Re: [PyMOL] Selection of chains based on PDB header
Dear Julian
You can also try the PDB plugin which places each chain into a selection
automatically for you.
https://pymolwiki.org/index.php/PDB_plugin
Regards
John
PDBe
On 12/06/2017 17:10, Thomas Holder wrote:
Hi Julian,
A one-liner to create chain selections looks like this:
for c in cmd.get_chains(): cmd.select("chain_" + c, "chain " + c)
PyMOL doesn't provide access to the PDB header fields. In principle PyMOL
provides a way to access everything inside mmCIF files, see:
https://pymolwiki.org/index.php/Cif_keepinmemory
However, instead of doing this, I recommend to use the PDBe web API which provides the
data in a friendly JSON data structure. I've attached a Python script which creates
molecule (or chain) selections for 5n61 as an example. I recommend to load PDB structures
from mmCIF or MMTF format, which not only have chain identifiers, but also molecule
identifiers ("segi" field in PyMOL).
Hope that helps.
Cheers,
Thomas
On Jun 12, 2017, at 12:21 PM, Julian Reitz <julianr1...@gmail.com> wrote:
Dear all,
I have a pdb-file with multiple chains (5N61).
Is there an easy way to create selections for all the chains that are defined
in the pdb-header (A to U) without doing it manually for every chain (select A,
chain A)?
Is it also possible to use the MOLECULE information from the header to name the
selections?
Thank you in advance,
Julian
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] Pymol crash when raytracing empty graphics
Dear Spencer It is possible to work this out using the PDBe API. for our interactive API see: http://www.ebi.ac.uk/pdbe/api/doc/ The molecules url will give you this information: http://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/1a1q entity 1 has ca_p_only: true, which means cartoon will not work for this chain - so we use ribbon instead with the command pymol.cmd.set(ribbon_trace_atoms, 1) This test allows us to make images such as those shown on the entry page for 1a1q at PDBe http://www.ebi.ac.uk/pdbe/entry/pdb/1a1q The images are made with pymol (currently 1.6, but also works in 1.7) Regards John PDBe On Monday 17 August 2015 15:40:14 Spencer Bliven wrote: We have a pipeline that uses pymol to create images using the headless command line interface. I've discovered that PyMOL 1.7.4 and 1.7.6 (at least) crash if you try to ray-trace an empty viewport. Example: pymol -q -c -d 'fetch 1a1q,async=0;as cartoon;ray' This particular example only has CA atoms, so the cartoon mode doesn't show anything. In interactive mode I would `set cartoon_trace_atoms,1` but when batch processing there isn't a good way of detecting whether anything is showing or not. The error is: *** glibc detected *** /home/user/software/packages/pymol-v1.7.4.4/pymol.exe: double free or corruption (out): 0x7f11f8744f40 *** I've reproduced the error on Redhat 6 and Ubuntu 14.04, with PyMOL 1.7.4.1 through 1.7.6.3. Attached is a stack trace. Any suggestions on ensuring that there are some polygons in frame would also be appreciated. Say, if there was a way to detect that cartoon would fail so that I can switch to a lines or nonbonded representation (I wish that was the default fallback for cartoon). Thanks, Spencer -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 -- ___ 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] shadows on floors
I am try to create a picture with shadows visible on the background of the image. I have so far managed to create a floor, following the example of David Cooper (movies section of pymol web site) and create shadows on a grey and blue backgound. Is this the best way of creating a background, or is there a better way? But, I don't seem to be able to make a white background with shadows on (rgb 1,1,1 is white?). Is this possible? Is it possible to create your own background colours (set_color doesn't seem to work in the floor.py script in the example by David Cooper). Also as a side note, what are the rgb codes that pymol uses, are they standard 0 to 1 (the same as molscript) or 0 to 255? Using some of the rgb codes from molscript only seems to produce a grey background. Thank you John -- John Berrisford Department of Molecular Biology and Biotechnology University of Sheffield email: j.berrisf...@sheffield.ac.uk
[PyMOL] sphere sizes
I am trying to create a picture containing a metal ion and water molecules. The problem that I am having is that I wish to display them both as spheres, but of different sizes. Pymol (version 0.93 and 0.95 beta 11 ) seems to only use the last sphere size command i.e. set sphere_scale, 0.1 in the script and effectively ignore any previous sphere_scale command. Am I doing something wrong and there is another, better way of doing this, for example linking the size command to an object? I have been so far unable to work out how to do this. Thanks John -- John Berrisford Department of Molecular Biology and Biotechnology University of Sheffield email: j.berrisf...@sheffield.ac.uk
RE: [PyMOL] drawing hydrogen bonds or dashes
Thanks that works fine apart from one thing: I wish to display lines between 97AOE1 and MN in two overlapped structures, with identical chain identification, in two different colours. Using the below command draws two lines in the same colour. Is there a way a specifying a line between the two below atoms only within a specific pdb file (defined as an object). eg line between A97OE1 and MN only within object e4_final. I hope this is clear thanks John Quoting Warren DeLano war...@delanoscientific.com: John, Welcome to PyMOL! I wish to do the equivalent to the following molscript command line position res-atom A97 OE1 to position res-atom M200 MN; dist my_line, a/97/OE1, M/200/MN hide labels Also note that PyMOL can draw hydrogen-bonds automatically using its limited chemical intuition according to the global h_bond_... settings. (Sorry guys, that isn't documented -- I am thinking about creating a new command for it since dist isn't the right place for this). dist hbnd, all, all, mode=2 hide labels (But I don't think that will help with MN.) If you don't want dashes, then set dash_length, 3 set dash_gap, 0 Seems to work for me... Cheers, Warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of John Berrisford Sent: Thursday, February 19, 2004 10:09 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] drawing hydrogen bonds or dashes I have searched the manual and forum and cannot find how to draw a hydrogen bond between two specific atoms. I wish to do the equivalent to the following molscript command line position res-atom A97 OE1 to position res-atom M200 MN; which draws a line between two atoms A97 OE1 and Mn200. So not a hydrogen bond but a specific line. Is this possible in pymol? I have read posts on changing the thickness of a dash and the number of dashes in a line. But none on how to draw the line. Can anyone help me, i'm a new user by the way! thanks John --- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356alloc_id=3438op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- John Berrisford Department of Molecular Biology and Biotechnology University of Sheffield email: j.berrisf...@sheffield.ac.uk
[PyMOL] drawing hydrogen bonds or dashes
I have searched the manual and forum and cannot find how to draw a hydrogen bond between two specific atoms. I wish to do the equivalent to the following molscript command line position res-atom A97 OE1 to position res-atom M200 MN; which draws a line between two atoms A97 OE1 and Mn200. So not a hydrogen bond but a specific line. Is this possible in pymol? I have read posts on changing the thickness of a dash and the number of dashes in a line. But none on how to draw the line. Can anyone help me, i'm a new user by the way! thanks John
[PyMOL] selecting multiple atoms ie oxygen
I wish to select multiple oxygens (labelled O1, O2 etc.. within my pdb file) and colour them red for example. Is there any easy way of doing this other than typing out a list of all the oxygens I wish to select? eg. color red, (5paa and (name o1+o1a+o2+o3+o4+o5+o1p+o2p+o3p)) I know in molscript its posible to use a o* label to select all oxygens, is such a switch possible in pymol. It doesn't work, or I am using the wrong syntax if its possible. Any thoughts would be appreciated. John
