[PyMOL] PyMOL 1.7.2 on Ubuntu 15.04
Hi, In response to an error I reported here about POV-Ray rendering giving blank PNGs I decided to get rid of my source installation of PyMOL 1.7.6 and go with the 1.7.2 version found in the Ubuntu repository. So I ran this script: set ray_opaque_background, 1 png Trimethoprim_img0003.png, dpi=500, ray=1, width = 4000, height = 2325 to render a structure of Trimethoprim I had loaded. While the rendering was somewhat better than that generated on 1.7.6, as it wasn't blank, it was far from perfect as the output image Trimethoprim_img0003.png was 1146px by 668px in size, not the 4000px by 2325px I specified in this script. Anyone know of any difference in 1.7.2 that would explain this besides a bug in the Deb package available for Ubuntu? -- Thanks for your time, Brenton -- ___ 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 ray tracing errors
Hi, I installed PyMOL on 32 bit Ubuntu 15.04 by following the Linux install guide on PyMOL Wiki. Although I ended up redoing it using the tarball available at Source Forge instead of the directory downloaded via Subversion (SVN) as SVN downloads an unstable release 1.7.7.1 which I found was unresponsive to colouring commands for secondary structures displayed in cartoon mode: color red, ss s color yellow, ss h color blue, ss l+ Here’s the code I used to install the tarball: cd /tmp wget -c http://internode.dl.sourceforge.net/project/pymol/pymol/1.7/pymol-v1.7.6.0.tar.bz2 tar -xvf pymol-v1.7.6.0.tar.bz2 rm /tmp/pymol-v1.7.6.0.tar.bz2 sudo chmod 777 -R pymol cd pymol # Configuration and installation prefix=/opt/pymol-svn modules=$prefix/modules # enable c++11 export CPPFLAGS=-std=c++0x sudo python setup.py build install \ --home=$prefix \ --install-lib=$modules \ --install-scripts=$prefix sudo chmod 777 -R /tmp/pymol python setup.py build install \ --home=$prefix \ --install-lib=$modules \ --install-scripts=$prefix sudo python setup.py build install \ --home=$prefix \ --install-lib=$modules \ --install-scripts=$prefix you may wish to know why I repeated the python setup.py build install line three times. Well I find that if I use just one it jams in the layer1 directory (which I believe to be the result of the /build subdirectory of /tmp/pymol having writes permission issues, which is why I added the chmod line after it). For whatever reason doing one more build install line with sudo in front doesn’t suffice and gives errors, so I do it without the sudo and then do the sudo command afterwards because otherwise it gives permission errors as it can’t write to /opt/pymol-svn without root permissions. This bash script successfully installs PyMOL, but for whatever reason rendering ball and stick models using POV-Ray doesn't seem to work, although I can render cartoon models using POV-Ray without a problem. I can save the ball and stick models in PNG format via the GUI without a problem though. This is the script I'm using to create the ball-and-stick models I'm attempting to render with POV-Ray: delete all load 2hyy.pdb1 hide everything h_add r. STI show sticks, r. STI show spheres, r. STI set stick_radius, .07 set sphere_scale, .18 set sphere_scale, .13, elem H set bg_rgb=[1, 1, 1] set stick_quality, 50 set sphere_quality, 4 color black, elem C and organic color red, elem O and organic color slate, elem N and organic color white, elem H and organic set stick_color, black set ray_trace_mode, 1 set ray_texture, 2 set antialias, 3 set ambient, 0.5 set spec_count, 5 set shininess, 50 set specular, 1 set reflect, .1 set dash_gap, 0 set dash_color, black set dash_gap, .15 set dash_length, .05 set dash_round_ends, 0 set dash_radius, .05 set valence, 2 set valence_size, 0.2 python preset.ball_and_stick(r. STI) python end orient r. STI and this is the PML script I use to render the model using POV-Ray: set ray_opaque_background, 0 png 2HYY_img0001.png, dpi=500, ray=1, width = 4000, height = 2325 This gives a blank transparent PNG output, namely this http://i.imgur.com/FYsDSCl.png. Thanks for your time, Brenton -- ___ 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] What legal license does PyMOL's logo available under?
