Re: [ccp4bb] Problem with making covalent bonds in phenix by LINK or edits file
Dear Xiaoming, I would try using the graphical interface within phenix refine to add in the bond length/angle constraints for your link. This seemed to work fine with our system without actually needing a link record. J -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Xiaoming Ren Sent: Friday, 4 April 2014 9:17 a.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Problem with making covalent bonds in phenix by LINK or edits file Dear all: I am encountering a problem. I built a monomer model which is a modified nucleotide with Sketcher in ccp4 suite and generated the .cif file of this monomer. However, I could not make it bind with other nucleotides in the nucleic acid chain. I have tried to write LINK lines into PDB file, and also edited .edits file for phenix.refine. In both conditions, phenix.refine works except that it wouldn't add covalent bonds between the residues as I expected. I have used .edits file for covalent binding between residues before, and it worked well. So there must be something wrong with my input files. But I couldn't fighure out where the problem is. Thanks a lot and best regards! Xiaoming
Re: [ccp4bb] Problem with making covalent bonds in phenix by LINK or edits file
Xiaoming Can you send me the three residues in question (or the whole model) and the files you have so I can point you in the right direction. Cheers Nigel On Thu, Apr 3, 2014 at 1:17 PM, Xiaoming Ren wrote: > Dear all: > > I am encountering a problem. I built a monomer model which is a modified > nucleotide with Sketcher in ccp4 suite and generated the .cif file of this > monomer. However, I could not make it bind with other nucleotides in the > nucleic acid chain. I have tried to write LINK lines into PDB file, and > also edited .edits file for phenix.refine. In both conditions, > phenix.refine works except that it wouldn't add covalent bonds between the > residues as I expected. > > I have used .edits file for covalent binding between residues before, and > it worked well. > > So there must be something wrong with my input files. But I couldn't > fighure out where the problem is. > > Thanks a lot and best regards! > Xiaoming > -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : nwmoria...@lbl.gov Fax : 510-486-5909 Web : CCI.LBL.gov
[ccp4bb] Problem with making covalent bonds in phenix by LINK or edits file
Dear all: I am encountering a problem. I built a monomer model which is a modified nucleotide with Sketcher in ccp4 suite and generated the .cif file of this monomer. However, I could not make it bind with other nucleotides in the nucleic acid chain. I have tried to write LINK lines into PDB file, and also edited .edits file for phenix.refine. In both conditions, phenix.refine works except that it wouldn't add covalent bonds between the residues as I expected. I have used .edits file for covalent binding between residues before, and it worked well. So there must be something wrong with my input files. But I couldn't fighure out where the problem is. Thanks a lot and best regards! Xiaoming
Re: [ccp4bb] First stucture of FCFV
Those who use lysozyme as a model protein should note that fungal spores of an unknown strain can have a dramatic effect on lysozyme crystal nucleation, as noticed by my student many years ago (I wasn't completely happy with the report because we never knew what we were working with!). Chayen, N. E., Radcliffe, J. W., & Blow, D. M. (1993). Control of nucleation in the crystallization of lysozyme. *Protein Science*, *2*(1), 113-118. http://onlinelibrary.wiley.com/doi/10.1002/pro.5560020112/full I've often wondered why crystallization experiments at room temp don't become a sea of bacteria and fungi within a week. Is it because the high precipitant concs used stop growth? After all, medical saline is only 150 mM - much less than the average NaCl conc used for crystallization, which is about 1.7M. I guess not many bugs can grow in 20% PEG either. Patrick On 3 April 2014 15:25, Reza Khayat wrote: > I think fungus dependent crystallization has occurred for some > labs. A paper that pops into mind is from my graduate > laboratory (not my work though): > > http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2225192/ > > Reza > > Reza Khayat, PhD > Assistant Professor > The City College of New York > Department of Chemistry, MR-1135 > 160 Convent Avenue > New York, NY 10031 > Tel. (212) 650-6070 > www.khayatlab.org > > > Original message > >Date: Thu, 3 Apr 2014 06:36:37 -0700 > >From: CCP4 bulletin board (on behalf > of Chad Brautigam ) > >Subject: Re: [ccp4bb] First stucture of FCFV > >To: CCP4BB@JISCMAIL.AC.UK > > > > I once encountered mold-dependent crystallization of > > a protein. Wouldn't that have made for a lively > > Methods section? > > Luckily, we determined the structure from crystals > > derived from a different, non-moldy condition. > > Whew. > > Chad > > From: Artem Evdokimov > > To: CCP4BB@JISCMAIL.AC.UK > > Sent: Thursday, April 3, 2014 7:55 AM > > Subject: Re: [ccp4bb] First stucture of FCFV > > Common molds like aspergillus or penicillium. After > > a while you sometimes get sporangia, then you can > > tell with more certainty. .. > > A. > > On Apr 3, 2014 3:50 AM, "Bernhard Rupp" > >wrote: > > > > Several people were asking what this FCFV > > tentacles actually might be. I think it is some > > fungus/yeast growing out of nutritious drops. Does > > resemble fungus/mushroom mycelium. I have also > > some that look like huge bacteriophages with nice > > heads on them, probably yeast buds. There is also > > a yeast lab next to the Xtallization facility :-/ > > *** feel free to speculate. > > > > Best, BR > > > > > -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
Re: [ccp4bb] loggraph not popping up after refmac5 ccp4-6.4
Hi all ..
loggraph seems to be broken on Redhat 6.5 . It may be a "blt" error. Can
someone confirm that they can get loggraph to work on Redhat Enterprise 6.5
with the ccp4 provided binaries.
