Re: [ccp4bb] Alignment software
Another alignment tool worth to keep an eye on is this one: http://foldit.wikia.com/wiki/Alignment_Tool They are still debugging, but the plan is to release a standalone version after CASP9. Or at least a version that runs in a standalone FoldIt version. On Tue, May 25, 2010 at 15:18, Victor Alves vdal...@fmv.utl.pt wrote: Hi Charlie I am so sorry I assumed development had halted, but I'm glad one of the authors of ALINE has stepped in to restore the truth, and even more that ALINE is still being taken care of. Hopefully those needed funds will materialize, for your sake and also for the benefit of all the scientific community. I will e-mail you some suggestions. Cheers, Victor Alves __ VICTOR DIOGO ALVES, DVM PhD Professor Auxiliar Faculdade de Medicina Veterinária UTL - Lisboa __ -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Charlie Bond Sent: terça-feira, 25 de Maio de 2010 4:48 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Alignment software Hi Victor, Thanks for recommending ALINE. It is not exactly true that development has stopped. It is just glacially slow as funding for such utilities is not easily obtained! Recommendations for improvements (to improve that potential) are well-received and a keen user can write their own plug-ins to achieve new functionality. Cheers, Charlie Victor Alves wrote: Hi Mohd You can also check: ALINE (An Extensible WYSIWYG Protein Sequence Alignment Editor for Publication Quality Figures) http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/ It’s quite nice and has a lot of potential, although unfortunately it seems that development of the software as stopped :-( Cheers Victor Alves *From:* CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] *On Behalf Of *Salameh, Mohd A., Ph.D. *Sent:* sexta-feira, 21 de Maio de 2010 16:11 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Alignment software Dear All, I’m trying to prepare an alignment figure of 2 proteins that highlight conserved and similar residues and probably secondary structures; I will greatly appreciate it if anybody can recommend a software that I can use. Thanks, Mohd -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310 35 Stirling Highway Crawley WA 6009 Australia charles.b...@uwa.edu.au +61 8 6488 4406
Re: [ccp4bb] Alignment software
Another tool you can use is RAPIDO (http://webapps.embl-hamburg.de/rapido). It identifies rigid bodies between the two structures and already produces pyMol scripts for the superposition both on the entire structure and on the single rigid bodies. A more complete list of the tools you can use can be found here: http://en.wikipedia.org/wiki/Structural_alignment_software
Re: [ccp4bb] Alignment software
Thanks Roger, that worked perfectly! I'll try and have fun with aline now. ciao, s On May 25, 2010, at 7:56 PM, Roger Dodd wrote: Hi there, I just got this working a couple of days ago under Mac OS X 10.6.3. I manually compiled and installed Perl-Tk from CPAN. Steps taken: 1. Download and ungzip / untar: http://search.cpan.org/CPAN/authors/id/S/SR/SREZIC/Tk-804.028_501.tar.gz (the newer -503 version didn't work) 2. Change into the directory 3. Execute perl Makefile.PL 4. make 5. make test 6. sudo make install Hopefully that should get things working. Cheers, Roger On 25 May 2010 17:50, Sebastiano Pasqualato sebastiano.pasqual...@ifom-ieo-campus.it wrote: Hi there, I remember a friend of mine showing me Aline, and it looked very nice. However, I can't make it work on my MacBook Pro (Mac OS X 10.6.3). With respect to the instruction I found on the website, I had to change the export lines to be added to the .bashrc in order not to get error messages. That's how I added the path info: export ALINEHOME='/sw64/share/xtal/aline_011208' export PATH=$PATH:$ALINEHOME/bin however, I still get an error while trying to run aline: s...@host005:~ aline Can't locate Tk.pm in @INC (@INC contains: /sw64/lib/perl5 /sw64/lib/perl5/darwin /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0 .) at /sw64/share/xtal/aline_011208/bin/aline line 37. BEGIN failed--compilation aborted at /sw64/share/xtal/aline_011208/bin/aline line 37. s...