[ccp4bb] Refmac5, error
Dear Everybody, it would have been nice to know how to overcome the following error of Refmac5 refinement (both for Rigidbody and Restrainst) C:/Ccp4Temp/CCP4/DepositFiles/unknown/unknown061110:19:35:08.refmac has no associated file name $$ Open failed: Unit: 9, File: C:/Ccp4Temp/CCP4/DepositFiles/unknown/unknown061110:19:35:08.refmac (logical: C:/Ccp4Temp/CCP4/DepositFiles/unknown/unknown061110:19:35:08.refmac) Refmac_5.5.0102: Open failed: File: C:/Ccp4Temp/CCP4/DepositFiles/unknown/unknown061110:19:35:08.refmac ast system error message: Unknown error Refmac_5.5.0102: Open failed: File: C:/Ccp4Temp/CCP4/DepositFiles/unknown/unknown061110:19:35:08.refmac Thanks
[ccp4bb] Fix hydrogen in PDB and use of "reduce"
If anybody have used "reduce" (http://kinemage.biochem.duke.edu/software/reduce.php) to fix hydrogens to residues in PDB, then I highly appeciate suggestion on my problem as follows. Running "reduce" (new version 3.13) I can see hydrogens are fixed to protein residues. But if ligand is covalently or non-covantly bound to protein, then how hydrogen is fixed to protein residue covalently bound to ligand or noncovalent ligand using "reduce". I did not get any result on HETATM in the PDB running "reduce" in the same way. Thanks. Sam. _ Introducing Live Search cashback . It's search that pays you back! http://search.live.com/cashback/?&pkw=form=MIJAAF/publ=HMTGL/crea=introsrchcashback
Re: [ccp4bb] How many reflections for Rfree?
I use CCP4i, refmac5 for the refinement using data of 2.45 angstrom. My R and Rfree is 0.182 and 0.267 respectively. For calculating Rfree ,5% of random data (1715 reflections) was used . So I see there is a difference of about 8.5% between R and Rfree. Is this difference reasonable ? Any idea how can I improve Rfree and difference between R and Rfree gets less than 5%. Thanks, _ Need to know now? Get instant answers with Windows Live Messenger. http://www.windowslive.com/messenger/connect_your_way.html?ocid=TXT_TAGLM_WL_Refresh_messenger_062008
[ccp4bb] adding hydrogens without altering coordinates of non-hydrogen atoms
Any idea is appreciated how to add Hs (hydrogens) stereochemically to protein or peptide without altering the coordinates of non-hydrogen atoms. Does COOT have any option to do this ? Thanks. Sam. _ Need to know now? Get instant answers with Windows Live Messenger. http://www.windowslive.com/messenger/connect_your_way.html?ocid=TXT_TAGLM_WL_Refresh_messenger_062008
Re: [ccp4bb] Coot and Hs
Hi Paul, How can I add Hs (hydrogens) stereochemically to protein or peptide using COOT without altering the coordinates of non-hydrogen atoms. Thanks. Sam. > Date: Thu, 19 Jun 2008 15:57:46 +0100 > From: [EMAIL PROTECTED] > Subject: Re: [ccp4bb] Coot and Hs > To: CCP4BB@JISCMAIL.AC.UK > > Dear Roberto, > > Roberto Steiner wrote: >> Dear all, >> >> a problem possibly at the coot/mmdb interface... > > Indeed. > >> If one uploads a pdb file (from phenix.refine in the example below) >> that contains Hs into Coot and then writes it out (with or without any >> modification done on it) Coot shifts the HG2n of THR on the right by >> one column space. Because column 17 is kept empty the result is three >> identical HG2 THR protons. > > Technical answer: > > The current PDB parser in Coot is from mmdb and is for PDB format > version 2.3. Phenix.refine and other modern programs