Sadly Redhat nor Activestate provide "blt" replacements
In all cases the loggraph starts a blank window ready to plot a graph and
then fails with the error
"Error in startup script: syntax error in expression "10 11 12 + 12": extra
tokens at end of expression
while executing
"expr [string trim $ele] + $data(NCOLUMNS) "
(procedure "extract_tables_from_GRAPH" line 44)
invoked from within
"extract_tables_from_$filetype $input $arrayname"
(procedure "extract_tables_from_file" line 31)
invoked from within
"extract_tables_from_file $system(SCRIPT) $system(FORMAT) data"
invoked from within
"if { $system(SCRIPT) != "" } {
if { ![ElementExists system FORMAT] || $system(FORMAT) == "" } {
set system(FORMAT) [GetFileFormat $system(SCRI..."
(file
"/home/yong.tang/ccp4_root/ccp4-6.4.0/share/ccp4i/loggraph/loggraph.tcl"
line 2324)
invoked from within
"source [file join $env(CCP4I_TOP) loggraph loggraph.tcl]"
(file
"/home/yong.tang/ccp4_root/ccp4-6.4.0/share/ccp4i/bin/loggraph.tcl" line 83)
"
Sadly We cannot go back to using Ubuntu where this was working.
The CCP4 provided blt, bltsh and wish binaries seem to work fine ..its
only loggraph that fails .
We are using the current ccp4 installed yesterday.
I also tried using Activestate wish and combining it with ccp4 provided
bltsh ..but in that case I get the error :
package require blt
Thanks
Hari ( and Yong)
On Wed, Apr 2, 2014 at 2:33 PM, Yong Tang wrote:
> Hello All,
>
> Further to my earlier email..I am running ccp4 6.4 , on 64 bit Redhat
> Linux 6.5
>
> I cannot see loggraphs with View-Files-From-Job - View Log Graphs--
>
> That throws an error in the shell. This is the same error I see when coot
> finishes refmac5 as well.
> It seems that the loggraph tcl script is broken somehow.
>
> Any ideas on how to fix.
> Thank you for your help
>
>
> Yong
>
>
> Top level CCP4 directory is /home/yong/ccp4_root/ccp4-6.4.0
> Using CCP4 programs from /home/yong/ccp4_root/ccp4-6.4.0/bin
> Error in startup script: syntax error in expression "10 11 12 + 12": extra
> tokens at end of expression
> while executing
> "expr [string trim $ele] + $data(NCOLUMNS) "
> (procedure "extract_tables_from_GRAPH" line 44)
> invoked from within
> "extract_tables_from_$filetype $input $arrayname"
> (procedure "extract_tables_from_file" line 31)
> invoked from within
> "extract_tables_from_file $system(SCRIPT) $system(FORMAT) data"
> invoked from within
> "if { $system(SCRIPT) != "" } {
> if { ![ElementExists system FORMAT] || $system(FORMAT) == "" } {
> set system(FORMAT) [GetFileFormat $system(SCRI..."
> (file
> "/home/yong.tang/ccp4_root/ccp4-6.4.0/share/ccp4i/loggraph/loggraph.tcl"
> line 2324)
> invoked from within
> "source [file join $env(CCP4I_TOP) loggraph loggraph.tcl]"
> (file
> "/home/yong.tang/ccp4_root/ccp4-6.4.0/share/ccp4i/bin/loggraph.tcl" line 83)
>
>
>
> On Wed, Apr 2, 2014 at 2:22 PM, Yong Tang wrote:
>
>> Hi ,
>> I have just switched to a new computer with ccp4 6.4 and binary coot
>> installed from Paul Emsleys nightlies.
>>
>> When I run refmac5 inside coot or run refmac5 inside ccp4, the loggraph
>> does not pop-up at the end of a refmac run. I looked everywhere in settings
>> inside ccp4i or inside coot and could not re-enable loggraph popup.
>>
>> Can someone tell me what setting I need to change to have the old style
>> loggraphs popup ? .