@host005:~ I even tried with the perl -MCPAN -e 'install Tk' command, as suggested by the website, but nothing changed. Any idea of what's wrong here? Thanks a lot for the tips, ciao s On May 25, 2010, at 5:47 AM, Charlie Bond wrote: Hi Victor, Thanks for recommending ALINE. It is not exactly true that development has stopped. It is just glacially slow as funding for such utilities is not easily obtained! Recommendations for improvements (to improve that potential) are well-received and a keen user can write their own plug-ins to achieve new functionality. Cheers, Charlie Victor Alves wrote: Hi Mohd You can also check: ALINE (An Extensible WYSIWYG Protein Sequence Alignment Editor for Publication Quality Figures) http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/ It’s quite nice and has a lot of potential, although unfortunately it seems that development of the software as stopped :-( Cheers Victor Alves *From:* CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] *On Behalf Of *Salameh, Mohd A., Ph.D. *Sent:* sexta-feira, 21 de Maio de 2010 16:11 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Alignment software Dear All, I’m trying to prepare an alignment figure of 2 proteins that highlight conserved and similar residues and probably secondary structures; I will greatly appreciate it if anybody can recommend a software that I can use. Thanks, Mohd -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310 35 Stirling Highway Crawley WA 6009 Australia charles.b...@uwa.edu.au +61 8 6488 4406 -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 9437 5990 -- Roger B. Dodd, PhD. Cambridge Institute for Medical Research Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY UK -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 9437 5990
Re: [ccp4bb] How to calculate real-space CC by section?
You might find some useful examples in $CCP4/examples/unix/runnable
OVERLAPMAP is used in mapcorrelation_procedures, overlapmap.exam,
waterpeaks.
As I understand it, CORR SECT does a map correlation by map section, so
you get a single CC value per map section.
This mode does not use MAPIN3, and doesn't use atom or residue
information. So yes, it will ignore the CHAIN keyword.
section refers to map section:
Number of columns, rows, sections ... 96 152 17
and not a section of your atomic model.
HTH
Martyn
On Tue, 2010-05-25 at 23:51 -0400, Hailiang Zhang wrote:
Hi,
I am working on a real space correlation on a specif protein section using
CCP4 OVERLAPMAP. I am using the following scripts, not sure whether it is
good or not (didn't find in OVERLAPMAP documentation).
overlapmap \
mapin1 ${PDB}-1.map\
mapin2 ${PDB}-2.map\
mapin3 ${PDB}-mask.map \
eof
CORR SECT
CHAIN A $START $END
END
There is no error message, but the results make no difference no matter
how I change $START and $END. I am not sure whether the above script is
ok.
By the way, more importantly to me, if corr sect works at all, will it
print out a single CC value by integrating over the WHOLE region define by
the section range?
Thanks!
Best Regards, Hailiang
--
***
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
* Fax: +44 1925 603634Skype name: martyn.winn *
* URL: http://www.ccp4.ac.uk/martyn/ *
***
Re: [ccp4bb] Structure Based Sequence Alignment
Muhammed bashir Khan wrote: Dear All; Can some body tell me a website for structure based sequence alignment, which can also pin point the similar and identical residues in different colors. regards Bashir PISA does just this - go to the ebi web site and select pisa
Re: [ccp4bb] how to read the ascii map converted by MAPTONA4 and MAPEXCHANGE
mapdump does this if you select the right flags. But as Ian says you will get a LOT of numbers. You dont say why you want this information, but if it is to find the electron density at an atom site overlapmap will do that if you ask for real space rfactor eleanor Hailiang Zhang wrote: Hi, I wanted to convert a binary ccp4 map file to a readable format so that I can retrieve the electron density at each real space grid point. Just tried MAPTONA4 and MAPEXCHANGE, but the resulting ascii file are not readable, and I didn't find any documentataion about how to read them. Could somebody give me any hint? Thanks a lot! Best Regards, Hailiang
Re: [ccp4bb] How to calculate real-space CC by section?
If you ask for CORR SECTion then overlapmap does just that - the CC will
have a certain value for each section regardless of the CHAIN
parameters. If you want correlation residue by residue you must ask for
CORR RESI
As someone said - a lousy model will give poor CCs even if the map is
brilliant..
But once your refinement is finished it is intresting to go back and
check the CC of the initial maps.
There is a belief that you need a CC of 0.5 to be able to build the
structure but different problems and different builders achieve
different results..
