Re: [PyMOL] How to plot residu with a number 9999
Stephane, What I've done in these situations is broken the many-residue blocks (typically water) into different chainID's and segid's. Then select with by both residue number and segid (or chainID or both). That said, I don't think segid's are a part of the official pdb specification anymore (although pymol doesn't have a problem with them). As for getting around the 5-digit limit in overall atoms, I think different packages have different tricks, including * (not particularly useful) and hexadecimal (vmd/namd). Overall, this points out a glaring problem with fixed-width fields, but that's another discussion... Regards, David - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm -Original Message- From: Warren DeLano [mailto:war...@delsci.com] Sent: Monday, June 08, 2009 8:01 PM To: Stephane Abel; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] How to plot residu with a number Stephane, As per http://www.wwpdb.org/documentation/format32/sect9.html , the PDB residue identifier field is only four characters wide. So how could you possibly have a PDB file with residue identifiers larger than ? Cheers, Warren -Original Message- From: Stephane Abel [mailto:stephane.a...@cea.fr] Sent: Monday, June 08, 2009 7:30 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] How to plot residu with a number Hi pymol users It seems that the command select, residue xxx to plot residue xxx where xxx is greater than does not work in pymol version 0.99rc6 Indeed for a pdb file with ~ 13800 residue, if i use the command: select water1846, residue 1846 - the water molecule with the residue number 1846 is plotting But when i use the same command (say select water11100, residue 11100) for plotting the residue 11100 the previous command does not work How to tackle this problem. Thanks in advance for your help Stephane -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ 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 -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ 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 -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ 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 plot residu with a number 9999
Stephane, Okay, I see -- you're just spilling the top digit into the chain id. So for residue 10123, you can issue a selection like: zoom chain 1 and resi 0123 Looking over the code, I note that PyMOL has a hardcoded resi field of just four characters plus a null. Given how C compilers pack structs, I suspect we could extend that to 7 characters plus a null without adversely impacting PyMOL's memory use characteristics... Cheers, Warren -Original Message- From: ABEL Stephane 175950 [mailto:stephane.a...@cea.fr] Sent: Tuesday, June 09, 2009 12:34 AM To: Warren DeLano Subject: RE : [PyMOL] How to plot residu with a number Warren, Thank you for your response Indeed, you are right and this is a well known limitation of the pdb format. But as you can see with the file i join in this message obtained from a molecular dynamics software, you can also use the field 22 - 26 to extend the resSeq to 9 and this with pymol and rasmol. -- Stéphane Abel, PhD CEA Saclay DSV/IBITEC-S/SB2SM 91191 Saclay, FRANCE website: http://www.st-abel.com -- Message d'origine De: Warren DeLano [mailto:war...@delsci.com] Date: mar. 09/06/2009 02:01 À: ABEL Stephane 175950; pymol-users@lists.sourceforge.net Objet : RE: [PyMOL] How to plot residu with a number Stephane, As per http://www.wwpdb.org/documentation/format32/sect9.html , the PDB residue identifier field is only four characters wide. So how could you possibly have a PDB file with residue identifiers larger than ? Cheers, Warren -Original Message- From: Stephane Abel [mailto:stephane.a...@cea.fr] Sent: Monday, June 08, 2009 7:30 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] How to plot residu with a number Hi pymol users It seems that the command select, residue xxx to plot residue xxx where xxx is greater than does not work in pymol version 0.99rc6 Indeed for a pdb file with ~ 13800 residue, if i use the command: select water1846, residue 1846 - the water molecule with the residue number 1846 is plotting But when i use the same command (say select water11100, residue 11100) for plotting the residue 11100 the previous command does not work How to tackle this problem. Thanks in advance for your help Stephane -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ 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-users Digest, Vol 37, Issue 7
PyMOLers,
This example was just too cool not to be made into a script. See
http://www.pymolwiki.org/index.php/FindSurfaceResidues
-- Jason
Message: 3
Date: Mon, 8 Jun 2009 19:01:01 -0700
From: Warren DeLano war...@delsci.com
Subject: Re: [PyMOL] Hi all...
To: Yasser Almeida Hernandez pedro...@fenhi.uh.cu,
pymol-users@lists.sourceforge.net
Message-ID:
896b75251ba19745a529b1b867893fa50eb...@planet.delsci.local
Content-Type: text/plain; charset=US-ASCII
As for the your general question: can you import pymol; from pymol
import cmd; pymol.finish_launching(); etc?
Answer 1: Yes, if you manually compile PyMOL open-source code into an
existing Python interpreter.
Or
Answer 2: Yes, if you run your Python script using PyMOL's built-in
Python interpreter (launch PyMOL as follows):
./pymol your-script.py # with full 3D GUI
./pymol -qc your-script.py # command-line only (in a terminal)
Or
Answer 3: Yes, if you call your Python script from a PyMOL script via
the run or spawn commands inside PyMOL.
However,
Answer 4: No, if you want precompiled PyMOL build to work with an
external precompiled Python build. This approach has proved impractical
due unavoidable application binary interface (ABI) version mismatches
between PyMOL, Python, and the host environment.
