Re: [ccp4bb] changing names of many files
I don't know where this comes from, but its called rename-alot. Its a
perl script. I'm guessing Larry is Larry Wall, but who knows. chmod a
+x it and then put it in your path (~/bin)
You run it like this
rename-alot 's/1105 A/A/' *.osc
The above will change all files that look like this: 1105 A0176.osc
to this A0176.osc.
The script is everything between, but not including, the equals signs.
Your system probably has perl on it unless you are running Mac OS 9 or
prior or any version of Windows.
==
#!/usr/bin/perl -w
# rename - Larry's filename fixer
$op = shift or die Usage: rename-alot expr [files]\n .
eg: % rename-alot \'s/abc /abc-/\' abc*txt\n ;
chomp(@ARGV = STDIN) unless @ARGV;
for (@ARGV) {
$was = $_;
eval $op;
die $@ if $@;
rename($was,$_) unless $was eq $_;
}
==
James
On Mar 11, 2008, at 6:32 PM, Raja Dey wrote:
Hi,
How I can change names of many files keeping the extension same. My
files are like this
1105 A0176.osc
1105 A0177.osc
1105 A0178.osc
1105 A0179.osc
1105 A0180.osc
I want to change them as
A0176.osc
A0177.osc
A0178.osc
A0179.osc
A0180.osc
I am using ubuntu linux.
Thanks...
RD
Raja Dey, Ph.D.
Research Associate
Molecular and Computational Biology
University of Southern California
1050 Childs Way, Los Angeles, CA 90089
Chat on a cool, new interface. No download required. Click here.
--
James Stroud
UCLA-DOE Institute for Genomics and Proteomics
Box 951570
Los Angeles, CA 90095
http://www.jamesstroud.com
Re: [ccp4bb] changing names of many files
There's a dead-ordinary linux command 'rename':
rename 1055 '' 1055*.osc
Saved my butt numerous times.
phx.
James Stroud wrote:
I don't know where this comes from, but its called rename-alot. Its a
perl script. I'm guessing Larry is Larry Wall, but who knows. chmod
a+x it and then put it in your path (~/bin)
You run it like this
rename-alot 's/1105 A/A/' *.osc
The above will change all files that look like this: 1105 A0176.osc
to this A0176.osc.
The script is everything between, but not including, the equals signs.
Your system probably has perl on it unless you are running Mac OS 9 or
prior or any version of Windows.
==
#!/usr/bin/perl -w
# rename - Larry's filename fixer
$op = shift or die Usage: rename-alot expr [files]\n .
eg: % rename-alot \'s/abc /abc-/\' abc*txt\n ;
chomp(@ARGV = STDIN) unless @ARGV;
for (@ARGV) {
$was = $_;
eval $op;
die $@ if $@;
rename($was,$_) unless $was eq $_;
}
==
James
On Mar 11, 2008, at 6:32 PM, Raja Dey wrote:
Hi,
How I can change names of many files keeping the extension same. My
files are like this
1105 A0176.osc
1105 A0177.osc
1105 A0178.osc
1105 A0179.osc
1105 A0180.osc
I want to change them as
A0176.osc
A0177.osc
A0178.osc
A0179.osc
A0180.osc
I am using ubuntu linux.
Thanks...
RD
Raja Dey, Ph.D.
Research Associate
Molecular and Computational Biology
University of Southern California
1050 Childs Way, Los Angeles, CA 90089
Chat on a cool, new interface. No download required. Click here.