Eleanor
Hailiang Zhang wrote:
Hi,
I am working on a real space correlation on a specif protein section using
CCP4 OVERLAPMAP. I am using the following scripts, not sure whether it is
good or not (didn't find in OVERLAPMAP documentation).
overlapmap \
mapin1 ${PDB}-1.map\
mapin2 ${PDB}-2.map\
mapin3 ${PDB}-mask.map \
eof
CORR SECT
CHAIN A $START $END
END
There is no error message, but the results make no difference no matter
how I change $START and $END. I am not sure whether the above script is
ok.
By the way, more importantly to me, if corr sect works at all, will it
print out a single CC value by integrating over the WHOLE region define by
the section range?
Thanks!
Best Regards, Hailiang
[ccp4bb] voltage gated Na channel
Does anyone know of the existence of a structure for a voltage gated Na (not K) channel? Rex Palmer Birkbeck College, London
Re: [ccp4bb] Structure Based Sequence Alignment
I believe SSM does just that: http://www.ebi.ac.uk/msd-srv/ssm/ Eugene On Tue, May 25, 2010 at 7:39 PM, Muhammed bashir Khan muhammad.bashir.k...@univie.ac.at wrote: Dear All; Can some body tell me a website for structure based sequence alignment, which can also pin point the similar and identical residues in different colors. regards Bashir -- Muhammad Bashir Khan Department for Biomolecular Structural Chemistry Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria Phone: +43(1)427752224 Fax: +43(1)42779522
[ccp4bb] BSA
Dear All, I am trying to calculate BSA (Buried surface area) for a protein complex. I am using CCP4 AreaIMol. I used Accessible surface area module and calculate areas for protein atoms only I know that the buried surface area (BSA) can be calculated as: BSA = ASA(A) + ASA(B) - ASA(AB) when two proteins A and B form a complex AB So when I run areaIMol for complex AB using AB.pdb, I get Total area of chain A Total area of chain A Total area Total contact area of chain A Total contact area of chain A Total contact area So, How do I get my BSA? Do I need to split PDB in to individual chains to get Accessible surface area for each chain [ ASA(A) and ASA(B)]? Is the total area I got above is the ASA (AB)? Are there are any applications which could help get BSA PISA server giver ASA for each interface and total, so how could I use them to calculate BSA? Thanks in advance Yogi
Re: [ccp4bb] BSA
You should take a look at DIFFMODE COMPARE keyword in AREAIMOL manual, it allows for buried surface area calculation (you have to prepare the two pdb files with complex and receptor only). If you can easily use command line and scripts (i.e. you are running CCP4 on non-micro$oft OS), try the following script. It takes three command line parameters: the name of the pdb file with complex structure, and two chain IDs (for receptor and ligand). Notice that if your current directory contains files named foo1.pdb and foo2.pdb, they will be replaced by the script and subsequently deleted. --- #!/usr/bin/env bash pdbset xyzin $1 xyzout foo2.pdb eof /dev/null select chain $2 $3 eof pdbset xyzin $1 xyzout foo1.pdb eof /dev/null select chain $2 eof areaimol xyzin foo2.pdb xyzin2 foo1.pdb eof | \ grep 'TOTAL AREA DIFFERENCE' | cut -d: -f 2 DIFFMODE COMPARE MODE NOHOH SMODE OFF REPORT CONTACT YES RESAREA NO PNTDEN 10 PROBE 1.4 END eof rm foo1.pdb rm foo2.pdb --- On Wed, 2010-05-26 at 08:45 -0400, Sollepura Yogesha wrote: Dear All, I am trying to calculate BSA (Buried surface area) for a protein complex. I am using CCP4 AreaIMol. I used Accessible surface area module and calculate areas for protein atoms only I know that the buried surface area (BSA) can be calculated as: BSA = ASA(A) + ASA(B) - ASA(AB) when two proteins A and B form a complex AB So when I run areaIMol for complex AB using AB.pdb, I get Total area of chain A Total area of chain A Total area Total contact area of chain A Total contact area of chain A Total contact area So, How do I get my BSA? Do I need to split PDB in to individual chains to get Accessible surface area for each chain [ ASA(A) and ASA(B)]? Is the total area I got above is the ASA (AB)? Are there are any applications which could help get BSA PISA server giver ASA for each interface and total, so how could I use them to calculate BSA? Thanks in advance Yogi -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
Re: [ccp4bb] BSA