use PDB format > version 3.0 [1] - released over a year ago. PDB version 3.0 > "Remediated" does not wrap the hydrogen (or other) names and so the > hydrogen name "unmangler" - which is what is tripping you up - need not > be executed. I'd like to make Coot compatible with the current PDB > standard. If CCP4 were to release a version of mmdb compatible with > Coot, I could do that right away [2]. I'm hoping that they will do so > today^H^H^H^H^H soon. > >> The only solution right now (that I know of) is to remove all Hs and >> generate them again (molprobity for example) prior to refinement. > > Bleugh. Non-optimal (no matter how fine Molprobity is). > > Paul. > > [1] or version 3.1? > [2] I imagine. _ Introducing Live Search cashback . It's search that pays you back! http://search.live.com/cashback/?&pkw=form=MIJAAF/publ=HMTGL/crea=introsrchcashback
[ccp4bb] How to create TLS file
Suggestion please. How TLS file is created to be used in Refmac refinement. Thanks. Sam _ Get Free (PRODUCT) RED™ Emoticons, Winks and Display Pics. http://joinred.spaces.live.com?ocid=TXT_HMTG_prodredemoticons_052008
[ccp4bb] fixing position in the refinement: Shelx, refmac5
How one can fix position of few residues when refining in SHELX or Refmac5. Thanks. Sam. _ Use video conversation to talk face-to-face with Windows Live Messenger. http://www.windowslive.com/messenger/connect_your_way.html?ocid=TXT_TAGLM_WL_Refresh_messenger_video_042008
[ccp4bb] Angle between NCS-axis and Crystallographic axis
Hi I appreciate suggestion how can I calculate angle (s) between NCS axis and crystallographic axis and their origins, starting with the coordinates from PDB. Thanks. Sam. _ Windows Live Hotmail is giving away Zunes. http://www.windowslive-hotmail.com/ZuneADay/?locale=en-US&ocid=TXT_TAGLM_Mobile_Zune_V3
[ccp4bb] Self rotation function and figures
Hi, I am using a native data of 2 angstrom and C2 space group, final R-merge is 0.059. I processed data using HKL2000. I highly appreciate suggestion how can I generate self-rotation function, get figures and save that in required format. Thanks, Sam _ Don't get caught with egg on your face. Play chicktionary! http://club.live.com/chicktionary.aspx?icid=chick_wlhmtextlink1_feb
[ccp4bb] Occupany in refmac and parameter file in CNS
Hi I like to know how fractional occupancies are refined in refmac5. I am using CCP4i interface. I like know how Parameter and Topology files are created for a ligand bonded covalently to Ser residue. I am trying to refine structure using CNS. I appreciate your suggestion and comments and help. Sam _ Windows Live Hotmail and Microsoft Office Outlook – together at last. Get it now. http://office.microsoft.com/en-us/outlook/HA102225181033.aspx?pid=CL100626971033
[ccp4bb] scalepack2mtz
I used to run "scalepack2mtz" succefully. now it is not working. Can anybody suggest the way to short it out. %chmod +x scalepack2mtz.exam (% is a unix/linux prompt). %scalepack2mtz.exam message is as follows. bash: scalepack2mtz.exam: command not found Although I sourced the path /opt/ccp4/ccp4-6.0/ccp4-6.0/bin , I still get the same message. Thanks any suggestion. Sam _ Gear up for Halo® 3 with free downloads and an exclusive offer. It’s our way of saying thanks for using Windows Live™. http://gethalo3gear.com?ocid=SeptemberWLHalo3_WLHMTxt_2
[ccp4bb] Refmac5, .cif file for ligans and restrain.