Hi, I would like to know the legal licensing of PyMOL's logo (i.e., this one https://a.fsdn.com/allura/p/pymol/icon), as I would like to upload it to Wikimedia Commons. Thanks for your time, Brenton -- ___ 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 ball stick representation of imatinib in 2HYY
Hi, I recently read this reply (http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg13248.html) to another users' query on this list so I went to the PyMOL Wiki page hyperlinked in the answer and found this piece of code: preset.ball_and_stick(selection='all', mode=1) set_bond stick_color, white, selection, selection set_bond stick_radius, 0.14, selection, selection set sphere_scale, 0.25, selection show sticks, selection show spheres, selection I want to customize it such that the selection that is changed in representation from the cartoon style (which is the present style for the macromolecule I'd like it to stay the representation style for the macromolecule) to ball-and-stick style, is just het ID STI (i.e., the imatinib ligand) in 2HYY. Any ideas of how I might achieve this? Thanks for your time, Brenton -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF___ 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] APBS plugin not working on both Ubuntu Windows 7
Hi, pdb2pqr.py doesn't exist in the pdb2pqr tar.gz file (for either 2.0.0 or 1.8 versions; in a previous question I was advised to use the 1.8 version) and consequently APBS tools doesn't work. I have tried turning the pdb2pqr.py.in into pdb2pqr.py by removing the in extension, but the APBS failed to set up the grid after I did this. Is there any way around this? Thanks for your time, Brenton -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ 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] Labelling ligands and amino acids
Hi, I have skimmed the Label http://pymolwiki.org/index.php/Label page on PyMOL Wiki and it only appears to give examples about how to label specific atoms and not whole ligands or residues. See I'd like to label residue 403 as Ser403, ceftaroline's open form (het ID AI8) as Open CFT and ceftaroline (het ID 1W8) as CFT in the structure that has the PDB ID 3ZG0. I presently have the PyMOL code: delete all load 3zg0.pdb1 hide show cartoon # Colouring secondary structure set_color blues, [0.0196078,0.7607843,0.7607843] color red, ss h color yellow, ss s color blues, ss l+ show sticks, r. 1w8 label (r. 1w8), CFT show sticks, r. ai8 label (r. ai8), open-chain CFT show sticks, r. mur show sticks, resi 403 color green, resi 403 label (resi 403), Ser403 h_add set valence, 0.2 set_color orange, [1, 0.5, 0] set_color fluorine, [0.5625,0.875,0.3125] set_color chlorine, [0.12109375,0.9375,0.12109375] set_color sulfur, [1,1,0.18750] # Colouring elements #color black, elem c and resi 69 and not name c+n+o color black, elem c and organic #color blue, elem n and resi 69 and not name c+n+o color blue, elem n and organic #color white, elem h and resi 69 and not name c+n+o color white, elem h and organic #color red, elem o and resi 69 and not name c+n+o color red, elem o and organic #color orange, elem p and resi 69 and not name c+n+o color orange, elem p and organic #color fluorine, elem f and resi 69 and not name c+n+o color fluorine, elem f and organic #color chlorine, elem cl and resi 69 and not name c+n+o color chlorine, elem cl and organic color sulfur, elem s and organic # Colour backgrond white bg_color white remove solvent With the relevant code indented. The result was http://i.imgur.com/lXoZmQA.png. The problem, however, is that as you can see in this image this code doesn't give just a single, individual label for each of the two ligands and serine 403, rather it appears to label each individual atom in each of these three molecules of interest. So my question is how do I get just a single label for each molecule of interest and not for every atom inside these molecules. Thanks for your time, Brenton -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF___ 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] Displaying covalent bonds between amino acids (within protein) and ligand
Hi, In the structure that goes by the PDB ID 1PWC (RCSB PDB http://www.pdb.org/pdb/explore/explore.do?structureId=1PWC, PDBe www.ebi.ac.uk/pdbe-srv/view/entry/1pwc/summary.html, download link for bio assembly 1 http://www.pdb.org/pdb/files/1PWC.pdb1.gz, which I am using) PNM http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=PNM (open chain benzylpenicillin) is covalently bonded to residue 62 (a serine; I base this on molecular modelling I've done in Accelrys Discovery Studio Visualizer [ADSV] and knowledge this is how penicillins interact with this penicillin-binding protein) but in PyMOL this bonding isn't shown. Is there any way of rendering the serine (and only the serine, the rest of the protein I want in cartoon mode) in sticks format and showing the covalent bond between the serine and PNM? Thanks for your time, Brenton -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ 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] Zoom animation
Hi,
I'd like to create a set of transparent PNG frames, with each frame
being more and more zoomed in on the PNM-ser62 complex found within the
PDB structure 1PWC. This is the code I have so far:
set ray_opaque_background, 0
png Image0001.png, width= 2000, height= 1162, dpi=500, ray=1
python
for iin range(2,61):
cmd.zoom(r. pnm, 20)
cmd.png(rImage{:04d}.png.format(i), width=2000, height=1162, dpi=500,
ray=1)
python end
Running this just creates frame one (i.e., the one outside the python
loop). If you're wondering what made me think that this might work, well
this was based on a rotate-based animation script (the original script
had cmd.rotate('y',6) instead of cmd.zoom...) I have created based on
input from others on this mailing list.