PISA's interface area is 1/2 of sum BSAs for the interfacing structures. If you go to interface details, you also get total area of structures and their individual BSAs. The latter I should think would be an overinterpretation if used. Eugene. On Wed, May 26, 2010 at 1:45 PM, Sollepura Yogesha yoge...@scripps.edu wrote: Dear All, I am trying to calculate BSA (Buried surface area) for a protein complex. I am using CCP4 AreaIMol. I used Accessible surface area module and calculate areas for protein atoms only I know that the buried surface area (BSA) can be calculated as: BSA = ASA(A) + ASA(B) - ASA(AB) when two proteins A and B form a complex AB So when I run areaIMol for complex AB using AB.pdb, I get Total area of chain A Total area of chain A Total area Total contact area of chain A Total contact area of chain A Total contact area So, How do I get my BSA? Do I need to split PDB in to individual chains to get Accessible surface area for each chain [ ASA(A) and ASA(B)]? Is the total area I got above is the ASA (AB)? Are there are any applications which could help get BSA PISA server giver ASA for each interface and total, so how could I use them to calculate BSA? Thanks in advance Yogi
[ccp4bb] Protein-DNA complex crystallisation
Hello all I am novice to this field and trying to crystallize a protein-protein complex verses DNA i.e a ternary complex of protein complex and DNA, which stochiometry is 2:!. I am wondering 1-what should be the DNA and protein ratio for the ternary complex like this typically for binary complex it is taken as 1.2 :1. 2- what should be the minimum concentation of DNA in the crystallization drop while protein-DNA complex (binary complex of protein-DNA) crystallization. similary what care should be taken for the ternary complex crystallisation. 3- What are the screen would be better to start the screening of crystallisation of the complex. 4- Whether crystallisation under oil could be done for the complexes or hanging drop would be better than the crystallisation under oil in this concern. I would really apprecitae the suggestions. Thanks in advance thomas
Re: [ccp4bb] voltage gated Na channel
Dear Rex, It might still be while before a structure of a full-length voltage-gated sodium channel (or voltage-gated calcium channel) comes along. Keep an eye on the NaChBac channel (originating from Bacillus species), as this prokaryotic sodium-selective channel will likely be the first to represent the sodium channel family. (Science.http://www.ncbi.nlm.nih.gov/pubmed/11743207 2001 ;294,2372-2375) There are structures of small cytoplasmic loop segments (PDB ID 2KAV, 1BYY, 1QG9), but these won't tell you anything about sodium selectivity. cheers Filip Van Petegem On Wed, May 26, 2010 at 4:50 AM, Rex Palmer rex.pal...@btinternet.comwrote: Does anyone know of the existence of a structure for a voltage gated Na (not K) channel? Rex Palmer Birkbeck College, London -- Filip Van Petegem, PhD Assistant Professor The University of British Columbia Dept. of Biochemistry and Molecular Biology 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 email: filip.vanpete...@gmail.com http://crg.ubc.ca/VanPetegem/
Re: [ccp4bb] How to calculate real-space CC by section?
I see. It is like the CC for each slide along the Z direction. But, do
you know does CCP4, or any other programs, calculate CC for a group of
residues at all?
Thanks!
Hailiang
You might find some useful examples in $CCP4/examples/unix/runnable
OVERLAPMAP is used in mapcorrelation_procedures, overlapmap.exam,
waterpeaks.
As I understand it, CORR SECT does a map correlation by map section, so
you get a single CC value per map section.
This mode does not use MAPIN3, and doesn't use atom or residue
information. So yes, it will ignore the CHAIN keyword.
section refers to map section:
Number of columns, rows, sections ... 96 152 17
and not a section of your atomic model.
HTH
Martyn
On Tue, 2010-05-25 at 23:51 -0400, Hailiang Zhang wrote:
Hi,
I am working on a real space correlation on a specif protein section
using
CCP4 OVERLAPMAP. I am using the following scripts, not sure whether it
is
good or not (didn't find in OVERLAPMAP documentation).
overlapmap \
mapin1 ${PDB}-1.map\
mapin2 ${PDB}-2.map\
mapin3 ${PDB}-mask.map \
eof
CORR SECT
CHAIN A $START $END
END
There is no error message, but the results make no difference no matter
how I change $START and $END. I am not sure whether the above script is
ok.
