc. or name CA) and i. {}'.format(stored.x)
Cheers,
Thomas
> On Jun 20, 2018, at 3:11 PM, Murpholino Peligro wrote:
>
> I have waters and ions in my structures.
>
> If I add the "sc." it works for non-glycine residues. (The error is
> "ExecutiveWindowZoom-Warning: selection doesn't specify any coordinates.")
> How to tweak it so that F1 works for all my residues?
>
> Ps I was thinking to include the alpha carbon in the selection so the
> sidechain does not look truncated
> sele = 'sc. and i. or name ca and i. {}'.format(stored.x)
> This works but it centers on the ca and not the sc. Plus... sticks are not
> drawn.
> Ps. Sorry for the delay. I was very sick.
>
>
>
> 2018-06-18 5:12 GMT-05:00 Thomas Holder :
>
> > It works ...but the F1 key now zooms farther away from the residues. :P
>
> Are there other atoms with residue number 1? Ligands? Solvent? I had removed
> the "sc." selector, so that it works on Glycine as well. You can add it back
> to the sele string in the zoomnext function.
>
> sele = 'sc. and i. {}'.format(stored.x)
>
> Cheers,
> Thomas
--
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PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] Orient every sidechain and make a movie
> It works ...but the F1 key now zooms farther away from the residues. :P
Are there other atoms with residue number 1? Ligands? Solvent? I had removed
the "sc." selector, so that it works on Glycine as well. You can add it back to
the sele string in the zoomnext function.
sele = 'sc. and i. {}'.format(stored.x)
Cheers,
Thomas
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] Orient every sidechain and make a movie
Hi Murpholino, How about an interactive version instead of a fix-speed movie? The attached script maps the F1 key to advance to the next residue, and F2 to go back. It also colors atoms by density fit (red if they don't fit into the 1.2 sigma shell). It will only show sticks for the current residue, to make it more visible. Cheers, Thomas sc_inspector_F1.pml Description: Binary data > On Jun 15, 2018, at 4:36 PM, Murpholino Peligro wrote: > > Dear PyMOL users.. > I found this bb_inspector at https://pymolwiki.org/index.php/MovieSchool_4 > It kinda does what I want, so I tweak it little bit ... (*.pml attached) > If you run the script and play the movie you'll see that sometimes the > sidechain is a little bit obscured by some density/atoms in the front. How do > I make them more visible? > > Lots of thanks > > > > > > 2018-06-15 8:31 GMT-05:00 Murpholino Peligro : > Dear PyMOL users... > > Is there a way to orient every sidechain and take a picture to produce a > movie? > > Idea: By aligning the pdbs and maps and having them in the grid mode, with > this movie I could f take a quick look at how well my electron density fits > to all my models... > > Thanks > > ------ -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] PyMOL Open-Source Fellowship - Call for Applications
Greetings, We are excited to announce that the Warren L. DeLano Memorial PyMOL Open-Source Fellowship program is now accepting applications for the 2018--2019 term. The Fellowship is awarded by Schrӧdinger to supplement the income of an outstanding member of the PyMOL open-source community to develop free resources to help scientific progress and the community as a whole. Details and application instructions can be found on https://pymol.org/fellowship The application deadline is August 26, 2018. We look forward to your submissions! Cheers, The PyMOL Team at Schrödinger -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] AutoDock plugin error
Hi all, I made a pull request to Pymol-script-repo where oldnumeric is replaced with numpy in the bundled ADT copy. Anyone willing to review and test this? https://github.com/Pymol-Scripts/Pymol-script-repo/pull/98 Cheers, Thomas > On Jun 13, 2018, at 11:24 AM, J.R. W wrote: > > Enrique, > > I don’t know a lot about AutoDock, but I do know a lot about python. That > error comes from using a new versions of numpy (1.14) that does not have old > numeric with it anymore (deprecated in 1.9). > > You can do a few things. Run the script within pymol which uses a earlier > release of numpy. rOr you could downgrade your numpy to 1.8 by using > > Pip install ‘numpy==1.8’ —force-reinstall > > > But I’d recommend you do that in an environment. This is the perfect time for > virtual environments > > https://realpython.com/python-virtual-environments-a-primer/ > > > >> On Jun 12, 2018, at 2:36 PM, Enrique Ordaz wrote: >> >> Dear everyone, >> I have recently installed the open-source Pymol 1.7.x on Ubuntu 16.04 >> sudo-apt-get install pymol >> >> I then added the Pymol-script-repo which includes the Autodock/Vina plugin >> and ADT. This has worked well for me in the past. However on this new >> installation I keep getting the following error: >> >> Batch: >> /home/enrique/Pymol-script-repo/modules/ADT/AutoDockTools/Utilities24/prepare_receptor4.py >> -r /home/enrique/pymol/receptor.1crl.pdb -o >> /home/enrique/pymol/receptor.1crl.pdbqt -A checkhydrogens >> Traceback (most recent call last): >> File >> "/home/enrique/Pymol-script-repo/modules/ADT/AutoDockTools/Utilities24/prepare_receptor4.py", >> line 10, in >> import MolKit.molecule >> File "/home/enrique/Pymol-script-repo/modules/ADT/MolKit/molecule.py", >> line 25, in >> from mglutil.util import misc >> File "/home/enrique/Pymol-script-repo/modules/ADT/mglutil/util/misc.py", >> line 19, in >> import numpy.oldnumeric as Numeric >> ImportError: No module named oldnumeric >> >> Hope someone can help me or point me in the right direction. >> >> Best regards, >> Enrique Ordaz -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Ambient occlusion on isosurface
Hi Gianluca, > is it possible to set ambient occlusion for isosurfaces? Unfortunately no, it's only implemented for molecular surfaces. Cheers, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Collada export with instances?
Hi Jared,
Only writing one sphere geometry per color makes a lot of sense, yes let's talk
about that offline! I also see some dispensable elements like with
identity matrix, which we could safely remove to reduce file size further.
Cheers,
Thomas
> On Jun 6, 2018, at 10:49 PM, Jared Sampson wrote:
>
> Hi Gary and Thomas -
>
> As Thomas mentioned, the sphere/cylinder/etc. primitives described in the
> COLLADA 1.5 spec as ("boundary representation") elements would be the
> best option for spheres and basically all other PyMOL representations except
> for molecular surfaces. Unfortunately COLLADA 1.5 is not well supported by
> other graphics applications. However, there is still room to optimize the
> storage within the constraints of COLLADA 1.4.
>
> After looking through a couple test .dae files to refresh my memory, I see
> that the output from PyMOL does use elements. However,
> as Gary has noticed, it defines a separate element for each sphere
> in the scene. This adds up quickly for scenes with many atoms represented as
> spheres. FWIW, the reasoning behind this when I originally wrote the COLLADA
> exporter was that color information is included in the definition,
> and it was easier to write a separate geometry for each sphere than to
> collect information about all the different colors of spheres.
>
> Of course, it is possible to do this more efficiently. Probably the simplest
> way to cut down the file size would be to write only a single sphere
> element *per color* of sphere present in the scene, and then use
> instances of those to represent all spheres that share the same color. The
> attached files each have two geometries (output by PyMOL with pseudoatom
> spheres at position=[0, 0, 0] and [1, 0, 0], in grey90 and red,
> respectively). The first file, "test.dae", was output directly by PyMOL and
> has one instance of each sphere, for a total file size of 21545 bytes.
> Manually adding a second instance of each sphere (translated by +/- 4Å along
> the X axis) in "test-added.dae" adds only 1147 bytes to the file (look for
> and in your
> favorite text editor), compared to adding 18174 bytes if the two additional
> spheres are exported from PyMOL with their additional geometries by adding
> additional pseudoatoms (that file not attached). That's an almost 94%
> reduction per added sphere; for scenes with many spheres, the storage savings
> would be substantial.
>
> On the other hand, if there is a way for color to be specified separately
> from the element (which I imagine must be possible, but I haven't
> found a clear example of how to do this), that would be the most preferred
> option, as it would allow us to use a single sphere element per
> output file.
>
> Thanks to Gary for bringing this up. Thomas, perhaps we can talk offline
> about what might be the best way to implement this?
>
> Cheers,
> Jared
>
>
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] PyMOL without OpenGL (OS X)?
