Re: [ccp4bb] ARP/wARP 7.0 error
Hi there -
That error is indeed something totally misleading from python.
Somehow, the error messages get hard-coded at compilation time and
list the directories
that compilation took place at (in this case Gerrit's laptop).
We will try and suppress this message since its totally misleading.
The error message is in the parsing of the Refmac log file
(Garib ... we should indeed do the XML one of these days !)
I think we have seen it before, but if you could send us a gzip of
the whole run dir,
or at least the last refmac log file, we will be able to tell you
exactly.
In a similar case, getting the newest refmac5 from York solved the
problem.
Since I can almost guarantee that any such anomalies are genuine bugs
in ARP/wARP 7.0
(and especially in the 'new' flex-warp module) it might be best to
email directly the authors,
so we can deal with it asap ...
(I am on ccp4bb detox, I read it once a day to avoid shouting to too
many people)
Tassos
On Jul 23, 2007, at 16:24, Craig McElroy wrote:
Hi all,
I am trying to use the new ARP/wARP to build a model starting from a
partially refined structure for the phases using the "Use pdb file
as it is"
option. When I run the program it quits after/during the first
REFMAC cycle
with the following message:
ERROR ('IndexError', ('list index out of range',), [' File
"/Users/gerrit/CProg/ARP_svn/pyWARP/CArc.py", line 78, in
checkAndProcess\n', ' File
"/Users/gerrit/CProg/ARP_svn/pyWARP/CRefmacController.py", line 43, in
checkAndProcess\n', ' File
"/Users/gerrit/CProg/ARP_svn/pyWARP/CRefmacController.py", line
107, in
_parse\n'])
--
ERROR => Ending JOB
--
I'm relatively sure I have everything installed properly, but it
seems the
program is trying to reference scripts that do not exist (i.e.
there is no
/Users/gerrit on my system and therefore no python scripts in
/Users/gerrit/CProg/ARP_svn/pyWARP/).
Any help that you could provide would
be appreciated. Thanks in advance.
Craig
--
Craig McElroy, Ph.D.
Department of Molecular and Cellular Biochemistry
Ohio State University
483 Hamilton Hall
1645 Neil Ave.
Columbus, OH 43210
(614) 688-8630
[ccp4bb] 21st Rhine-Knee Regiomeeting 2007
Registration for the 21st Rhine-Knee Regiomeeting 2007 in Hölstein (CH) is open until August 31th, 2007 under http://www.bioc.uzh.ch/index.php?204&L=1 . Best regards, Peer Mittl
Re: [ccp4bb] CCP4 Wiki
Yes, that is our intention. CCP4 would probably be at the third level of a hierarchy including: Macromolecular crystallographic techniques Structure solution, analysis and visualisation software The CCP4 suite So there would be room for other software packages at the same level as CCP4, and things like purification and crystallisation off of the top level. James Stroud wrote: Would a "CCP4 wiki" be different from a general crystallography wiki? Would it reflect, for instance, the breadth of topics on the CCP4BB? On Monday 23 July 2007 09:57, [EMAIL PROTECTED] wrote: Contributions from volunteers to establish and maintain the CCP4 wiki will be definitely appreciated.
