[PyMOL] arranging atom records in pdb file by resid
Dear PyMOL users/developers, Is there any way to rearrange the atom records in a .pdb file according to their residue ID? I have run Vina with flexible sidechains and then concatenated the rigid receptor part with the sidechain conformations for each pose. That resulted to .pdb files where the backbone atoms (apart from Ca) occur in the correct order but the flexible sidechain atoms are at the end of the file. That leads to some problems in visualization and analysis of the protein-ligand complexes that I'd like to overcome. If anyone know how to fix that problem either with PyMOL or any other program please let me know. thanks, Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with 2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1___ 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] arranging atom records in pdb file by resid
Hi Thomas,
Probably something like this should do something close to what you need:
sed -n '/^\(ATOM\|HETATM\)/s/^.\{16\}\(.\{10\}\)/\1 \0/p' file.pdb | sort
-n -k 3 | cut -b 11-
Hope it helps,
Tsjerk
On Thu, May 30, 2013 at 10:21 AM, Thomas Evangelidis teva...@gmail.comwrote:
Dear PyMOL users/developers,
Is there any way to rearrange the atom records in a .pdb file according to
their residue ID? I have run Vina with flexible sidechains and then
concatenated the rigid receptor part with the sidechain conformations for
each pose. That resulted to .pdb files where the backbone atoms (apart from
Ca) occur in the correct order but the flexible sidechain atoms are at the
end of the file. That leads to some problems in visualization and analysis
of the protein-ligand complexes that I'd like to overcome. If anyone know
how to fix that problem either with PyMOL or any other program please let
me know.
thanks,
Thomas
--
==
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tev...@pharm.uoa.gr
teva...@gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
--
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[PyMOL] how to get cealign outputs for mulitple structures
Hi all, can anyone suggest a straightforward way of collecting the cealign output in bulk, (RMS, #atoms compared), using alignto doesn't even print this to screen (I tried adjusting quiet=, to no avail). thanks in advance jacob https://owa.einstein.yu.edu/owa/?ae=Itema=Opent=IPM.Noteid=RgDDT2ZJXulBTI8H5G%2fACk3UBwBPSkr8RdqeRa4tSfsjXcRlSCziAABPSkr8RdqeRa4tSfsjXcRlAAAPdWIns=Draftpspid=_1369930182703_402002554# https://owa.einstein.yu.edu/owa/?ae=Itema=Opent=IPM.Noteid=RgDDT2ZJXulBTI8H5G%2fACk3UBwBPSkr8RdqeRa4tSfsjXcRlSCziAABPSkr8RdqeRa4tSfsjXcRlAAAPdWIns=Draftpspid=_1369930182703_402002554# -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with 2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1___ 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 cealign outputs for mulitple structures
Hi Jacob, Use the result from cmd.cealign and an alignment object. Here's an example: # fetch two proteins fetch 1cll 1ggz, async=0 # use a python block python # cealign the two structures and create a corresponding alignment object result = cmd.cealign(1cll, 1ggz, object=aln) # print out the values from the result print result.keys() for key in result: print %s: %s % (key, result[key]) # end the python block python end # now access those atoms in the alignment select 1cll and aln # or count the atoms in 1ggz and aln print cmd.count_atoms(1ggz and aln) Cheers, -- Jason On Thu, May 30, 2013 at 2:07 PM, Jacob Pessin jacob.pes...@einstein.yu.eduwrote: Hi all, can anyone suggest a straightforward way of collecting the cealign output in bulk, (RMS, #atoms compared), using alignto doesn't even print this to screen (I tried adjusting quiet=, to no avail). thanks in advance jacob https://owa.einstein.yu.edu/owa/?ae=Itema=Opent=IPM.Noteid=RgDDT2ZJXulBTI8H5G%2fACk3UBwBPSkr8RdqeRa4tSfsjXcRlSCziAABPSkr8RdqeRa4tSfsjXcRlAAAPdWIns=Draftpspid=_1369930182703_402002554# https://owa.einstein.yu.edu/owa/?ae=Itema=Opent=IPM.Noteid=RgDDT2ZJXulBTI8H5G%2fACk3UBwBPSkr8RdqeRa4tSfsjXcRlSCziAABPSkr8RdqeRa4tSfsjXcRlAAAPdWIns=Draftpspid=_1369930182703_402002554# -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with 2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1 ___ 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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with 2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1___ 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