--
James Stroud
UCLA-DOE Institute for Genomics and Proteomics
Box 951570
Los Angeles, CA 90095
http://www.jamesstroud.com
Re: [ccp4bb] changing names of many files
for me following works (just an example):
The objective was to remane all 336 images files to 760D6a0001(to 336).img
to 760D6a0_001(to _336).img
Just save the script below (like filename.com) and run as sh filename.com
***
for i in 760D6a0***.img
do
mv $i ${i%760D6a0***}760D6a0_${i#760D6a0}
done
Rajesh
On Wednesday 12 March 2008 02:32, Raja Dey wrote:
CCP4BB@jiscmail.ac.uk
--
Rajesh Kumar Singh, PhD
Institut fur Biochemie
Universitat Greifswald
Felix-Hausdorff-Str. 4
D-17489 Greifswald
Germany
E.Mail: [EMAIL PROTECTED]
Phone: +49-3834- 86 4392
[ccp4bb] Feature of CCP4i for 6.0.99 (SIGF/Weight label menu)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello; While using the CCP4 version 6.0.99 during the Bangalore workshop, I realised that it is not any more possible to freely choose the weight/sigma labels from a mtz input file. In particular when trying to use phases coming from refmac (after MR + rigid body) with there FoM as input to DM (for NCS averaging) it is not possible to select the FOM from refmac as the weight for PHIC... While I fill that the 6.0.99 implemetation is safer in the way that it prevents easy wrong input of the weight/sigma, it is sometime necessary to be able to select 'non-standard' weight/sigma (using ie. the list labels possibilities present in 6.0). I've discussed the matter with Martyn during the workshop, but don't hesitate to ask me for more details if this messag is not clear enough. Cheers; Serge. *** Dr. Serge COHEN GPG Key ID: 0B5CDAEC N.K.I. Department of Molecular Carcinogenesis Plesmanlaan 121 1066 CX Amsterdam; NL E-Mail: [EMAIL PROTECTED] Tel : +31 20 512 2053 *** -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.3 (Darwin) iD8DBQFH16v5lz6UVQtc2uwRAqt6AJ0QRykg9/r77ANuuFsyPLSs1WaCMgCgpg02 eR6mUdvM0LCKyOV6w3oykoY= =994v -END PGP SIGNATURE-
Re: [ccp4bb] changing names of many files
Just for the sake of completeness:
mmv is also a package available for some linux distributions (SuSE at
least), so you don't need the alias.
If you like doing so using shell features, you could, with bash, issue
for i in 1105\ A*; do mv $i ${i#1105\ } ; done
This might work in many POSIX-sh-compliant shells, not only bash (which
the obsolete (t)csh is not ;- )
Cheers, Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Wed, 12 Mar 2008, Raja Dey wrote:
Hi,
How I can change names of many files keeping the extension same. My files are
like this
1105 A0176.osc
1105 A0177.osc
1105 A0178.osc
1105 A0179.osc
1105 A0180.osc
I want to change them as
A0176.osc
A0177.osc
A0178.osc
A0179.osc
A0180.osc
I am using ubuntu linux.
Thanks...
RD
Raja Dey, Ph.D.
Research Associate
Molecular and Computational Biology
University of Southern California
1050 Childs Way, Los Angeles, CA 90089
-
Chat on a cool, new interface. No download required. Click here.
[ccp4bb] Procheck, MolProbity
Dear all, What is the currently accepted view on the percentage of residues in disallowed regions of the Ramachandran plot (for publication purposes) ? This is because I have a structure where there are several stretches of not so well defined density. As a consequence there are about 5% of the residues in disallowed regions of the plot. I know this is high, otherwise the geometry is well defined. Thank you for your input regarding this query. Best, Fred. begin:vcard fn:Fred. Vellieux (Ph.D) n:Vellieux (Ph.D);Fred. email;internet:[EMAIL PROTECTED] tel;work:+33 438789605 version:2.1 end:vcard
[ccp4bb] Postdoctoral Researcher Crystallography/Biochemistry
University of Oxford Weatherall Institute of Molecular Medicine Department of Molecular Oncology Cell Signalling Group Postdoctoral Researcher Crystallography/Biochemistry University Grade 7: £26,666 - £32,796 p.a A highly motivated postdoctoral researcher is sought for our team to work on a project involving crystallography of protein interaction domain complexes, computational screening for small inhibitor molecules and various biochemical and biological assays with the aim to generate new protein structures and to search for and analyse lead compounds for cancer therapy. The ideal candidate will have experience in protein crystallography and in silico screening as well as in biochemical techniques and the desire to apply structural data to find new concepts and leads for disease therapy. You should be able to work independently and in a multi- disciplinary team, communicate effectively and provide substantial input into the conceptual and day-to-day development of the project, which is funded by Cancer Research UK. The position is available immediately for up to 36 months. The salary range is Grade 7, £26,666 - £32,796pa. The Cell Signalling Group at the Weatherall Institute of Molecular Medicine (WIMM; www.imm.ox.ac.uk) in Oxford studies signalling proteins and pathways related to cancers with biological, biochemical and biophysical methods. Objects of main interest are protein - protein interactions, especially SH3 domains and the signalling pathway heterogeneity in cancer cells (www.imm.ox.ac.uk/pages/research/cancer_research/signaling.ht m). The university offers a variety of benefits to their employees (further details