By the way, more importantly to me, if corr sect works at all, will it
print out a single CC value by integrating over the WHOLE region define
by
the section range?
Thanks!
Best Regards, Hailiang
--
***
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
* Fax: +44 1925 603634Skype name: martyn.winn *
* URL: http://www.ccp4.ac.uk/martyn/ *
***
Re: [ccp4bb] how to read the ascii map converted by MAPTONA4 and MAPEXCHANGE
Dear Eleanor: Yes, this is something I want to do (RSR and CC). But I just want to do the calculation based on a group of residues or atoms, and it seems OVERLAPMAP doesn't do it, so I think I have to find other ways. Hailiang mapdump does this if you select the right flags. But as Ian says you will get a LOT of numbers. You dont say why you want this information, but if it is to find the electron density at an atom site overlapmap will do that if you ask for real space rfactor eleanor Hailiang Zhang wrote: Hi, I wanted to convert a binary ccp4 map file to a readable format so that I can retrieve the electron density at each real space grid point. Just tried MAPTONA4 and MAPEXCHANGE, but the resulting ascii file are not readable, and I didn't find any documentataion about how to read them. Could somebody give me any hint? Thanks a lot! Best Regards, Hailiang
Re: [ccp4bb] How to calculate real-space CC by section?
Hi Eleanor:
Do you have some references in mind that discussed the value of CC (say
0.5) to be able to build the structure? Didn't find one for right now:-(
By the way, probably a weak question, In the case a lousy model will
give poor CCs even if the map is brilliant, we still accept this model
dispite the poor CC, right? Sorry that I didn't get practically involved
too much in real model building, but I just heard that model is more
frequently built manually by eyes, not CC etc.
Best Regards, Hailiang
If you ask for CORR SECTion then overlapmap does just that - the CC will
have a certain value for each section regardless of the CHAIN
parameters. If you want correlation residue by residue you must ask for
CORR RESI
As someone said - a lousy model will give poor CCs even if the map is
brilliant..
But once your refinement is finished it is intresting to go back and
check the CC of the initial maps.
There is a belief that you need a CC of 0.5 to be able to build the
structure but different problems and different builders achieve
different results..
Eleanor
Hailiang Zhang wrote:
Hi,
I am working on a real space correlation on a specif protein section
using
CCP4 OVERLAPMAP. I am using the following scripts, not sure whether it
is
good or not (didn't find in OVERLAPMAP documentation).
overlapmap \
mapin1 ${PDB}-1.map\
mapin2 ${PDB}-2.map\
mapin3 ${PDB}-mask.map \
eof
CORR SECT
CHAIN A $START $END
END
There is no error message, but the results make no difference no matter
how I change $START and $END. I am not sure whether the above script is
ok.
By the way, more importantly to me, if corr sect works at all, will it
print out a single CC value by integrating over the WHOLE region define
by
the section range?
Thanks!
Best Regards, Hailiang
Re: [ccp4bb] How to calculate real-space CC by section?
Hailiang Zhang wrote: Hi Eleanor: Do you have some references in mind that discussed the value of CC (say 0.5) to be able to build the structure? Didn't find one for right now:-( Lunin and Woolfson, (1993) http://scripts.iucr.org/cgi-bin/paper?he0076
Re: [ccp4bb] how to read the ascii map converted by MAPTONA4 and MAPEXCHANGE
OVERLAPMAP will do this, but you need to calculate a label map with SFALL first and provide that to OVERLAPMAP as mapin3, as MW and others have pointed out already. RTFM: http://www.ccp4.ac.uk/dist/html/overlapmap.html#notes_mapin3 http://www.ccp4.ac.uk/dist/html/sfall.html#mode_atmmap_resmod -James Holton MAD Scientist Hailiang Zhang wrote: Dear Eleanor: Yes, this is something I want to do (RSR and CC). But I just want to do the calculation based on a group of residues or atoms, and it seems OVERLAPMAP doesn't do it, so I think I have to find other ways. Hailiang mapdump does this if you select the right flags. But as Ian says you will get a LOT of numbers. You dont say why you want this information, but if it is to find the electron density at an atom site overlapmap will do that if you ask for real space rfactor eleanor Hailiang Zhang wrote: Hi, I wanted to convert a binary ccp4 map file to a readable format so that I can retrieve the electron density at each real space grid point. Just tried MAPTONA4 and MAPEXCHANGE, but the resulting ascii file are not readable, and I didn't find any documentataion about how to read them. Could somebody give me any hint? Thanks a lot! Best Regards, Hailiang
Re: [ccp4bb] How large should the real space correlation coefficient be?