Thanks for your time,
Brenton
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[PyMOL] Fwd: Location of pdb2pqr.py file for PyMOL use on Windows 7
Hi, I've had some trouble with the APBS tools plugin, please see the email below which I sent to the pdb2pqr-users list and I felt as I haven't received a response so far (granted I only sent it 2 hours ago) I felt I should forward this message to PyMOL-users too. Forwarded Message Subject:Location of pdb2pqr.py file for PyMOL use on Windows 7 Date: Thu, 26 Mar 2015 16:01:26 +1000 From: Brenton Horne brentonhorn...@gmail.com To: pdb2pqr-us...@lists.sourceforge.net Hi, I downloaded pdb2pqr-windows-bin64-2.0.0.zip http://jaist.dl.sourceforge.net/project/pdb2pqr/pdb2pqr/pdb2pqr-2.0.0/pdb2pqr-windows-bin64-2.0.0.zip, unzipped it and realized that pdb2pqr.py was missing from the zipped file directory (as I understand it pdb2pqr should be ready to go the way it is without running any msi/exe files?). Now I need a pdb2pqr.py python script in my PDB2PQR installation to point to in order for PyMOL to work for me (as running Set grid without it gives the error described below), so my question is, How do I get such a script or otherwise overcome this error? The PyMOL error described above was: /Error: could not import pdb2pqr, please check pdb2pqr.py location./ Thanks for your time, Brenton -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ 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] Colouring nucleic acids, without changing the colouring of amino acids
Hi, I've seen this (Example 1 on 3DNA http://www.pymolwiki.org/index.php/3DNA) and I noticed to colour each nucleic acid differently they used something like: set cartoon_color, green, resn G for each of the four different nucleic acids. When I ran this for 2XCT bio assembly 1 it coloured amino acids with the same single letter codes as the four nucleic acids (e.g., G for guanine [nucleic acid] and glycine [amino]) and I wanted to know how to run it just for nucleic acids. I thought that something like this for each chain containing nucleic acids: set cartoon_color, green, /2XCT//Eand resn G would do the trick but that would take forever seeing how 8 separate chains contain nucleic acids. While we're on this topic I'd also like to know how to colour the backbone and sugars via a more efficient method than doing something like this: color pink, /2XCT//Eand bb. for each chain containing nucleic acids. Thanks for your time, Brenton -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ 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] Fetching PDBs; how to load .cifs provided instead of .pdbs
Hi, I have noticed that for some PDBs wwPDB doesn't contain PDB files (e.g., 4V7Y http://www.rcsb.org/pdb/explore/explore.do?structureId=4V7Y), but rather they have mmCIF files instead and I was wondering if it was possible to get the fetch command to fetch these mmCIFs instead of PDBs. Now to be clear, I do understand how to load mmCIFs that I have downloaded manually from wwPDB by going to |File-Open...| but I'd like to know how to get PyMOL to fetch these files from wwPDB and load them. Thanks for your time, Brenton -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ 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] Removing chloride ions from CIF files
Hi, I've been loading a methylphenidate structure I created using crystallography data and it has a chloride ion I'd like to remove, how do I do this using PyMOL scripts? I tried remove [Cl] hoping it would do something similar to what it does for PDB files if Cl is replaced by a metal ion's symbol (e.g., Zn, or Mg). Thanks for your time, Brenton -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ 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 installation on Windows 7
Oh, I have something else. Running in command prompt in admin mode I receive this error when running these whl installation commands: Traceback (most recent call last): File C:\Python27\lib\runpy.py, line 162, in _run_module_as_main __main__, fname, loader, pkg_name) File C:\Python27\lib\runpy.py, line 72, in _run_code exec code in run_globals File C:\Python27\Scripts\pip2.exe\__main__.py, line 5, in module ImportError: No module named pip On 13/03/2015 9:04 PM, Brenton Horne wrote: Hi, I have tried installing PyMOL via pip wheel files (found here http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol) using python 2.7.9 and while no obvious errors occurred during the execution of the |pip install ...| commands I have no new files in |C:\Python27|, my python directory. I have allowed for the fact that pip for me is at |C:\Python27\Scripts\pip2.exe| instead of |C:\Python27\Scripts\pip.exe| like I understand it usually is, as far as adjusting the PYTHONPATH variable accordingly. Any ideas on how to install PyMOL on my 64 bit Windows 7 SP1 OS? I have VisualStudio 2010 installed on my PC if relevant. If you need any other details please ask! Thanks for your time, Brenton -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ 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 -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ 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 colouring specific chains according to secondary structure