at www.ox.ac.uk/staff/index.html). Oxford provides a vibrant and highly stimulating research environment and offers excellent central facilities for robot-supported protein crystallography (www.oppf.ox.ac.uk) and a brand new synchrotron in close proximity (www.diamond.ac.uk). Applications, consisting of a detailed CV, the contact details of three referees one of whom must be the current or most recent employer, and a letter setting out examples of how you meet the selection criteria for the post including your future aspirations should be sent to Claire Russell, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DS or email: [EMAIL PROTECTED] Please quote reference number H808007 on all applications The closing date for applications is 28th March 2008. The University is an Equal Opportunities Employer. --- End of forwarded message --- Claire Russell Personnel and Studentship Officer Weatherall Institute of Molecular Medicine University of Oxford Tel: 01865 222453 --- End of forwarded message --- Claire Russell Personnel and Studentship Officer Weatherall Institute of Molecular Medicine University of Oxford Tel: 01865 222453 --- End of forwarded message --- Claire Russell Personnel and Studentship Officer Weatherall Institute of Molecular Medicine University of Oxford Tel: 01865 222453
[ccp4bb] Staff Position Available: Macromolecular Crystallography Laboratory Manager
This is a re-post (the previous ad had an incorrect job requisition number - my apologies for any confusion this might have caused): Macromolecular Crystallography Laboratory Manager. The University of Oklahoma Department of Chemistry and Biochemistry seeks an individual with a doctorate in Chemistry, Biochemistry, or Physics (or a related relevant field) OR a combination of education and experience (e.g. M.S. degree with several years of macromolecular crystallography experience). Experience in both X-ray crystallographic hardware maintenance and computer software support is required. The Manager of the Macromolecular Crystallography Laboratory (MCL) is responsible for: (i) operation and routine maintenance of the departmental X-ray instrumentation used by structural biologists (which includes a Rigaku/MSC RUH3 rotating anode generator, RAXIS IV++ image plate detector system, Osmic confocal optics, and an Oxford Cryosystem Series 700) and (ii) training and supervising users. The successful candidate will have the opportunity to engage in collaborative research in structural biology with users of the X-ray facilities and is also expected to actively participate in structural biology group meetings and spearhead efforts at writing external proposals for instrument upgrades or replacement. The successful candidate should have excellent interpersonal, communication and organizational skills. Experience with all aspects of macromolecular structure determination by X-ray crystallography is highly desirable. The position is available immediately and will remain open until filled. A competitive salary will be offered, commensurate with experience. Applicants MUST apply for this position on-line at https://jobs.ou.edu. Computers and personal assistance are available at the Office of Human Resources, 905 Asp Avenue, Room 205, Norman, OK 73019. Refer to the job requisition #4933 on all correspondence. Applicants should submit a cover letter, CV, and at least three letters of reference addressed to: Professor Ann H. West, Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019. Alternatively, applications in PDF format can be sent to Ms. Sandy Fisher ([EMAIL PROTECTED]). For further information on this or other OU job opportunities, please call (405) 325-1826, or access our web site at http://hr.ou.edu. The University of Oklahoma is an Affirmative Action/Equal Opportunity employer and encourages diversity in the workplace. See also: http://chem.ou.edu/images/openings/mcl_x-ray_position.pdf --
[ccp4bb] X6A @ NSLS: Beam time available
Beam time available @ X6A http://protein.nsls.bnl.gov The NIGMS beam line X6A at the National Synchrotron Light Source provides FAST access to beam time through out the year. To apply submit a short proposal to http://protein.nsls.bnl.gov at any time. Proposals are continuously reviewed and beam time can be scheduled within a week. For comments or further questions please contact the scientific staff at: [EMAIL PROTECTED] or call: +1 (631) 344 8375 Vivian Stojanoff National Synchrotron light Source Brookhaven National Laboratory Bldg 725D Upton, NY 11973 USA Email: [EMAIL PROTECTED]; [EMAIL PROTECTED] phone: +1 631 344 8375 fax: +1 631 344 3238
Re: [ccp4bb] changing names of many files
Beware that 'rename' on Fedora/Redhat and the like works differently
from 'rename' on Debian/Ubuntu etc. Both are in /usr/bin but the former
is an executable and the latter is a Perl script (it's apparently
installed with Perl), and is probably descended from your 'rename-alot'
(the syntax appears to be identical).
Personally I think the Debian/Perl version is much more powerful, i.e.
you can do anything that's allowed by the Perl regexp rules. For
example the executable version only changes the *first* occurrence of a
search string, whereas with the 's/.../.../g' modifier you can change
multiple occurrences (assuming that's what you want of course!).