I appreciate if anybody suggest following. I am trying to fit a ligand into a protein (covalently bonded) and refine using refmac5. I made .cif file (ligand.cif) using ccp4i which I provide to refmac5 during the refinement. Question is how can I restrain the geometrical paramers of the similar bonds, angles and/or torsions of the ligand(s) during this refinement? My second question is if anybody wants to fit more than one ligand (different types), then how can s/he mention two or more .cif files in the refmac5 refiments ? I see it has only one place for providing .cif file as Library. Thanks Sam _ Kick back and relax with hot games and cool activities at the Messenger Café. http://www.cafemessenger.com?ocid=TXT_TAGLM_SeptWLtagline
[ccp4bb] few organophophates coordiantes
Hi, Thanks for the reply to my earlier query. I am looking for the coordinates of few organophosphates which can bond covalently to protein as follows . 1) Para-oxon: O,O-Diethyl-O-para-nitrophenyl phosphate 2) Sarin: 2-(fluoro-methyl-phosphoryl)oxypropane 3) Soman: 3-(fluoro-methyl-phosphoryl)oxy-2,2-dimethyl-butane 4) Tabun: Ethyl N,N-dimethylphosphoramidocyanidate 5) DFP: 2-(fluoro-(1-methylethoxy)phosphoryl)oxypropane 6) VX: O-ethyl-S-[2(diisopropylamino)ethyl] methylphosphonothiolate I would like to know if anybody know the correct "hiccup' site. I searched a similar site though google, but I did not find any good hit. JL Susman and Charles Millard groups did some studies with few of these organophosphates, but I donot see any complete structure of the organophosphates in their submitted PDBs. Appreciate suggestion/notes. Sam _ Explore the seven wonders of the world http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-US&form=QBRE
[ccp4bb] covalently bonded Ligand fit
Hi I am trying fit a ligand (organo phosphate) covalently bonded to residue Serine 250 in my structure. How can I connect this phosphate to Ser-O and during refinement (refmac and CNS), how should I mention in the ligand in the input and how should I number it? I use COOT as graphics. Thanks for suggestion. Sam. _ Invite your mail contacts to join your friends list with Windows Live Spaces. It's easy! http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/friends.aspx&mkt=en-us
Re: [ccp4bb] Pymol, labels, maps
Hi, I like to short out how I can see map in pymol and bobscript. When I am using pymol, I cann't see map file. Same map file I can see in Coot. Map file (created for O using from .fcf shelxpro) is also not coming; extenstion .xplor (or .dsn6) not working either. message: Crystal: Unit Cell Volume 845180. ExecutiveLoad: "popp_fcf_sigmaa1_FP1_map.ccp4" loaded as "popp_fcf_sigmaa1_FP1_map", through state 0. How one can label symbols in pymols. Example shown at "http://www.pymolwiki.org/index.php/Label"; does not give symbolic label. In bobscript when I use map file (created using shelxpro for O format) as per the example shown in "http://www.strubi.ox.ac.uk/bobscript/example3.html"; error message comes. message: . contouring map shelx at 4.00 Error: no graphical segments to output end_plot line number 36 Maximum actual usage of allocated memory: 60606 out of 120 "map" points used (leaving 4.3 Mb unused) Line number 36 is "end_plot". I am not sure why is this error for, Appreciate suggestion and help. Thanks Sam _ PC Magazine’s 2007 editors’ choice for best web mail—award-winning Windows Live Hotmail. http://imagine-windowslive.com/hotmail/?locale=en-us&ocid=TXT_TAGHM_migration_HMWL_mini_pcmag_0707
Re: [ccp4bb] how to convert matrix to angle
In this connection I like to know how symmetry (in degrees and translation) is calculated between two or more molecules in the asymmetric unit (A.U.).Suppose if I download a PDB then I like to know the symmetry axis and center coordinate of symmetry axis between two or more molecules in A.U. ThanksDate: Sun, 8 Jul 2007 09:45:30 +0800From: [EMAIL PROTECTED]: Re: [ccp4bb] how to convert matrix to angleTo: [EMAIL PROTECTED] a lot. You are so kind. On 7/7/07, Kay Diederichs <[EMAIL PROTECTED]> wrote: Jiamu Du schrieb:> Dear all:> I want to calculate the rotation angle between two similar domains. By > using Coot, I can superposr the two domain and get the rotation matrix.> But > how to convert this matrix to an angle. Is there any program can> calculate > this ?> Thanks.>Jiamu Du, If you have the rotation matrixa11 a12 a13a21 a22 a23a31 a32 a33then(a11 + a22 + a33 - 1) / 2is the cosine of the angle you're looking for.HTH,Kay--Kay Diederichs http://strucbio.biologie.uni-konstanz.deemail: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz-- Jiamu DuState Key Laboratory of Molecular BiologyInstitute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS) _ Local listings, incredible imagery, and driving directions - all in one place! Find it! http://maps.live.com/?wip=69&FORM=MGAC01