Re: [ccp4bb] resolution and solvent accessible surface area
Hi Hyunchul Kim, the paper that Miguel quotes concludes that the ASA doesn't show any correlation with resolution, but i would like to respectfully disagree. In the paper, the authors limit themselves to structures determined at a resolution no lower than 2.3 A. Many complex structures though are determined at much lower resolution. Especially below 3 Angstrom, many side chains are less well defined, and tend to fold onto the main chain. As a result, one is often forced to build the interface by hand, even though hydrogen bonds at that resolution are hard to determine. So I would take any (S)ASA calculation (per residue) on a structure at a resolution lower than 3 A with a grain of biodegradable salt. In fact, any structure that misses the first solvation shell around the protein is suspect. Cheers, Rob Meijers Synchrotron Soleil Hyunchul Kim <[EMAIL PROTECTED]> wrote: Hello Miguel, Thank you for your reply. It's related to the total SASA of a protein structure but not that of per residue. However, it still give me a hint. :) Best, Hyunchul Kim On Tue, 2007-07-24 at 08:12 +0200, Miguel Ortiz-Lombardía wrote: > Hello Hyunchul Kim, > > I found this paper very interesting: > > Novotny M, Seibert M, Kleywegt GJ. > On the precision of calculated solvent-accessible surface areas. > Acta Crystallogr D Biol Crystallogr. 2007 Feb;63(Pt 2):270-4. Epub > 2007 Jan 16. > PMID: 17242521 [PubMed - indexed for MEDLINE] > > http://www.ncbi.nlm.nih.gov/sites/entrez?Db=PubMed&Cmd=ShowDetailView&TermToSearch=17242521&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum > > It discusses most of the topics you mentioned. > There are many programs around to do that type of calculations. I tend > to use naccess. > > Best, > > > > Miguel > > > 2007/7/24, Hyunchul Kim : > I am interested in the SASA per residue. > > On Tue, 2007-07-24 at 14:43 +0900, Hyunchul Kim wrote: > > Hi all, > > > > Resolution doesn't matter when solvent accessible surface > area(SASA) is > > calculated? > > > > If resolution is poor, I think that the SASA is not likely > to be > > reliable. Then, is there any resolution cut-off for SASA > calculation? > > > > Also, when you calculate SASA, do you include NMR data, too? > > > > Any comments are welcome :) > > > > Thank you in advance. > > > > Best, > > Hyunchul Kim > > > > > > -- > correo-e: [EMAIL PROTECTED] > ~~~ > Je suis de la mauvaise herbe, > Braves gens, braves gens, > Je pousse en liberté > Dans les jardins mal fréquentés! > > Georges Brassens - Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user panel and lay it on us.
[ccp4bb] mosflm error
Date: Tue, 24 Jul 2007 11:49:35 +0100 From: Stephen Brian Carr <[EMAIL PROTECTED]> To: ccp4bb@jiscmail.ac.uk Subject: mosflm error Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear ccp4bb-ers, I have started encountering an error in mosflm (version 6.2.6 with ccp4 6.0.2), after integration ipmosflm is crashing with the error message Open failed: Unit: 10, File: COORDS (logical: COORDS) Last system error message: Success ipmosflm: Open failed: File: COORDS ipmosflm: Open failed: File: COORDS I'm sure there is a simple fix so does anybody know how to prevent this from happening. The message occurs with any data set I have tried to integrate today (even those which I have processed previously with no problems). Thanks very much, Steve ~~~ Dr Stephen Carr Astbury Centre for Structural Molecular Biology University of Leeds Leeds LS2 9JT
Re: [ccp4bb] mosflm error
Hi, >From the error message if seems that the programs is trying to read in a file that should be specified with the COORDS keywords. It is trying COORDS as a filename, which is usually a sign that the filename itself is missing. When writing out a file that should not be too much of a problem as the file will simply be called as the keyword but when reading in it would fail. Hope this can help -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: 24 July 2007 11:50 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] mosflm error Date: Tue, 24 Jul 2007 11:49:35 +0100 From: Stephen Brian Carr <[EMAIL PROTECTED]> To: ccp4bb@jiscmail.ac.uk Subject: mosflm error Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear ccp4bb-ers, I have started encountering an error in mosflm (version 6.2.6 with ccp4 6.0.2), after integration ipmosflm is crashing with the error message Open failed: Unit: 10, File: COORDS (logical: COORDS) Last system error message: Success ipmosflm: Open failed: File: COORDS ipmosflm: Open failed: File: COORDS I'm sure there is a simple fix so does anybody know how to prevent this from happening. The message occurs with any data set I have tried to integrate today (even those which I have processed previously with no problems). Thanks very much, Steve ~~~ Dr Stephen Carr Astbury Centre for Structural Molecular Biology University of Leeds Leeds LS2 9JT