-- Ian
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Frank von Delft
Sent: 12 March 2008 07:42
To: James Stroud
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] changing names of many files
There's a dead-ordinary linux command 'rename':
rename 1055 '' 1055*.osc
Saved my butt numerous times.
phx.
James Stroud wrote:
I don't know where this comes from, but its called
rename-alot. Its a
perl script. I'm guessing Larry is Larry Wall, but who
knows. chmod
a+x it and then put it in your path (~/bin)
You run it like this
rename-alot 's/1105 A/A/' *.osc
The above will change all files that look like this: 1105
A0176.osc
to this A0176.osc.
The script is everything between, but not including, the
equals signs.
Your system probably has perl on it unless you are running
Mac OS 9 or
prior or any version of Windows.
==
#!/usr/bin/perl -w
# rename - Larry's filename fixer
$op = shift or die Usage: rename-alot expr [files]\n .
eg: % rename-alot \'s/abc /abc-/\' abc*txt\n ;
chomp(@ARGV = STDIN) unless @ARGV;
for (@ARGV) {
$was = $_;
eval $op;
die $@ if $@;
rename($was,$_) unless $was eq $_;
}
==
James
On Mar 11, 2008, at 6:32 PM, Raja Dey wrote:
Hi,
How I can change names of many files keeping the extension
same. My
files are like this
1105 A0176.osc
1105 A0177.osc
1105 A0178.osc
1105 A0179.osc
1105 A0180.osc
I want to change them as
A0176.osc
A0177.osc
A0178.osc
A0179.osc
A0180.osc
I am using ubuntu linux.
Thanks...
RD
Raja Dey, Ph.D.
Research Associate
Molecular and Computational Biology
University of Southern California
1050 Childs Way, Los Angeles, CA 90089
Chat on a cool, new interface. No download required. Click here.
--
James Stroud
UCLA-DOE Institute for Genomics and Proteomics
Box 951570
Los Angeles, CA 90095
http://www.jamesstroud.com
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Cambridge CB4 0QA under number 3751674
[ccp4bb] PostDoc / Research Engineer available at the University Kiel (Germany)
A Postdoctoral Research position / Senior Research Engineer is available from May, 1st 2008 in the Department of Structural Biology, University Kiel, Germany. The position is initially on a 3-year contract. The position involves research in structural biology of medical relevant proteins (www.strubio.uni-kiel.de), teaching (4 SWS) in biophysics and biochemistry at the advanced level of the Master study program (www.zbm.uni-kiel.de/bcmb) and technical assistance within the equipment pool of the LMB (www.zbm.uni-kiel.de/lmb). For more information see: http://www.uni-kiel.de/stellen/extern/wiss/Scheidig.htm A Ph.D. in Biochemistry or an allied discipline and previous research experience in protein biochemistry is required. Preference will be given to applicants with advanced experience in X-ray crystallography. Salary and benefits are determined by experience and age according to the E 13 TV-L scale. The university seeks to increase the number of women in those areas where they are underrepresented and therefore explicitly encourages women to apply. Applications from disabled individuals are especially welcome. Closing date for applications is March, 31st 2008. The application should include a CV (including in particular any experience relevant to the position announced) as well as the names and contact details of three references, together with a cover letter stating why the applicant has a special interest in this position. Applications must be sent to: Prof. Dr. Axel J. Scheidig Zoologisches Institut - Strukturbiologie Zentrum fuer Biochemie und Molekularbiologie Christian-Albrechts-Universitaet Am Botanischen Garten 1-9 24118 Kiel Germany The cover letter and CV may be submitted by e-mail to axel.scheidig'at'strubio.uni-kiel.de, whereas all supporting documentation must be submitted by regular mail.