[ccp4bb] Multiple conformation of ligand, shelx, refmac5, CNS
Hi I am refining a structure of protein, 2 molecules in the asymmetric unit. I like to know whether it is possible to crystallize two different conformations of a molecule in the same crystal.When I am trying to fit n-octyl-beta-D-glucopyranoside into the density, I see sugar part of the ligand takesBOAT conformation in A molecule of asymmetric unit (A.U.) and CHAIR conformation in B molecule.Is it normal, because I thought only one conformation of a molecule is favoured in the crystallization?When I refine in Shelx, should I use two sets of description of DFIX and DANG restraints for two different molecules of A.U. ? If refinement is done by refmac5 or CNS, how does it distinguish two different conformation between boat and chair form of sugar ?I appreciate any suggestions, comments.Sam _ Don't get caught with egg on your face. Play Chicktionary! http://club.live.com/chicktionary.aspx?icid=chick_wlmailtextlink
[ccp4bb] Molscript and symbolic label
Hi I would appreciate knowing how to make label of symbolic letters like alpha, beta, pi etc. using molscript. Thanks. Sam _ Make every IM count. Download Windows Live Messenger and join the i’m Initiative now. It’s free. http://im.live.com/messenger/im/home/?source=TAGWL_June07
Re: [ccp4bb] Ligand fitting in COOT and SHELX refinement
My following question relates to the fitting and refinemt of a ligand, n-octyl-beta-D-glucopyranoside. Sam > Date: Fri, 22 Jun 2007 06:27:45 + > From: [EMAIL PROTECTED] > Subject: [ccp4bb] Ligand fitting in COOT and SHELX refinement > To: CCP4BB@JISCMAIL.AC.UK > > Hi > I would like to know following issue for a ligand. > A ligand of a long alkyl chain can have multiple conformation. > In coot in order to fit any protein residues into "difference Density", we > can select a specific "rotamer" conformation and refine. > For fitting ligand of above kind, how does it work out. > Taking the PDB with ligand when we go to refine in SHELX, how restraints like > (DFIX, DANG etc) are mentioned for such kind of ligand which can have > multiple conformation (particularly for the long alkyl chain) and during > refinement values can deviate a lot from a particular value taken from the > literature. > I appreciate suggestion and comments. > Many Thanks > Sam > _ > With Windows Live Hotmail, you can personalize your inbox with your favorite > color. > www.windowslive-hotmail.com/learnmore/personalize.html?locale=en-us&ocid=TXT_TAGLM_HMWL_reten_addcolor_0607 _ Hotmail to go? Get your Hotmail, news, sports and much more! Check out the New MSN Mobile! http://mobile.msn.com
[ccp4bb] Ligand fitting in COOT and SHELX refinement
Hi I would like to know following issue for a ligand. A ligand of a long alkyl chain can have multiple conformation. In coot in order to fit any protein residues into "difference Density", we can select a specific "rotamer" conformation and refine. For fitting ligand of above kind, how does it work out. Taking the PDB with ligand when we go to refine in SHELX, how restraints like (DFIX, DANG etc) are mentioned for such kind of ligand which can have multiple conformation (particularly for the long alkyl chain) and during refinement values can deviate a lot from a particular value taken from the literature. I appreciate suggestion and comments. Many Thanks Sam _ With Windows Live Hotmail, you can personalize your inbox with your favorite color. www.windowslive-hotmail.com/learnmore/personalize.html?locale=en-us&ocid=TXT_TAGLM_HMWL_reten_addcolor_0607
[ccp4bb] Fitting molecule B7G or B8G using COOT