Nvm I figured it out: |delete all|| ||fetch 2Y7Q|| ||as cartoon|| ||bg_color white|| || ||color pink, /2Y7Q//B|| ||color green, /2Y7Q//D|| || ||set_color blues, [0.0196078,0.7607843,0.7607843]|| || ||color red, 2Y7Q and segi and c. A and ss h|| ||color yellow, 2Y7Q and segi and c. A and ss s|| ||color blues, 2Y7Q and segi and c. A and ss l+| does the trick. On 5/03/2015 11:55 AM, Brenton Horne wrote: Hi, I'd like to colour chain A of 2Y7Q according to secondary structure but this code didn't work (where chain B D are coloured pink and green respectively, the background is white, the structure is rendered as cartoons, etc.): |delete all|| ||fetch 2Y7Q|| ||as cartoon|| ||bg_color white|| || ||color pink, /2Y7Q//B|| ||color green, /2Y7Q//D|| || ||set_color blues, [0.0196078,0.7607843,0.7607843]|| || ||color red, /2Y7Q//A/ss_h|| ||color yellow, /2Y7Q//A/ss_s|| ||color blues, /2Y7Q//A/ss_l+| Giving this output: http://i.imgur.com/7dc2yl6.png. I also tried |delete all||| |||fetch 2Y7Q||| |||as cartoon||| |||bg_color white||| |||color pink, /2Y7Q//B||| |||color green, /2Y7Q//D||| |||set_color blues, [0.0196078,0.7607843,0.7607843]||| |||color red, /2Y7Q//A/ ss h||| |||color yellow, /2Y7Q//A/ ss s||| |||color blues, /2Y7Q//A/ ss l+| and this just coloured every other chain according to the colour scheme at the end, with chain A coloured 'blues'. Thanks for your time, Brenton -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ 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 -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ 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 colouring specific chains according to secondary structure
Hi, I'd like to colour chain A of 2Y7Q according to secondary structure but this code didn't work (where chain B D are coloured pink and green respectively, the background is white, the structure is rendered as cartoons, etc.): |delete all|| ||fetch 2Y7Q|| ||as cartoon|| ||bg_color white|| || ||color pink, /2Y7Q//B|| ||color green, /2Y7Q//D|| || ||set_color blues, [0.0196078,0.7607843,0.7607843]|| || ||color red, /2Y7Q//A/ss_h|| ||color yellow, /2Y7Q//A/ss_s|| ||color blues, /2Y7Q//A/ss_l+| Giving this output: http://i.imgur.com/7dc2yl6.png. I also tried |delete all||| |||fetch 2Y7Q||| |||as cartoon||| |||bg_color white||| |||color pink, /2Y7Q//B||| |||color green, /2Y7Q//D||| |||set_color blues, [0.0196078,0.7607843,0.7607843]||| |||color red, /2Y7Q//A/ ss h||| |||color yellow, /2Y7Q//A/ ss s||| |||color blues, /2Y7Q//A/ ss l+| and this just coloured every other chain according to the colour scheme at the end, with chain A coloured 'blues'. Thanks for your time, Brenton -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ 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 syntax .properties file for SciTE
Hi, I'd like to know if anyone has a .properties file for the PyMOL syntax for use in SciTE. Currently I'm using python .properties for highlighting PyMOL code but as you's know PyMOL syntax isn't 100% consistent with python syntax. Thanks for your time, Brenton -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ 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] How to delete specific chains
Hi, I've got this pml code: |delete all|| ||fetch 1Z92, type=pdb1|| ||as cartoon|| ||bg_color white|| || ||color red, ss h|| ||color yellow, ss s|| ||color green, ss l+|| || ||delete /1Z92//A| But it doesn't delete chain A as I'd like it to. Any ideas of how I can delete chain A without removing any other parts of the structure? Thanks for your time, Brenton -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ 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] Embeddable version of PyMOL
Hi, PyMOL is probably my favourite 3D molecule viewer and I'm wondering if there's any way to embed it into HTML web pages (sort of like JSmol can) and if not is it possible it could be sometime in the foreseeable future? Thanks for your time, Brenton -- Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ 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] Selecting specific ligands for colouring