>>
>> Thanks
>>
>> Yong
>>
>> --
>> Yong Tang
>>
>
>
Re: [ccp4bb] First stucture of FCFV
I think fungus dependent crystallization has occurred for some labs. A paper that pops into mind is from my graduate laboratory (not my work though): http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2225192/ Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 www.khayatlab.org Original message >Date: Thu, 3 Apr 2014 06:36:37 -0700 >From: CCP4 bulletin board (on behalf of Chad Brautigam ) >Subject: Re: [ccp4bb] First stucture of FCFV >To: CCP4BB@JISCMAIL.AC.UK > > I once encountered mold-dependent crystallization of > a protein. Wouldn't that have made for a lively > Methods section? > Luckily, we determined the structure from crystals > derived from a different, non-moldy condition. > Whew. > Chad > From: Artem Evdokimov > To: CCP4BB@JISCMAIL.AC.UK > Sent: Thursday, April 3, 2014 7:55 AM > Subject: Re: [ccp4bb] First stucture of FCFV > Common molds like aspergillus or penicillium. After > a while you sometimes get sporangia, then you can > tell with more certainty. .. > A. > On Apr 3, 2014 3:50 AM, "Bernhard Rupp" >wrote: > > Several people were asking what this FCFV > tentacles actually might be. I think it is some > fungus/yeast growing out of nutritious drops. Does > resemble fungus/mushroom mycelium. I have also > some that look like huge bacteriophages with nice > heads on them, probably yeast buds. There is also > a yeast lab next to the Xtallization facility :-/ > *** feel free to speculate. > > Best, BR > >
Re: [ccp4bb] First stucture of FCFV
I once encountered mold-dependent crystallization of a protein. Wouldn't that have made for a lively Methods section? Luckily, we determined the structure from crystals derived from a different, non-moldy condition. Whew. Chad From: Artem Evdokimov To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, April 3, 2014 7:55 AM Subject: Re: [ccp4bb] First stucture of FCFV Common molds like aspergillus or penicillium. After a while you sometimes get sporangia, then you can tell with more certainty. .. A. On Apr 3, 2014 3:50 AM, "Bernhard Rupp" wrote: Several people were asking what this FCFV tentacles actually might be. I think it is some fungus/yeast growing out of nutritious drops. Does resemble fungus/mushroom mycelium. I have also some that look like huge bacteriophages with nice heads on them, probably yeast buds. There is also a yeast lab next to the Xtallization facility :-/ … feel free to speculate. > >Best, BR > >
Re: [ccp4bb] First stucture of FCFV
Common molds like aspergillus or penicillium. After a while you sometimes get sporangia, then you can tell with more certainty. .. A. On Apr 3, 2014 3:50 AM, "Bernhard Rupp" wrote: > Several people were asking what this FCFV tentacles actually might be. I > think it is some fungus/yeast growing out of nutritious drops. Does > resemble fungus/mushroom mycelium. I have also some that look like huge > bacteriophages with nice heads on them, probably yeast buds. There is also > a yeast lab next to the Xtallization facility :-/ ... feel free to speculate. > > > > Best, BR > > > > >
[ccp4bb] PhD position in Structural Biology in Norway
Dear all, A 4-year PhD position in Structural Biology starting August 2014 is available at University of Oslo, Department of Biosciences, Section for Biochemistry and Molecular Biology. The position is funded by the Research Council of Norway and the University of Oslo. The project is dealing with different redox proteins (haem, flavin, iron-sulfur, and di-metal proteins) with a focus on flavodoxins, ferredoxins, ferredoxin/flavodoxin reductases and redox partner enzymes. The project is in the field of structural biology and biochemistry with a strong focus on protein crystallography in combination with other biochemical and biophysical methods including single-crystal spectroscopy. More information about the project, position and application procedure is found on the website: http://uio.easycruit.com/vacancy/1149343/96323?iso=no Applicants must hold a Master’s degree or equivalent in protein crystallography, structural biology, biochemistry or molecular biology. The successful applicant should have skills and experience in working with proteins. It would be advantageous with hands-on experience within topics like cloning, protein expression, purification, crystallisation, protein crystallography, spectroscopy, protein-protein interactions, enzyme kinetics, redox- and co-factor proteins and teaching. Candiates without a Master's Degree have until 30 June, 2014 to complete the final exam. Application deadline is 20th April 2014 through the website: http://uio.easycruit.com/vacancy/1149343/96323?iso=no For further information please contact: Dr. Hans-Petter Hersleth, (h.p.hersl...@ibv.uio.no) -- Hans-Petter Hersleth, PhD Department of Biosciences, University of Oslo Section for Biochemistry and Molecular Biology P.O.Box 1066 Blindern, NO-0316 Oslo, Norway http://www.mn.uio.no/ibv/personer/vit/hphersle/index.html ---
Re: [ccp4bb] First stucture of FCFV
Several people were asking what this FCFV tentacles actually might be. I think it is some fungus/yeast growing out of nutritious drops. Does resemble fungus/mushroom mycelium. I have also some that look like huge bacteriophages with nice heads on them, probably yeast buds. There is also a yeast lab next to the Xtallization facility :-/ . feel free to speculate. Best, BR