Hi David, PyMOL uses OpenGL on macOS, so if Apple drops it, we're screwed :-( For now they have deprecated it, let's hope that they ship the libraries for a couple more years... Thomas > On Jun 6, 2018, at 6:23 PM, David Mathog wrote: > > As reported here: > > https://arstechnica.com/gadgets/2018/06/the-end-of-opengl-support-other-updates-apple-didnt-share-at-the-keynote/ > > Apple has declared that they are dropping support for OpenGL from OS X. How > will that affect PyMOL on OS X? Does that version already use metal (or > something else) or is it still OpenGL based? > > Thanks, > > David Mathog > mat...@caltech.edu > Manager, Sequence Analysis Facility, Biology Division, Caltech -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Collada export with instances?
Hi Gary, Do you know an application which can actually read COLLADA files with sphere primitives? We've faced the problem that most tools only handle COLLADA 1.4, so if PyMOL would use COLLADA 1.5 features, the programs we know wouldn't read the exported files. See https://pymolwiki.org/index.php/COLLADA#Limitations I fully agree that sphere primitives and other COLLADA 1.5 features would be better (smaller files, precise sphere representation, etc.). Thomas > On Jun 6, 2018, at 1:19 PM, Gary Oberbrunner > wrote: > > The collada file exported by pymol would be smaller and export/import faster, > I think, if it used geometry_instance for spheres rather than giving each > sphere its own geometry/mesh/accessors/etc.. Has that been discussed before? > > -- > Gary Oberbrunner -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] pymol and gromacs
Hi Paul, Looks like they are working on a new version of the plugin: https://github.com/makson96/Dynamics/pull/95 You could give this modified version a try: https://github.com/speleo3/Dynamics/blob/no-tk-mainloop/pymol_plugin_dynamics.py Cheers, Thomas > On May 17, 2018, at 1:50 PM, Paul Buscemi <busce...@umn.edu> wrote: > > > Dear Users, > > I’ve been able to use Pymol 1.7 with Gromacs plugin ( ppa download and > install ), but have not found a plugin/method to use version2.1.1 ( > Schrodinger maintained ). > Is a plugin for v 2.1.1 available ? > > System is linux Mint 18.1 > > Regards > Paul -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] export smoother spheres to Collada?
Hi Gary, "sphere_quality" works for me, for both regular atom sphere representation and for CGO spheres. What exactly did you do where it had no effect? Cheers, Thomas > On May 15, 2018, at 10:14 PM, Gary Oberbrunner <ga...@darkstarsystems.com> > wrote: > > How can I get more sphere subdivision into the Collada export? I've tried > sphere_quality 2 and cgo_sphere_quality 2, they seem to have no effect. > > -- > Gary Oberbrunner -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Pymol 2.1 graphics error
Hi Andy,
> thanks for the responses. The -M option did the trick. What does it do?
Great! The -M ("mono") option skips the attempt to detect hardware stereo
(a.k.a. quad buffered, available with Nvidia Quadro cards and 3D vision).
Did you install pymol with conda? Recently, pyqt=5.9 packages appeared in the
default anaconda channel, but unfortunately PyQt >5.6 doesn't handle the stereo
request properly on non-stereo hardware. Downgrading helps (conda install
pyqt=5.6).
Cheers,
Thomas
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] Add ACE and NME terminals
Hi Roja,
Which PyMOL version do you use? The "attach_amino_acid" function had a bug in
old versions, it was fixed in PyMOL 1.8.0.
A capped poly-threonine alpha helix can be built in PyMOL (1.8+) like this:
from pymol import cmd, editor
cmd.set('retain_order', 0)
cmd.fab('T' * 40, ss=1)
editor.attach_amino_acid("last name C", 'nme')
editor.attach_amino_acid("first name N", 'ace')
Cheers,
Thomas
> On May 10, 2018, at 8:53 AM, roja rahmani <roja.r...@gmail.com> wrote:
>
> Dear Thomas,
>
> I tried both builder and command. But the problem is an NME doesn't connect
> to last C, even when i remove the last OXT.
>
> Let me ask in different way. Please help me to build poly threonine(consist
> of 40 threonine amino acids) in alpha helical structure which is capped by
> NME and ACE. How can i exactly build it?