Hi, I know I must be getting annoying, although I must say this mailing list and its users have been very helpful for me so thank you all. My question this time is how do I select specific ligands? Like I am using PDB ID 2HYY and I'd like to set the imatinib (STI600) ligand as the only visible ligand, plus I'd like to colour it according to the CPK scheme, except with carbons coloured black. Now I've tried: select 2hyy/A/STI based on the Selection Algebra http://pymolwiki.org/index.php/Selection_Algebra page on PyMOL Wiki but this returned the result: Selector: selection sele defined with 0 atoms. ps. is there are any PDF document showing complete up-to-date command-line syntax for PyMOL because I think this will really help me. PyMOL Wiki I find generally only gives a snippet of the command-line syntax for a given topic. Plus I generally find the really general format of the syntax (e.g., show reprentation [,object] ) with the square brackets PyMOL sometimes shows is confusing to me, unless it's accompanied by an example of how that code appears for a specific example. Thanks for your time, Brenton -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net___ 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] Scripting attempts
Hi, I've been executing the pml script I wrote: set ray_opaque_background, 0 png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - imatinib\PyMOL movie\Image0001.png, dpi=300, ray=1 for i in range(2, 60) rotate y, 6 png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - imatinib\PyMOL movie\Image%4d.png, dpi=300, ray=1 The desired result from this script is a series of 60 transparent pngs taken at 6 degrees apart (rotated around the y axis) with name Image0001.png, Image0002.png, Image0003.png, ..., Image0060.png. Sadly however I only got two PNGs: Image0001.png and Image%4d.png. How do I overcome this problem? Thanks for your time, Brenton -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net ___ 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] eMovie extension
Hi eMovie isn't working for me on Ubuntu 14.04, and whenever I open the plugin manager I get the pop-up window, here http://imgur.com/jxJ94Jl. How do I overcome this? Thanks for your time, Brenton -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net ___ 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 png movie creation from command line
Hi, I'd like to know how to create a series of PNGs of customized width, height and dpi taken at a customizable angle between frames. I've tried using eMovie but I don't know how to set the image resolution for each frame using this extension. A command line-based way of creating these serial PNGs I think would be best with me, if it is possible. Thanks for your time, Brenton -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net ___ 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] Is it possible to write PNG images in PyMOL of higher resolution than the viewing window?
Hi, I'd like to know if it is possible to save PNG images of a structure that have a higher resolution (in terms of pixels, e.g., 4000 px wide as opposed to my usual of 1146 px wide). I ask this because I know that Accelrys DS Visualizer (if you're unfamiliar with this software it's another software capable of displaying 3D structures of biomolecules) can write PNG files of higher resolution than screen resolution and these images are often clearer when I upload them to my Wiki and I'm wondering if PyMOL is capable of producing similarly higher resolution images than screen resolution. If I'm not clear in my question, please do ask me to clarify. Thanks for your time, Brenton -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net ___ 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] Is it possible to set the number of frames in a movie?
Hi, I've just started using PyMOL and although I rather like the movie-making function I would like to know if it is possible to set the number of frames and the exact angle between frames (i.e., I usually rotate about the y axis in these movies I capture). Please keep in mind I am a noob when it comes to python scripting so please boil any instructions down to simple instructions. Thanks for your time, BRenton -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151iu=/4140/ostg.clktrk___ 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