Re: [ccp4bb] changing names of many files
This is also easily done using midnight commander. http://en.wikipedia.org/wiki/Midnight_Commander http://linuxgazette.net/issue23/wkndmech_dec97/mc_article.html Here are the details on changing names. http://www.chm.tu-dresden.de/edv/mc/mc4.5/manual1.html#45
[ccp4bb] Missing reflections
Dear CCP4bb, I was looking through the REFMAC manual today and found the following advice: Completing the data to include all possible hkls. Should do this after data reduction, and certainly before using REFMAC. This is now done with the uniqueify script. It is best done using CCP4i. http://www.ccp4.ac.uk/dist/html/refmac5/usage/examples.html#exam0 Is it a good idea to always run uniqueify on data before running REFMAC - what about other refinement programs such as SHELX, CNS or phenix.refine? Simon
Re: [ccp4bb] Missing reflections
All these programs only refine against reflections that were actually measured. REFMAC, but not SHELXL, provides the 'Sigma-A' weight coefficients for Coot to use DFc instead of 2mFo-DFc for the reflections for which Fo is not known (or is reserved for the free R) to calculate a map. This will in general improve the appearence of the map at the cost of introducing a little model bias. As far as I know these 'unobserved' reflections are not used in calculating the difference map. CNS is probably like SHELXL, I'm not sure what phenix.refine does. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Wed, 12 Mar 2008, Simon Kolstoe wrote: Dear CCP4bb, I was looking through the REFMAC manual today and found the following advice: Completing the data to include all possible hkls. Should do this after data reduction, and certainly before using REFMAC. This is now done with the uniqueify script. It is best done using CCP4i. http://www.ccp4.ac.uk/dist/html/refmac5/usage/examples.html#exam0 Is it a good idea to always run uniqueify on data before running REFMAC - what about other refinement programs such as SHELX, CNS or phenix.refine? Simon
Re: [ccp4bb] Feature of CCP4i for 6.0.99 (SIGF/Weight label menu)
Dear Serge -- While using the CCP4 version 6.0.99 during the Bangalore workshop, I realised that it is not any more possible to freely choose the weight/sigma labels from a mtz input file. In particular when trying to use phases coming from refmac (after MR + rigid body) with there FoM as input to DM (for NCS averaging) it is not possible to select the FOM from refmac as the weight for PHIC... While I fill that the 6.0.99 implemetation is safer in the way that it prevents easy wrong input of the weight/sigma, it is sometime necessary to be able to select 'non-standard' weight/sigma (using ie. the list labels possibilities present in 6.0). I've discussed the matter with Martyn during the workshop, but don't hesitate to ask me for more details if this messag is not clear enough. you can't do it at all, or is it only restricted to the interface (ie scripting still ok)? I'm currently still using 6.0, but some students here are using 6.0.99 and might have this problem, although not reported yet. Leo Chavas Leonard, Ph.D. Research Associate Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED]
Re: [ccp4bb] Missing reflections
Thanks for the reply, Does this mean REFMAC/Coot does need the missing number flags (and thus you will get improved maps ONLY if uniqueify is run) or does REFMAC/Coot recognise when a reflection is missing and use DFc regardless (in which case there is no point running uniqueify)? Simon On 12 Mar 2008, at 16:00, George M. Sheldrick wrote: All these programs only refine against reflections that were actually measured. REFMAC, but not SHELXL, provides the 'Sigma-A' weight coefficients for Coot to use DFc instead of 2mFo-DFc for the reflections for which Fo is not known (or is reserved for the free R) to calculate a map. This will in general improve the appearence of the map at the cost of introducing a little model bias. As far as I know these 'unobserved' reflections are not used in calculating the difference map. CNS is probably like SHELXL, I'm not sure what phenix.refine does. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Wed, 12 Mar 2008, Simon Kolstoe wrote: Dear CCP4bb, I was looking through the REFMAC manual today and found the following advice: Completing the data to include all possible hkls. Should do this after data reduction, and certainly before using REFMAC. This is now done with the uniqueify script. It is best done using CCP4i. http://www.ccp4.ac.uk/dist/html/refmac5/usage/examples.html#exam0 Is it a good idea to always run uniqueify on data before running REFMAC - what about other refinement programs such as SHELX, CNS or phenix.refine? Simon
Re: [ccp4bb] Missing reflections