Hi everybody, I am trying to short out to fit a molecule into a density but having problem. It is n-beta-octyl-glucopyranoside into a electron density of my structure. The coordinate of this molecule I got from different from PDB. n-beta-octyl-glucopyranoside was present in the crystallization condition. I named it as "B8G" in the PDB. In COOT under "file:monomer search library" I find "beta-heptyl-glucopyranoside" and named as "B7G". But when I tried to fit B8G in COOT and use "real space refine zone", its not working out but I get the following warning message. "INFO:: using standard CCP4 Refmac dictionary to search for B8G WARNING:: Failed to find restraints for :B8G: " I appreciate help to overcome this. Sam _ Live Earth is coming. Learn more about the hottest summer event - only on MSN. http://liveearth.msn.com?source=msntaglineliveearthwlm
Re: [ccp4bb] conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 format
Deliang, That's right, coot closes if you want to open map from shelxpro which is readable only in O. In order to read map in coot it is necessary to convert it into ccp4 format, but I am also unable to do it by mapman, although I increased memory size (10-20 times) still I am having the error. sam > Date: Thu, 14 Jun 2007 17:29:19 -0700 > From: [EMAIL PROTECTED] > Subject: Re: [ccp4bb] conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 > format > To: CCP4BB@JISCMAIL.AC.UK > > Hi Inari, > I just tried 2Fo-Fc map generated from fcf file in shelxpro. You know what > happened when COOT opened this map? COOT automatically shut itself off! > Maybe shelxpro only generates the map in a way COOT can't handle. > Help, anybody! > Deliang > - Original Message - > From: Inari Kursula > To: U Sam > Cc: deliang > Sent: Wednesday, June 13, 2007 11:12 PM > Subject: Re: [ccp4bb] conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 > format > Dear Sam, > you can use shelxpro to calculate maps with different coefficients from your > .fcf file. Have never used these maps in coot (only O and Xtalview), but I > can't see a reason why they shouldn't work. > Kind regards, > Inari > > Inari Kursula, Ph. D. > Div. of Molecular Structural Biology > Dept. of Medical Biochemistry and Biophysics > Karolinska Institutet > 17177 Stockholm > Sweden > > On Jun 13, 2007, at 6:12 PM, U Sam wrote: > Hi > I would like to create ccp4 format 2fo-fc and fo-fc map from .fcf file > created in shelex. > I can load .fcf file in coot to see the map. But I want to create map files > manually by ccp4. > I appreciate if anybody suggest the script of CCP4 or CCP4i to make such map > files. > Thanks > Sam > > Play free games, earn tickets, get cool prizes! Join Live Search Club. Join > Live Search Club! _ Hotmail to go? Get your Hotmail, news, sports and much more! Check out the New MSN Mobile! http://mobile.msn.com
[ccp4bb] RMSD of Bond Length, angle and torsion and shelx
I like to know, Which parameters of shelx output (like .lst) indicate RMSD of Bond length, angles and torsion? Thanks _ With Windows Live Hotmail, you can personalize your inbox with your favorite color. www.windowslive-hotmail.com/learnmore/personalize.html?locale=en-us&ocid=TXT_TAGLM_HMWL_reten_addcolor_0607
Re: [ccp4bb] Fw: [ccp4bb] conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 format
Hi Deliang,I use FMAP 2 in shelx. The .fcf file created can be loaded into coot and as a result it generates SigmaA and Difference Sigma Maps.During this time .fcf.cif file also created. In CCP4i this .fcf.cif file is converted into MTZ followed by fft to make map files. This way 2FoFc map is same as SigmaA map mentioned above and but fofc map is very different from Difference Sigma map. I am not sure how to correlated the difference between these two maps.SamDate: Wed, 13 Jun 2007 14:00:07 -0700From: [EMAIL PROTECTED]: [ccp4bb] Fw: [ccp4bb] conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 formatTo: CCP4BB@JISCMAIL.AC.UK - Original Message - From: deliang To: U Sam Sent: Wednesday, June 13, 2007 10:46 AM Subject: Re: [ccp4bb] conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 format Hi Sam, I also have some similar questions . When I generate fcf file in shelx, it seems no matter which FMAP code I am using in the ins file (FMAP 2 is Fo-Fc; FMAP 4 is 2Fo-Fc), I will always end up with the Fo-Fc map when this fcf file is loaded in COOT. Anyone has experience in both shelx and COOT can help? Thanks a lot. Deliang - Original Message - From: U Sam To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, June 13, 2007 9:12 AM Subject: [ccp4bb] conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 format Hi I would like to create ccp4 format 2fo-fc and fo-fc map from .fcf file created in shelex.I can load .fcf file in coot to see the map. But I want to create map files manually by ccp4. I appreciate if anybody suggest the script of CCP4 or CCP4i to make such map files.ThanksSam Play free games, earn tickets, get cool prizes! Join Live Search Club. Join Live Search Club! _ Play free games, earn tickets, get cool prizes! Join Live Search Club. http://club.live.com/home.aspx?icid=CLUB_wlmailtextlink