Hi Hailiang, On 5/25/10 8:14 PM, Hailiang Zhang wrote: Have seen the real-space correlation used widely judging the map quality. Generally or empirically, in order to say an map (area) has good quality, how large should the real space correlation coefficient be? Say, is 0.8 good enough on a residue base? Any references about this will be greatly appreciated! why don't you just familiarize yourself with the map CC values computed per atom or per residue, for a few different structures at different resolutions? It might take you a few hours but from that point on you will have some reference between the map CC values and actual map appearance. phenix.model_vs_data or phenix.real_space_correlation can compute all these values for you. I did it at some point to educate myself and never regretted about the time I spent doing this -:) Pavel.
Re: [ccp4bb] how to read the ascii map converted by MAPTONA4 and MAPEXCHANGE
Hi James: Actually I did OVERLAPMAP calculation in this way. I first flagged the map grid points by using the provided pdb information, which serves as mapin3 for the OVERLAPMAP calculation. However, the calculated CCs or RSRs are either based on each individual atom, residue or map section, but it didn't calculate a single CC or RSR by integrating over the whole region encomprassed by a group of residues as I wanted. Maybe there is something I didn't discovered in OVERLAPMAP to do this? I appreicate if you could point out which key word I need to use. This will save me lots of time in coding on the map:-( Thanks a lot! Best Regards, Hailiang OVERLAPMAP will do this, but you need to calculate a label map with SFALL first and provide that to OVERLAPMAP as mapin3, as MW and others have pointed out already. RTFM: http://www.ccp4.ac.uk/dist/html/overlapmap.html#notes_mapin3 http://www.ccp4.ac.uk/dist/html/sfall.html#mode_atmmap_resmod -James Holton MAD Scientist Hailiang Zhang wrote: Dear Eleanor: Yes, this is something I want to do (RSR and CC). But I just want to do the calculation based on a group of residues or atoms, and it seems OVERLAPMAP doesn't do it, so I think I have to find other ways. Hailiang mapdump does this if you select the right flags. But as Ian says you will get a LOT of numbers. You dont say why you want this information, but if it is to find the electron density at an atom site overlapmap will do that if you ask for real space rfactor eleanor Hailiang Zhang wrote: Hi, I wanted to convert a binary ccp4 map file to a readable format so that I can retrieve the electron density at each real space grid point. Just tried MAPTONA4 and MAPEXCHANGE, but the resulting ascii file are not readable, and I didn't find any documentataion about how to read them. Could somebody give me any hint? Thanks a lot! Best Regards, Hailiang
Re: [ccp4bb] How large should the real space correlation coefficient be?
Hi Pavel: This is actually something I am doing right now. Yes, sometimes it is always better to try it practically. Best Regards, Hailiang Hi Hailiang, On 5/25/10 8:14 PM, Hailiang Zhang wrote: Have seen the real-space correlation used widely judging the map quality. Generally or empirically, in order to say an map (area) has good quality, how large should the real space correlation coefficient be? Say, is 0.8 good enough on a residue base? Any references about this will be greatly appreciated! why don't you just familiarize yourself with the map CC values computed per atom or per residue, for a few different structures at different resolutions? It might take you a few hours but from that point on you will have some reference between the map CC values and actual map appearance. phenix.model_vs_data or phenix.real_space_correlation can compute all these values for you. I did it at some point to educate myself and never regretted about the time I spent doing this -:) Pavel.