>
> (I want to use its .pdb file as an input for amber99ff in GROMACS.)
>
> Best regards
> -Roja
>
> On Thu, 10 May 2018, 00:47 Thomas Holder, <thomas.hol...@schrodinger.com>
> wrote:
> Hi Roja,
>
> This could be useful for you:
> 18 Nov 2017, NME and ACE capping from script
> https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg14812.html
>
> I couldn't quite follow your description, which interface were you using? The
> "Builder" panel? The following works for me:
> 1) Click "Builder" button in the upper right
> 2) Click "Protein" tab
> 3) Click "NMe"
> 4) Click on the last C atom (C-terminus)
>
> If there is an OXT atom, remove that first (e.g. with: "remove name OXT")
>
> Hope that helps.
>
> Cheers,
> Thomas
>
> > On May 9, 2018, at 9:11 PM, roja rahmani <roja.r...@gmail.com> wrote:
> >
> > Hi,
> >
> > I'm beginner in PYMOL. I want to add ACE and NME terminals to helical poly
> > amino acid which is made by Peptide builder. I load the poly AA pdb file to
> > pymol. Then:
> >
> > Edit first (name N)
> >
> > Then i didn't know how to add residue so i got help from taps and select
> > ACE.
> > But when i used this command,
> > Edit last (name C)
> > And then select NME from tabs, the NME were not connected to the last
> > carbon and was completely separated.
> > Would you please help me how solve this problem?
> >
> > Best regards
> > Roja
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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Re: [PyMOL] Add ACE and NME terminals
Hi Roja, This could be useful for you: 18 Nov 2017, NME and ACE capping from script https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg14812.html I couldn't quite follow your description, which interface were you using? The "Builder" panel? The following works for me: 1) Click "Builder" button in the upper right 2) Click "Protein" tab 3) Click "NMe" 4) Click on the last C atom (C-terminus) If there is an OXT atom, remove that first (e.g. with: "remove name OXT") Hope that helps. Cheers, Thomas > On May 9, 2018, at 9:11 PM, roja rahmani <roja.r...@gmail.com> wrote: > > Hi, > > I'm beginner in PYMOL. I want to add ACE and NME terminals to helical poly > amino acid which is made by Peptide builder. I load the poly AA pdb file to > pymol. Then: > > Edit first (name N) > > Then i didn't know how to add residue so i got help from taps and select ACE. > But when i used this command, > Edit last (name C) > And then select NME from tabs, the NME were not connected to the last carbon > and was completely separated. > Would you please help me how solve this problem? > > Best regards > Roja -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Pymol 2.1 graphics error
Hi Andy, Does it help if you launch PyMOL with "-M"? pymol -M If not, can you be more specific about the symptoms? Is it just slow or do you get flickering, wrong rendering, crashes, etc.? Thanks, Thomas > On May 9, 2018, at 8:01 PM, Andreas Tosstorff > <andreas.tossto...@cup.uni-muenchen.de> wrote: > > Hi all, > > I just installed PyMol 2.1 on my system (Centos 7) and there are some issues > with displaying any structures. > > I get the following error, however I'm not sure whether that's what's causing > the actual laggy graphics: > > "This Executable Build integrates and extends Open-Source PyMOL. > Detected OpenGL version 2.0 or greater. Shaders available. > Geometry shaders not available > SMAA not available > Detected GLSL version 1.30. > OpenGL graphics engine: > GL_VENDOR: Intel Open Source Technology Center > GL_RENDERER: Mesa DRI Intel(R) HD Graphics 530 (Skylake GT2) > GL_VERSION: 3.0 Mesa 17.0.1 > GL_ERROR : 1282" > > I'm new to Pymol and Linux so please excuse me if I'm missing something. > > Thanks, > > Andy > > > -- > M.Sc. Andreas Tosstorff > Lehrstuhl für Pharmazeutische Technologie und Biopharmazie > Department Pharmazie > LMU München > Butenandtstr. 5-13 ( Haus B) > 81377 München > Germany > Tel.: +49 89 2180 77059 > > -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Multiple PyMOL Instances in Python Script
> On Apr 24, 2018, at 7:17 PM, Yang Su <s...@crystal.harvard.edu> wrote: > > OK, thanks. If you don't mind, I can add it to the wiki: > https://pymolwiki.org/index.php/Launching_From_a_Script Sure, that would be great. Thanks a lot! Cheers, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Multiple PyMOL Instances in Python Script
Hi Yang,
Very good questions. I don't think that it's documented anywhere. Reference
counting is maintained, I fixed that up as best as I could before the PyMOL 2.0
release (in PyMOL 1.x it leaks references). Looks like there is no way to
introspect whether start() has been called already.