[ccp4bb] conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 format
Hi I would like to create ccp4 format 2fo-fc and fo-fc map from .fcf file created in shelex.I can load .fcf file in coot to see the map. But I want to create map files manually by ccp4. I appreciate if anybody suggest the script of CCP4 or CCP4i to make such map files.ThanksSam _ Play free games, earn tickets, get cool prizes! Join Live Search Club. http://club.live.com/home.aspx?icid=CLUB_wlmailtextlink
Re: [ccp4bb] COOT (version 0.2, Jan 2007) and .FCF file
Hi Paul,coot, version 0.3.1 finally have given me the map from .fcf file, but at the begining error messages are same as version 0.2.> Date: Thu, 7 Jun 2007 09:39:45 +0100> From: [EMAIL PROTECTED]> Subject: Re: [ccp4bb] COOT (version 0.2, Jan 2007) and .FCF file> To: CCP4BB@JISCMAIL.AC.UK> > On Thu, 2007-06-07 at 05:39 +, U Sam wrote:> > Hi would appreciate suggestion/comments.> > I am having a problem of opening .fcf file (created by shelx) in a new version of COOT (0.2, January 2007) > > ((safe_scheme_command) Error in proc: key: unbound-variable args: > > (#f Unbound variable: ~S (read-cif-data-with-phases) #f))> > This looks a bit like problem reported by George Sheldrick and fixed in> later versions - my memory is hazy about ancient coots.> > > /usr/bin/awk> > exit status: 0> > This is coot checking that awk is available (it's running which awk)> > > Finally chances are that coot uses an environment variable to call > > coot. > > Sounds like a cool idea - there's a lot of recursion in coot. Not> implemented yet :)> > So Sam, please try 0.3.1 - if that fails then I'll do something about> it.> > Paul. _ Make every IM count. Download Windows Live Messenger and join the i’m Initiative now. It’s free. http://im.live.com/messenger/im/home/?source=TAGWL_June07
[ccp4bb] COOT (version 0.2, Jan 2007) and .FCF file
Hi would appreciate suggestion/comments. I am having a problem of opening .fcf file (created by shelx) in a new version of COOT (0.2, January 2007) installed in newer version of Linux operating system (CentOS 4.4), and can not see the map. Same file .fcf I could open and see map in the older version of COOT in Linux Red Hat 8.0 series operating system. In both cases it uses CCP4 version 6.0. For the first case I am getting the following message dataset filename: /home/usx/shelex/pab.fcf DEBUG:: getting f_phi_columns... >> CCP4 library signal mtz:File not identified as MTZ (Error) raised in MtzGet << CCP4MTZfile: open_read - File missing or corrupted: /home/usx/shelex/pab.fcf INFO:: not an mtz file: /home/usx/shelex/pab.fcf DEBUG:: getting f_phi_columns... >> CCP4 library signal mtz:File not identified as MTZ (Error) raised in MtzGet << CCP4MTZfile: open_read - File missing or corrupted: /home/usx/shelex/pab.fcf INFO:: not an mtz file: /home/usx/shelex/pab.fcf DEBUG:: getting f_phi_columns... >> CCP4 library signal mtz:File not identified as MTZ (Error) raised in MtzGet << CCP4MTZfile: open_read - File missing or corrupted: /home/usx/shelex/pab.fcf INFO:: not an mtz file: /home/usx/shelex/pab.fcf DEBUG:: in column_selector_using_cmtz got read success of 0 INFO:: data file /home/usx/shelex/pab.fcf is not a valid mtz file /home/usx/shelex/pab.fcf is not a .phs file INFO trying to read /home/usx/shelex/pab.fcf as a SHELX fcf file safe running: (handle-shelx-fcf-file "/home/usx/shelex/pab.fcf") /usr/bin/awk exit status: 0 ((safe_scheme_command) Error in proc: key: unbound-variable args: (#f Unbound variable: ~S (read-cif-data-with-phases) #f)) In the above process a .cif file created which COOT can read and I can see map as well. But I am not sure whether this is a correct map COOT I am getting with the above error message displaying. For the above problem when I talked to our system administrator he said there was no BUG or problem during installation of COOT of above version. So I look for the advice/suggestion and many thanks in advance. Sam. _ With Windows Live Hotmail, you can personalize your inbox with your favorite color. www.windowslive-hotmail.com/learnmore/personalize.html?locale=en-us&ocid=TXT_TAGLM_HMWL_reten_addcolor_0607