Refmac (and dm and pirate and probably some other programs like phaser too) will only restore missing reflections if there are entries (albeit bblank ones) for those reflections in the MTZ file. So it's not a matter of running uniquify before refmac, its a matter of running uniquify before you run *anything* - i,e. when you first create an mtz file. If you are importing from another format using the 'Convert to MTZ' task in the GUI, this will be done for you unless you specifically turn it off. However it looks as though 'Truncate' task doesn't seem to do it by default - you have to click the button if you came in by this route. Simon Kolstoe wrote: Dear CCP4bb, I was looking through the REFMAC manual today and found the following advice: Completing the data to include all possible hkls. Should do this after data reduction, and certainly before using REFMAC. This is now done with the uniqueify script. It is best done using CCP4i. http://www.ccp4.ac.uk/dist/html/refmac5/usage/examples.html#exam0 Is it a good idea to always run uniqueify on data before running REFMAC - what about other refinement programs such as SHELX, CNS or phenix.refine? Simon
[ccp4bb] ecoli outer membrane / yeast cell wall permeability
Dear Crystallographers, does anybody know the extent to which the outer membranes of e. coli and/or the cell walls of s. cerevisiae are permeable to various solutes? In particular, I was thinking of small, hydrophilic molecules. References would be great as well--I am not sure where to look... Thanks for forgiving the off-topic post (I hope), Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] ***
Re: [ccp4bb] Color of heme containing Xtals
On Mar 12, 2008, at 12:48 PM, Jan Schoepe wrote: Hello everybody, I wonder if anybody has experience with heme (or to be more precise: heme b) containing proteins which Xtals do not look red under the microscope. How might the technique for crystallization (e.g. sitting drop, hanging drop) influence the intensity of the color? Many thanks! If there is no metal in the heme, its color will be very different. If your crystallization buffer contains EDTA or other strong chelating agents, I imagine this might happen, though protein crystallization is not my area. Ian
Re: [ccp4bb] Color of heme containing Xtals
Crystals are supposed to be red if you have oxidized iron in the heme and deep pink/scarlet if the iron is reduced. If you removed the iron (for example EDTA during purification) or substituted with something during purification or crystallization, you could loose the color. It is trivial to check your crystals on the synchrotron beamline with fluorescence spectrum and see which metals are there. Cheers, Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT, Bld. 436, D007 Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Jan Schoepe Sent: Wednesday, March 12, 2008 2:49 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Color of heme containing Xtals Hello everybody, I wonder if anybody has experience with heme (or to be more precise: heme b) containing proteins which Xtals do not look red under the microscope. How might the technique for crystallization (e.g. sitting drop, hanging drop) influence the intensity of the color? Many thanks! Jan Lesen Sie Ihre E-Mails jetzt einfach von unterwegs. http://uk.rd.yahoo.com/evt=51524/*http://de.mobile.yahoo.com/interstiti al?refer=e00127 .
Re: [ccp4bb] Color of heme containing Xtals
Jan Are you saying that the protein you are starting with is not colored (heme is gone or damaged) or that the native protein is only weakly colored (low extinction coefficient at the Soret wavelength)? The former is more disturbing than the latter. For some heme proteins, like peroxidases, you can bleach the heme. DTT and some sulfide containing compound can do this quite easily and I have watched in horror as my brown crystals turned clear (and lost diffraction). If the heme ligand is a histidine, you might knock out a non-covalently bound heme during purification on a Ni-/Co-chelation column. However, the heme is usually tightly bound in most, but not all, heme proteins under non-denaturing conditions. If the problem is the latter, cyanide, carbon monoxide, and other heme ligands can shift the Soret band to a different lambda and, occasionally, enhance the extinction coefficient. Normally, crystallizing heme proteins is not a problem with respect to the heme behavior if the heme is in its resting ferric state. Just avoid detrimental heme ligands and possible reductants (unless you want the ferrous state) and oxidants. But to answer your question better, more information is needed. Cheers, Michael * R. Michael Garavito, Ph.D. Professor of Biochemistry Michigan State University East Lansing, MI 48824-1319 517-355-9724 (Office) 517-353-9334 (Fax) [EMAIL PROTECTED] * Hello everybody, I wonder if anybody has experience with heme (or to be more precise: heme b) containing proteins which Xtals do not look red under the microscope. How might the technique for crystallization (e.g. sitting drop, hanging drop) influence the intensity of the color? Many thanks! Jan - Lesen Sie Ihre E-Mails jetzt einfach von unterwegs..