Cheers,
Thomas
> On Apr 24, 2018, at 6:16 PM, Yang Su <s...@crystal.harvard.edu> wrote:
>
> Thanks Thomas. The code snippet works. Does start(), stop() maintain
> reference counting? Is there a way to know if it's already started/stopped?
> Is this API documented somewhere?
>
> Thanks,
> Yang
>
>
> On Mon, Apr 23, 2018 at 1:15 PM, Thomas Holder
> <thomas.hol...@schrodinger.com> wrote:
> Hi Yang,
>
> Yes it's possible to have independent instances. The API has actually been
> around for a long time. For some reason it was never widely adopted and thus
> is not very thoroughly tested. Please report any bugs you encounter.
>
> Example:
>
> import pymol2
> p = pymol2.PyMOL()
> p.start()
> p.cmd.fragment('ala')
> p.cmd.show_as('sticks')
> p.cmd.zoom()
> p.cmd.png('/tmp/ala.png', 1000, 800, dpi=150, ray=1)
> p.stop()
>
> Cheers,
> Thomas
>
> > On Apr 19, 2018, at 3:33 PM, Yang Su <s...@crystal.harvard.edu> wrote:
> >
> > Hi,
> >
> > Is it possible to start multiple independent pymol backend processes in a
> > python script/jupyter notebook? Now with PyMOL 2.1 I can 'import pymol' and
> > call a pymol.cmd function to start a backend process, but this is kind of
> > 'global'. I'm looking for a way to manage multiple PyMOL sessions in
> > parallel, each manipulating its own structures.
> >
> > Thanks,
> > Yang
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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Re: [PyMOL] Anaglyph stereo output from command line
Thanks Jared and Cody! There is not much I can add, yes this looks like a bug and we should fix it. Cheers, Thomas > On Apr 23, 2018, at 11:51 PM, Jared Sampson <jared.samp...@columbia.edu> > wrote: > > Hi Cody - > > I can confirm that I see similar behavior on 2.1.0 (stereo rendered properly > from the GUI but not in batch mode) but the issue is not limited to just > anaglyph stereo. Rather, (admittedly not having tested all stereo_mode > options) it seems stereo in general doesn't get rendered as expected in batch > mode. I imagine Thomas will chime in as well, but I would file a bug report > with pymol-dev-gr...@schrodinger.com and/or via > https://sourceforge.net/p/pymol/bugs/. > > Cheers, > Jared > > On April 23, 2018 at 6:59:03 PM, Cody Jackson (cjack...@scripps.edu) wrote: > >> Hi Everyone, >> >> I'm trying to make anaglyph 3D figures and movies in command line mode and >> I'm having some trouble - using incentive version 2.1.1 right now. >> >> It seems like anaglyph stereo is only ray traced when the GUI is open. >> Here's a quick example adapted from the wiki, it saves the desired red-cyan >> png when I run it with @script.pml in the GUI, but I only get the 2D output >> when I run pymol -c script.pml. Is there a trick to getting stereo images in >> the command line/batch mode? Is it not possible? >> >> -- >> fetch 1ESR, async=0 >> as cartoon >> set cartoon_smooth_loops >> spectrum >> bg white >> stereo anaglyph >> ray 640,480 >> png demo.png >> -- >> >> Thank you for any input. >> >> Best, >> Cody Jackson -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Multiple PyMOL Instances in Python Script
Hi Yang,
Yes it's possible to have independent instances. The API has actually been
around for a long time. For some reason it was never widely adopted and thus is
not very thoroughly tested. Please report any bugs you encounter.