Re: [ccp4bb] how to read the ascii map converted by MAPTONA4 and MAPEXCHANGE
The easiest thing to do is to make a PDB file that contains ONLY the residues you are interested in and set all the residue numbers to 1. Use this PDB file to calculate the MODE ATMMAP and the MODE ATMMAP RESMOD maps with SFALL. Then OVERLAPMAP (in correlate residue mode) will give you a CC and RSR for resiude 1, which is your region-of-interest. -James Holton MAD Scientist zhan...@umbc.edu wrote: Hi James: Actually I did OVERLAPMAP calculation in this way. I first flagged the map grid points by using the provided pdb information, which serves as mapin3 for the OVERLAPMAP calculation. However, the calculated CCs or RSRs are either based on each individual atom, residue or map section, but it didn't calculate a single CC or RSR by integrating over the whole region encomprassed by a group of residues as I wanted. Maybe there is something I didn't discovered in OVERLAPMAP to do this? I appreicate if you could point out which key word I need to use. This will save me lots of time in coding on the map:-( Thanks a lot! Best Regards, Hailiang OVERLAPMAP will do this, but you need to calculate a label map with SFALL first and provide that to OVERLAPMAP as mapin3, as MW and others have pointed out already. RTFM: http://www.ccp4.ac.uk/dist/html/overlapmap.html#notes_mapin3 http://www.ccp4.ac.uk/dist/html/sfall.html#mode_atmmap_resmod -James Holton MAD Scientist Hailiang Zhang wrote: Dear Eleanor: Yes, this is something I want to do (RSR and CC). But I just want to do the calculation based on a group of residues or atoms, and it seems OVERLAPMAP doesn't do it, so I think I have to find other ways. Hailiang mapdump does this if you select the right flags. But as Ian says you will get a LOT of numbers. You dont say why you want this information, but if it is to find the electron density at an atom site overlapmap will do that if you ask for real space rfactor eleanor Hailiang Zhang wrote: Hi, I wanted to convert a binary ccp4 map file to a readable format so that I can retrieve the electron density at each real space grid point. Just tried MAPTONA4 and MAPEXCHANGE, but the resulting ascii file are not readable, and I didn't find any documentataion about how to read them. Could somebody give me any hint? Thanks a lot! Best Regards, Hailiang
Re: [ccp4bb] how to read the ascii map converted by MAPTONA4 and MAPEXCHANGE
Dear James: This is really the easiest and a very smart way to get around this problem. I generated a PDB only only my interest region, which serves to produce a mask encomprassing only this region. The last Total line in the output should be it. Everything is cool except that some terminal residues in my region is a little bit different from the complete PDB results, which I think should be due to changing of flag labels on the map grids around the terminal residues. Anyway, I think this issue has been solved based on your suggestion. Thanks a lot! Best Regards, Hailiang The easiest thing to do is to make a PDB file that contains ONLY the residues you are interested in and set all the residue numbers to 1. Use this PDB file to calculate the MODE ATMMAP and the MODE ATMMAP RESMOD maps with SFALL. Then OVERLAPMAP (in correlate residue mode) will give you a CC and RSR for resiude 1, which is your region-of-interest. -James Holton MAD Scientist zhan...@umbc.edu wrote: Hi James: Actually I did OVERLAPMAP calculation in this way. I first flagged the map grid points by using the provided pdb information, which serves as mapin3 for the OVERLAPMAP calculation. However, the calculated CCs or RSRs are either based on each individual atom, residue or map section, but it didn't calculate a single CC or RSR by integrating over the whole region encomprassed by a group of residues as I wanted. Maybe there is something I didn't discovered in OVERLAPMAP to do this? I appreicate if you could point out which key word I need to use. This will save me lots of time in coding on the map:-( Thanks a lot! Best Regards, Hailiang OVERLAPMAP will do this, but you need to calculate a label map with SFALL first and provide that to OVERLAPMAP as mapin3, as MW and others have pointed out already. RTFM: http://www.ccp4.ac.uk/dist/html/overlapmap.html#notes_mapin3 http://www.ccp4.ac.uk/dist/html/sfall.html#mode_atmmap_resmod -James Holton MAD Scientist Hailiang Zhang wrote: Dear Eleanor: Yes, this is something I want to do (RSR and CC). But I just want to do the calculation