As for your specific question, this is something you could do with a
plain old script without even introducing the complexity of Python:
load $TUT/1hpv.pdb, query
remove not polymer
create tmp, query
set dot_solvent
get_area tmp, load_b=1
# threshold on what one considers an exposed atom (in A**2):
remove tmp and b2.5
tmp_dict = {}
iterate tmp, tmp_dict[(chain,resv)]=1
select exposed
exposed = tmp_dict.keys()
exposed.sort()
print Solvent exposed residues (chain,residue):
for res in exposed: print res
select exposed, query in tmp
dele tmp
# visual confirmation
color white
color red, byres exposed
set sphere_solvent
as spheres
orient
Cheers,
Warren
--
Jason Vertrees, PhD
Dartmouth College : j...@cs.dartmouth.edu
Boston University : jas...@bu.edu
PyMOLWiki : http://www.pymolwiki.org/
--
Crystal Reports - New Free Runtime and 30 Day Trial
Check out the new simplified licensing option that enables unlimited
royalty-free distribution of the report engine for externally facing
server and web deployment.
http://p.sf.net/sfu/businessobjects
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[PyMOL] Subject: Re: Hi all...
PyMOLers,
This example was just too cool not to be made into a script. See
http://www.pymolwiki.org/index.php/FindSurfaceResidues
-- Jason
Message: 3
Date: Mon, 8 Jun 2009 19:01:01 -0700
From: Warren DeLano war...@delsci.com
Subject: Re: [PyMOL] Hi all...
To: Yasser Almeida Hernandez pedro...@fenhi.uh.cu,
pymol-users@lists.sourceforge.net
Message-ID:
896b75251ba19745a529b1b867893fa50eb...@planet.delsci.local
Content-Type: text/plain; charset=US-ASCII
As for the your general question: can you import pymol; from pymol
import cmd; pymol.finish_launching(); etc?
Answer 1: Yes, if you manually compile PyMOL open-source code into an
existing Python interpreter.
Or
Answer 2: Yes, if you run your Python script using PyMOL's built-in
Python interpreter (launch PyMOL as follows):
./pymol your-script.py # with full 3D GUI
./pymol -qc your-script.py # command-line only (in a terminal)
Or
Answer 3: Yes, if you call your Python script from a PyMOL script via
the run or spawn commands inside PyMOL.
However,
Answer 4: No, if you want precompiled PyMOL build to work with an
external precompiled Python build. This approach has proved impractical
due unavoidable application binary interface (ABI) version mismatches
between PyMOL, Python, and the host environment.
As for your specific question, this is something you could do with a
plain old script without even introducing the complexity of Python:
load $TUT/1hpv.pdb, query
remove not polymer
create tmp, query
set dot_solvent
get_area tmp, load_b=1
# threshold on what one considers an exposed atom (in A**2):
remove tmp and b2.5
tmp_dict = {}
iterate tmp, tmp_dict[(chain,resv)]=1
select exposed
exposed = tmp_dict.keys()
exposed.sort()
print Solvent exposed residues (chain,residue):
for res in exposed: print res
select exposed, query in tmp
dele tmp
# visual confirmation
color white
color red, byres exposed
set sphere_solvent
as spheres
orient
Cheers,
Warren
--
Jason Vertrees, PhD
Dartmouth College : j...@cs.dartmouth.edu
Boston University : jas...@bu.edu
PyMOLWiki : http://www.pymolwiki.org/
--
Crystal Reports - New Free Runtime and 30 Day Trial
Check out the new simplified licensing option that enables unlimited
royalty-free distribution of the report engine for externally facing
server and web deployment.
http://p.sf.net/sfu/businessobjects
___
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 plot residu with a number 9999
Whoops, I misread my own code: In fact, PyMOL already supports 5-character residue identifiers! Here's how you use them, assuming a PDB file where the resi field spills into chain: load your_file.pdb alter all, resi=chain+resi sort # and off you go indicate resi 1: zoom resi 10123 Cheers, Warren -Original Message- From: Warren DeLano Sent: Tuesday, June 09, 2009 12:26 PM To: ABEL Stephane 175950 Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] How to plot residu with a number Stephane, Okay, I see -- you're just spilling the top digit into the chain id. So for residue 10123, you can issue a selection like: zoom chain 1 and resi 0123 Looking over the code, I note that PyMOL has a hardcoded resi field of just four characters plus a null. Given how C compilers pack structs, I suspect we could extend that to 7 characters plus a null without adversely impacting PyMOL's memory use characteristics... Cheers, Warren -Original Message- From: ABEL Stephane 175950 [mailto:stephane.a...@cea.fr] Sent: Tuesday, June 09, 2009 12:34 AM To: Warren DeLano Subject: RE : [PyMOL] How to plot residu with a number Warren, Thank you for your response Indeed, you are right and this is a well known limitation of the pdb format. But as you can see with the file i join in this message obtained from a molecular dynamics software, you can also use the field 22 - 26 to extend the resSeq to 9 and this with pymol and rasmol. -- Stéphane Abel, PhD CEA Saclay DSV/IBITEC-S/SB2SM 91191 Saclay, FRANCE website: http://www.st-abel.com -- Message d'origine De: Warren DeLano [mailto:war...@delsci.com] Date: mar. 09/06/2009 02:01 À: ABEL Stephane 175950; pymol-users@lists.sourceforge.net Objet : RE: [PyMOL] How to plot residu with a number Stephane, As per http://www.wwpdb.org/documentation/format32/sect9.html , the PDB residue identifier field is only four characters wide. So how could you possibly have a PDB file with residue identifiers larger than ? Cheers, Warren -Original Message- From: Stephane Abel [mailto:stephane.a...@cea.fr] Sent: Monday, June 08, 2009 7:30 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] How to plot residu with a number Hi pymol users It seems that the command select, residue xxx to plot residue xxx where xxx is greater than does not work in pymol version 0.99rc6 Indeed for a pdb file with ~ 13800 residue, if i use the command: select water1846, residue 1846 - the water molecule with the residue number 1846 is plotting But when i use the same command (say select water11100, residue 11100) for plotting the residue 11100 the previous command does not work How to tackle this problem. Thanks in advance for your help Stephane -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ 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 -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ 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