[ccp4bb] Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB
Hi, I am looking over a number of models from the PDB but have been unable to reproduce the R-factors for any model that was refined with Refmac and contains TLS parameters. I usually can't get within 5% of the reported value. On the other hand, I usually do pretty well for models w/o TLS. An example is the model 1nkz. The PDB header gives an R value of 17% but even when I use tlsanal in CCP4i to generate a PDB with anisotropic B's that mimic the TLS parameters I get an R value of 22.4% using SFCheck. (I'm not implying that I suspect any problem with 1nkz, in fact I have every reason to believe this is the great model its published stats indicate.) I've found a CCP4 BB letter that stated that SFCheck does not pay attention to anisotropic B's but that letter was dated 2002. I hope this limitation has been removed, or at least the output would mention this limitation. Setting up a refinement in Refmac involves a large overhead, since even for zero cycles of refinement the program insists on a complete stereochemical definition for the strange and wondrous groups in this model. I would just like to verify the R factor and calculate a proper map for inspection in Coot. Since I have many models I would like to look at, I would like a simple procedure. I did set up a Refmac run for another model, for which I do have all the .cif's required, but even after refinement I was not close to the reported R. I see that the models I'm interested in are not present in the Electron Density Server, so I suspect I'm not alone in fighting this battle. Any advice would be appreciated, Dale Tronrud
Re: [ccp4bb] Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB
Dale, You raise a very important point. The electron density server will not put out the data unless there is a reasonable agreement between the Author reported R-factor and the calculated R-factor. I guess for the same reasons (and more - Gerard?). The question I have is - if we are going to ask people to deposit data with their model - what information should be deposited (and be in the header of the CIF or PDB file), that would allow us to reproduce the exact maps and statistics that the author reports? We have been struggling with that for some time now in my lab. If the community can come up with an answer, then I am sure we can convince PDB to add those information. Best, Rams. S. Ramaswamy Department of Biochemistry University of Iowa. On Wed, 2008-03-12 at 14:20 -0700, Dale Tronrud wrote: Hi, I am looking over a number of models from the PDB but have been unable to reproduce the R-factors for any model that was refined with Refmac and contains TLS parameters. I usually can't get within 5% of the reported value. On the other hand, I usually do pretty well for models w/o TLS. An example is the model 1nkz. The PDB header gives an R value of 17% but even when I use tlsanal in CCP4i to generate a PDB with anisotropic B's that mimic the TLS parameters I get an R value of 22.4% using SFCheck. (I'm not implying that I suspect any problem with 1nkz, in fact I have every reason to believe this is the great model its published stats indicate.) I've found a CCP4 BB letter that stated that SFCheck does not pay attention to anisotropic B's but that letter was dated 2002. I hope this limitation has been removed, or at least the output would mention this limitation. Setting up a refinement in Refmac involves a large overhead, since even for zero cycles of refinement the program insists on a complete stereochemical definition for the strange and wondrous groups in this model. I would just like to verify the R factor and calculate a proper map for inspection in Coot. Since I have many models I would like to look at, I would like a simple procedure. I did set up a Refmac run for another model, for which I do have all the .cif's required, but even after refinement I was not close to the reported R. I see that the models I'm interested in are not present in the Electron Density Server, so I suspect I'm not alone in fighting this battle. Any advice would be appreciated, Dale Tronrud
Re: [ccp4bb] Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB
Clearly a few interesting entries . 2) in the context of PX, only the total B factor contribution to Fcalc needs to be positive definite, the TLS component might not be (though it is satisfying if it is) 3) how do you calculate the TLS origin ? The PDB entries should contain the origin of the coordinate system to which the TLS parameters refer, and thus it is something you choose not something you calculate. You are perhaps comparing the origin used by refmac with the centre of reaction ?? Cheers Martyn -Original Message- From: CCP4 bulletin board on behalf of Pavel Afonine Sent: Wed 3/12/2008 10:48 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB Hi Dale, a few of my observations regarding this issue: 1) A quick run over all TLS containing models in PDB results in this list of models with incorrect TLS selections or other artifacts (see errors1 file, attached). 2) A lot of reported TLS matrices in PDB are not positive definite. You can easily verify it (I did). 3) Reported TLS origins are not always the same if you compute them yourself (see errors2 file, attached). This file shows the distance between reported and re-computed TLS origin for each group. 