[ccp4bb] R and Rfree
Hi Everybody, I have small query. I am feeding ions and correcting few residues into my final structure. If R increases and Rfree decreases or vice versa in the subsequent refinement, which one I should accept and go forward. Thanks. Sam _ Discover the new Windows Vista http://search.msn.com/results.aspx?q=windows+vista&mkt=en-US&form=QBRE
[ccp4bb] shelxl, refinement of occupany
I am looking for some advice. (1) In shelex what should I mention to refine occupancy. I have two molecule in asym unit. In A molecule residues 89-92 is present, but in B these residues are missing. So I believe in B these residues should not be with zero occupancy, although I donot find any prominent density (Fo-Fc). Occupancy could be anywhere between 0.0 to 1.0. How can I refine this parameter. Or, I should neglect this missing part of residues in B indicating a occupancy of 0.0 or keep a gap of these residues with no information including coordinates. Right now R1=14% and R1(free) =18%, without making water anisotropic. (2) I am using 1.4 A data. Should I refine water anisotropically ? If answer is yes, when. (3) Should I add hydrogen at this resolution. If yes, when should I do. Thanks Sam _ The average US Credit Score is 675. The cost to see yours: $0 by Experian. http://www.freecreditreport.com/pm/default.aspx?sc=660600&bcd=EMAILFOOTERAVERAGE
[ccp4bb] ANIS and SHELXL
Hi I am trying to refine my structure anisotropically by shelxl. When I use, "ANIS", all the atoms including water becomes anisotropic. (a) If I want to make only protein residues and ions (SO4 and Acetate) and not the waters, how should I declare ANIS in the .ins file. (b) If I modify or add any residues/ions, then in the next step how ANIS should be declared to make only modified residues/ions anisotropic after few cycle of isotropic refinement. Thanks for the suggestion/comments. Sam _ Find what you need at prices youll love. Compare products and save at MSN® Shopping. http://shopping.msn.com/default/shp/?ptnrid=37,ptnrdata=24102&tcode=T001MSN20A0701
[ccp4bb] shelxl/missing residues
Hi I would appreciate few things for my protein structure. Data is 1.5A. This protein is of 400 residues. 2 molecule in the asymm unit. Missing residues are : N-terminal 8 residues, C-terminal 5 residues and in the middle residues 87-93. Final R(working) = 21% after refmac refinement. Some (not all) waters created into the structure. I am taking this structure into Shelxl for further refinement and building the missing residues. (1) During Shexl refinement how the missing residues I can fix. what kind of keyword I should use to fix the missing residues with a reasonable Occunany and B value. (2) In COOT how can I build acetate ions in place of waters. Or any other way I can call acetate ions. Thanks Sam _ Win a Zunemake MSN® your homepage for your chance to win! http://homepage.msn.com/zune?icid=hmetagline
[ccp4bb] fromm .fcf to .map for coot
Hi everybody I would appreciate knowing how to create .map file (2fo-fc or fo-fc, suitable to display in COOT) from .fcf file generated by Shelxl. Thanks Sam _ The average US Credit Score is 675. The cost to see yours: $0 by Experian. http://www.freecreditreport.com/pm/default.aspx?sc=660600&bcd=EMAILFOOTERAVERAGE
[ccp4bb] axis of unit cell change
Hi I crystallized a protein in different condition than reported before and structure had been already reported by other group. In both cases space group is P21 21 2 Right now I am not interested in solving the structure, but to look for some other properties. I see a difference in cell dimension as follows. Reported structure a = 96.54 b = 121.95 c = 75.33 For my crystal a = 75.03 b = 96.50 c = 121.98 This the cell dimensions are ~equal in lengths but are associated with different axis compare to the reported crysta structure. I used HKL2000 for indexing. I would like to know why the above difference in cell dimensions. Is there any way I can index my data which would give cell parameters of reported structure? thanks in advance for any suggestion/comments. sam _ Find a local pizza place, movie theater, and more .then map the best route! http://maps.live.com/?icid=hmtag1&FORM=MGAC01