Example:
import pymol2
p = pymol2.PyMOL()
p.start()
p.cmd.fragment('ala')
p.cmd.show_as('sticks')
p.cmd.zoom()
p.cmd.png('/tmp/ala.png', 1000, 800, dpi=150, ray=1)
p.stop()
Cheers,
Thomas
> On Apr 19, 2018, at 3:33 PM, Yang Su <s...@crystal.harvard.edu> wrote:
>
> Hi,
>
> Is it possible to start multiple independent pymol backend processes in a
> python script/jupyter notebook? Now with PyMOL 2.1 I can 'import pymol' and
> call a pymol.cmd function to start a backend process, but this is kind of
> 'global'. I'm looking for a way to manage multiple PyMOL sessions in
> parallel, each manipulating its own structures.
>
> Thanks,
> Yang
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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Re: [PyMOL] Dashed/Dotted Lines for Ribbon Representation
Hi Yang, That's an interesting observation, I wasn't aware that cartoon dash and loop may be traced differently. Apparently the "cartoon_flat_sheets" setting only applies to dash, not loop. Turning it off will make them follow the same path: set cartoon_flat_sheets, 0 Cheers, Thomas > On Apr 19, 2018, at 4:15 PM, Yang Su <s...@crystal.harvard.edu> wrote: > > Also, 'cartoon dash' and 'cartoon loop' render beta-strands differently, so I > can't combine the two and get a consistent look and feel. The use case is to > show regions of the structure as dashed line to indicate 'not covered in > study'. I can't use different colors for this purpose because color coding is > already used to represent other properties. > > Best, > Yang > > On Thu, Apr 19, 2018 at 3:56 PM, Yang Su <s...@crystal.harvard.edu> wrote: > Thanks for the tip, Thomas. 'cartoon dash' works with cartoon representation, > but doesn't seem to affect the ribbon representation. For some use cases I > like the 'cornered' ribbon representation better than the smooth cartoon > representation, but cartoon is still a good alternative if it is not possible > to show ribbon as dashed/dotted lines. > > Thanks, > Yang > > > On Thu, Apr 19, 2018 at 1:54 PM, Thomas Holder > <thomas.hol...@schrodinger.com> wrote: > Hi Yang, > > Yes, since PyMOL 1.8.2 there is "cartoon dash". e.g.: > > fetch 1ubq, async=0 > as cartoon > cartoon dash > > See also: > https://pymolwiki.org/index.php/Cartoon#USAGE > > Cheers, > Thomas > > > On Apr 19, 2018, at 12:54 PM, Yang Su <s...@crystal.harvard.edu> wrote: > > > > Hi, > > > > Is there an option to show the ribbon as dashed or dotted lines in pymol? > > > > Thanks, > > > > Yang -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Dashed/Dotted Lines for Ribbon Representation
Hi Yang, Yes, since PyMOL 1.8.2 there is "cartoon dash". e.g.: fetch 1ubq, async=0 as cartoon cartoon dash See also: https://pymolwiki.org/index.php/Cartoon#USAGE Cheers, Thomas > On Apr 19, 2018, at 12:54 PM, Yang Su <s...@crystal.harvard.edu> wrote: > > Hi, > > Is there an option to show the ribbon as dashed or dotted lines in pymol? > > Thanks, > > Yang -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] carving MTZ map
Hi Paul, After loading the MTZ file, did any objects show up in the panel on the right? If PyMOL detects columns for 2fofc and/or fofc maps, and the file is named "foo.mtz", then you should get "foo.2fofc" and "foo.fofc" maps. Use one of these maps as the second argument to volume (or isomesh). If automatic column detection fails, use a loading option with manual column selection. Summary of MTZ loading options: 1) Command line with column auto detection for 2fofc and fofc: load file.mtz 2) Command line with manual column selections: load_mtz file.mtz, mapname, FP, PHIC 3) GUI, opens MTZ import dialog: File > Open ... In each case you should get one or more map objects, which you can use with volume or isomesh in the next step to get a visualization. Cheers, Thomas > On Apr 16, 2018, at 11:18 AM, Paul Miller <p...@strubi.ox.ac.uk> wrote: > > Hi > > I'm using Windows Pymol 2.0 and would like to show mtz (NOT ccp4!) file 2fofc > density around a ligand. Can anyone tell me how to do this? > > I found info on a website (below), which I modified in various ways but it > didn't work. Kept saying the some.2fofc file was not found. > volume abc, some.2fofc, 0, organic, 4., 1, 4 > > Cheers, Paul > > Paul Steven Miller (PhD) > Postdoctoral Researcher > University of Oxford > Wellcome Trust Centre for Human Genetics > Division of Structural Biology > Roosevelt Drive > Oxford > OX3 7BN -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Algorithm used to retrieve ss ?