4) Some files contain residual B-factors (Btotal-Btls), and some files contain total B-factors (Bresidual + Btls). ... I have a *very* long list. I re-refine all PDB models (for which data are available) from time to time -:). Let me know if interested. And finally, how you like the anisotropic B-factors in this file -:) http://www.rcsb.org/pdb/files/2atb.pdb Without some prior re-refinement you have almost no chances to reproduce the R-factors for most of these structures. Cheers, Pavel. --- Pavel V. Afonine, Ph.D. Lawrence Berkeley National Lab, Berkeley CA, USA (http://www.lbl.gov/) CCI: Computational Crystallography Initiative (http://cci.lbl.gov/) PHENIX (http://phenix-online.org/) On 3/12/2008 2:20 PM, Dale Tronrud wrote: Hi, I am looking over a number of models from the PDB but have been unable to reproduce the R-factors for any model that was refined with Refmac and contains TLS parameters. I usually can't get within 5% of the reported value. On the other hand, I usually do pretty well for models w/o TLS. An example is the model 1nkz. The PDB header gives an R value of 17% but even when I use tlsanal in CCP4i to generate a PDB with anisotropic B's that mimic the TLS parameters I get an R value of 22.4% using SFCheck. (I'm not implying that I suspect any problem with 1nkz, in fact I have every reason to believe this is the great model its published stats indicate.) I've found a CCP4 BB letter that stated that SFCheck does not pay attention to anisotropic B's but that letter was dated 2002. I hope this limitation has been removed, or at least the output would mention this limitation. Setting up a refinement in Refmac involves a large overhead, since even for zero cycles of refinement the program insists on a complete stereochemical definition for the strange and wondrous groups in this model. I would just like to verify the R factor and calculate a proper map for inspection in Coot. Since I have many models I would like to look at, I would like a simple procedure. I did set up a Refmac run for another model, for which I do have all the .cif's required, but even after refinement I was not close to the reported R. I see that the models I'm interested in are not present in the Electron Density Server, so I suspect I'm not alone in fighting this battle. Any advice would be appreciated, Dale Tronrud
Re: [ccp4bb] Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB
Hi Martin, 2) in the context of PX, only the total B factor contribution to Fcalc needs to be positive definite, the TLS component might not be (though it is satisfying if it is) Please correct me if I'm wrong My understanding was that the T and L matrices must be positive definite, otherwise they do not have physical sense. Yes, I understand that what's in the end important for the actual calculations is the positive definiteness of the total B-factor (since it goes as sqrt(det(B)) into denominator in electron density and gradients calculation). The PDB entries should contain the origin of the coordinate system to which the TLS parameters refer, and thus it is something you choose not something you calculate. OK, this partially the deviations I observe. Although, I'm still a bit puzzled about why some differences are so large? Isn't it true that the computed center of mass of a group should be pretty close to the chosen one (at least for large groups)? Cheers, Pavel. --- Pavel V. Afonine, Ph.D. Lawrence Berkeley National Lab, Berkeley CA, USA (http://www.lbl.gov/) CCI: Computational Crystallography Initiative (http://cci.lbl.gov/) PHENIX (http://phenix-online.org/)
[ccp4bb] Possible to make this movie?
Hello, I want to make a movie to show the process of ligand switch. In the movie, the first ligand will gradually be replaced by the second ligand(Include the conformation change such as the bond rotation when the second is approaching). possible to make this movie? I will use Pymol+eMovie to do it and I had the experience to make Pymol movie of middle complication some 2 years ago. Any help and suggestion is highly appreciated. Thank you again Yanming
[ccp4bb] eCheminfo Hands-on Drug Discovery Workshop in Oxford
The 5 Day eCheminfo Hands-on Drug Discovery Workshop Week will take place this year 21-25 July 2008 at the Medical Sciences Teaching Center, Oxford University, Oxford, UK. Topics to be covered include Virtual Screening Docking; Structure-based Drug Design; Ligand Optimisation Library Design; Structure Search, Similarity and Property Estimation; Data Mining, Analysis Visualisation; Pharmacophore Modelling for Lead Identification; Fragment-based Drug Design; QSAR-based Predictive Toxicology; and Quantitative Spectrometric Data-Activity Relationship Modelling. These workshops are aimed to provide a set of stimulating workshops using latest advanced modelling techniques of relevance to chemists, life scientists and modellers working in drug discovery. The workshop group studies problems with hands-on examples using leading-edge software and discusses complex issues highlighted by examples and case studies presented by instructors. A variety of leading drug discovery software packages and an IT classroom are used by instructors and participants to work through problems. Bursary: A Bursary Award sponsored by Tripos will be used to support the attendance of one academic participant, who may be working in any area of research related to drug discovery. To apply for the bursary please send an email with a) description of your research (ca. 500 words); b) your training needs (ca. 500 words), c) your CV to echeminfo -[at]- douglasconnect.com by 15 April 2008. The recipient of the award will be selected based on an evaluation of the quality and innovation of the described research and the potential positive impact of the training on their research progress and will be notified by 30 April. We gratefully acknowledge the sponsorship support of Tripos. More Information: Web: http://echeminfo.colayer.net/COMTY_training Blog: http://barryhardy.blogs.com/cheminfostream Correspondence:Please address any return correspondence on this workshop to echeminfo -[at]- douglasconnect.com best regards Barry Hardy eCheminfo Community of Practice Douglas Connect Switzerland Tel: +41 61 851 0170