based on a group of residues or atoms, and it seems OVERLAPMAP doesn't do it, so I think I have to find other ways. Hailiang mapdump does this if you select the right flags. But as Ian says you will get a LOT of numbers. You dont say why you want this information, but if it is to find the electron density at an atom site overlapmap will do that if you ask for real space rfactor eleanor Hailiang Zhang wrote: Hi, I wanted to convert a binary ccp4 map file to a readable format so that I can retrieve the electron density at each real space grid point. Just tried MAPTONA4 and MAPEXCHANGE, but the resulting ascii file are not readable, and I didn't find any documentataion about how to read them. Could somebody give me any hint? Thanks a lot! Best Regards, Hailiang
Re: [ccp4bb] Alignment software
Hi all. I'm rather surprised that Jalview has yet to be mentioned: http://www.jalview.org/ Although I've heard that ESPript can make the best looking figures, Jalview is also capable of generating very beautiful output, and I've found it reasonably intuitive and plenty powerful. I'm not fond of the command line, so the Jalview GUI is especially sweet for me. -Joel On Wed, May 26, 2010 at 2:13 AM, Sebastiano Pasqualato sebastiano.pasqual...@ifom-ieo-campus.it wrote: Thanks Roger, that worked perfectly! I'll try and have fun with aline now. ciao, s On May 25, 2010, at 7:56 PM, Roger Dodd wrote: Hi there, I just got this working a couple of days ago under Mac OS X 10.6.3. I manually compiled and installed Perl-Tk from CPAN. Steps taken: 1. Download and ungzip / untar: http://search.cpan.org/CPAN/authors/id/S/SR/SREZIC/Tk-804.028_501.tar.gz(the newer -503 version didn't work) 2. Change into the directory 3. Execute perl Makefile.PL 4. make 5. make test 6. sudo make install Hopefully that should get things working. Cheers, Roger On 25 May 2010 17:50, Sebastiano Pasqualato sebastiano.pasqual...@ifom-ieo-campus.it wrote: Hi there, I remember a friend of mine showing me Aline, and it looked very nice. However, I can't make it work on my MacBook Pro (Mac OS X 10.6.3). With respect to the instruction I found on the website, I had to change the export lines to be added to the .bashrc in order not to get error messages. That's how I added the path info: export ALINEHOME='/sw64/share/xtal/aline_011208' export PATH=$PATH:$ALINEHOME/bin however, I still get an error while trying to run aline: s...@host005:~ aline Can't locate Tk.pm in @INC (@INC contains: /sw64/lib/perl5 /sw64/lib/perl5/darwin /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0 .) at /sw64/share/xtal/aline_011208/bin/aline line 37. BEGIN failed--compilation aborted at /sw64/share/xtal/aline_011208/bin/aline line 37. s...@host005:~ I even tried with the perl -MCPAN -e 'install Tk' command, as suggested by the website, but nothing changed. Any idea of what's wrong here? Thanks a lot for the tips, ciao s On May 25, 2010, at 5:47 AM, Charlie Bond wrote: Hi Victor, Thanks for recommending ALINE. It is not exactly true that development has stopped. It is just glacially slow as funding for such utilities is not easily obtained! Recommendations for improvements (to improve that potential) are well-received and a keen user can write their own plug-ins to achieve new functionality. Cheers, Charlie Victor Alves wrote: Hi Mohd You can also check: ALINE (An Extensible WYSIWYG Protein Sequence Alignment Editor for Publication Quality Figures) http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/ It’s quite nice and has a lot of potential, although unfortunately it seems that development of the software as stopped :-( Cheers Victor Alves *From:* CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] *On Behalf Of *Salameh, Mohd A., Ph.D. *Sent:* sexta-feira, 21 de Maio de 2010 16:11 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Alignment software Dear All, I’m trying to prepare an alignment figure of 2 proteins that highlight conserved and similar residues and probably secondary structures; I will greatly appreciate it if anybody can recommend a software that I can use. Thanks, Mohd -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310 35 Stirling Highway Crawley WA 6009 Australia charles.b...@uwa.edu.au +61 8 6488 4406 -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 9437 5990 -- Roger B. Dodd, PhD. Cambridge Institute for Medical Research Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY UK -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 9437 5990