Hi Hélène, It's a custom algorithm developed by Warren DeLano. Some of the details are discussed in this post: https://sourceforge.net/p/pymol/mailman/message/7561993/ The implementation is in SelectorAssignSS in layer3/Selector.cpp: https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/layer3/Selector.cpp#l1885 Hope that helps. Cheers, Thomas > On Apr 4, 2018, at 11:59 AM, Hélène Kabbech <helene.kabb...@gmail.com> wrote: > > Dear pymol users, > > For a project based on proteins secondary structures (ss), I need to know > which algorithm/program does PyMol use to retrieve secondary structures from > a pdb file (when the ss datas are not display in the file). > > I retrieved ss using dssp program, and for some pdb files, it shows strands > or helix which are considered as loop by PyMol I guess. > > Thank you for your help. > > Best regards, > Hélène -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] how to get session to include CGO graphics objs?
Hi Gary & Jared,
PyMOL session files do not contain any graphics geometry. Export as COLLADA or
VRML are the best options.
The cmd.fetch() function is not asynchronous by default, only the fetch command
is. This is controlled by the quiet=0 argument which is passed to all commands.
Cheers,
Thomas
> On Mar 29, 2018, at 9:54 PM, Gary Oberbrunner <ga...@darkstarsystems.com>
> wrote:
>
> Thanks for the idea Jared, but no, still nothing but atoms.
>
> On Thu, Mar 29, 2018 at 3:31 PM, Jared Sampson <jared.samp...@columbia.edu>
> wrote:
> Hi Gary -
>
> `cmd.fetch()` runs asynchronously by default, meaning `cmd.show()` might
> execute before the structure is actually loaded. Try amending to:
>
> cmd.fetch(mol_id, async=0)
>
> Does that make a difference?
>
> Cheers,
> Jared
>
>
> On March 29, 2018 at 2:18:29 PM, Gary Oberbrunner (ga...@darkstarsystems.com)
> wrote:
>
>> I'm running pymol "headless" in a script. After initializing pymol and
>> calling finish_loading(), I do this:
>> cmd.fetch(mol_id)
>> cmd.show('spheres','all')
>> session = cmd.get_session()
>>
>> ... but my session object only includes one object, the cObjectMolecule. I'm
>> looking for it to include the graphics objects as well if that's possible.
>> Any hints?
>>
>>
>> --
>> Gary Oberbrunner -- CEO -- Dark Star Systems, Inc.
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] Protonation of small molecule amines
Hi Joel, Try this: 1) Click on "Builder" (upper right quick buttons) 2) Click "Charge: +1" 3) Click on the nitrogen atom This should put a positive charge (formal_charge) on the nitrogen and also add hydrogens to fill open valences. To add hydrogens to all atoms, click "Add H". Command line equivalent: PyMOL> alter name N, formal_charge=1 PyMOL> h_add Cheers, Thomas > On Mar 20, 2018, at 2:13 AM, Joel Tyndall <joel.tynd...@otago.ac.nz> wrote: > > Hi folks, > > Is pymol able to protonate an amine e.g. morphine i.e. when you add hydrogens > to a small molecule, ensure that the amine is charged (at it would be at > physiological pH? > > I have not been able to do it using the GUI. > > Cheers > > Joel > > Joel Tyndall | BSc(Hons) PhD > > Associate Professor in Medicinal Chemistry > School of Pharmacy | Te Kura Mātauraka Wai-whakaora > University of Otago | Te Whare Wānanga o Otāgo > PO Box 56 9054 > Dunedin | Ōtepoti > New Zealand | Aotearoa > Ph: 64 3 479 7293 > Skype: jtyndall > Website | pharmacy.otago.ac.nz -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