[ccp4bb] mosflm error follow up
Thanks for the replies so far. Here is some more information I should have included last time. The COORDS file is being written, but mosflm seems unable to read it. The simple things like the file permissions are all correct and there is plenty of free space on the disk. Thanks again Steve ~~~ Dr Stephen Carr Astbury Centre for Structural Molecular Biology University of Leeds Leeds LS2 9JT
Re: [ccp4bb] resolution and solvent accessible surface area
Hi Rob, Hyunchul Kim and Miguel, I was just about to write a comment on this, but Rob was quicker.. Rob is right, our dataset of hen egg-white lysozymes does not contain any structures with resolution lower than 2.3 Aone may say that these are all relatively high-resolution structures, therefore we can not claim there is no correlation between ASA and resolution in general. Nevertheless, we cannot see any correlation in our (limited) dataset. On the other hand, we also saw that two structures of the same protein differed by hundreds of sq A in their ASA just because a few residues could not be seen in one of these two structures. The conclusion of our paper was identical with Rob's last paragraph (although we forget to use the word "biodegradable"), and it is even more true when one look at individual residues. I think that The EDS server can provide some hints concerning the reliability of ASA values for individual residues...it allows to check how well are individual residues supported by experimental data, so if a deposited residue conformation is well supported by its electron density map, then its ASA can be quite reliable regardless resolution of a whole structure. However, proteins are dynamic and therefore ASA for individual residues will fluctuate substantially during time (regardless of resolution). best regards, --marian Marian Novotny Department of Animal Physiology and Developmental Biology Faculty of Natural Sciences Charles University in Prague Vinicna 7 Praha 2 128 43 Czech Republic GPS: 50¡4'20.07"N,14¡25'27.02"E mail: [EMAIL PROTECTED] tel:+420221951766 #
[ccp4bb] low b factors
I am working with a small protein in a relatively high space group p6322 and have good data to a modest 2.5 A resolution. During the first rounds of restrained refinement however the B factors drop to an average of 15 and as low as 2 A^3. This has the effect of producing large amounts of negative density in the voids of the structure. I have tried artificially rasing the b factors and setting a higher low cutoff but nothing seems to help. I have also chosen each of the b models of refinement (anisotropic, overall, etc.) but to no avail. Any suggestions? German Gomez Ready for the edge of your seat? Check out tonight's top picks on Yahoo! TV. http://tv.yahoo.com/
[ccp4bb] Help with coordinate file
Hello all, I have a coordinate file of an energy minimized molecule which was apparently done using Chem 3D Pro. Does anyone know how I can convert this to a pdb file? Thank you Mona Rahman -- Mona N. Rahman, Ph.D. Post-doctoral Fellow Botterell Hall, Room 634 Department of Biochemistry Queen's University Kingston, ON, K7L 3N6 Tel: 613-533-6392 E-mail: [EMAIL PROTECTED]
Re: [ccp4bb] Help with coordinate file
Hi Mona, No idea what format may be that file, but if you find it out, most often in these cases openbabel (http://openbabel.sourceforge.net/wiki/Main_Page) is your friend. M. 2007/7/24, Mona N. Rahman <[EMAIL PROTECTED]>: Hello all, I have a coordinate file of an energy minimized molecule which was apparently done using Chem 3D Pro. Does anyone know how I can convert this to a pdb file? Thank you Mona Rahman -- Mona N. Rahman, Ph.D. Post-doctoral Fellow Botterell Hall, Room 634 Department of Biochemistry Queen's University Kingston, ON, K7L 3N6 Tel: 613-533-6392 E-mail: [EMAIL PROTECTED] -- correo-e: [EMAIL PROTECTED] ~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens
Re: [ccp4bb] ARP/wARP 7.0 error
Thank you for the help. It seems as if the new Refmac5 has done the trick.
Thanks
Craig
Craig McElroy, Ph.D.
Department of Molecular and Cellular Biochemistry
Ohio State University
483 Hamilton Hall
1645 Neil Ave.
Columbus, OH 43210
(614) 688-8630
Anastassis Perrakis wrote:
Hi there -
That error is indeed something totally misleading from python.
Somehow, the error messages get hard-coded at compilation time and
list the directories
that compilation took place at (in this case Gerrit's laptop).
We will try and suppress this message since its totally misleading.
The error message is in the parsing of the Refmac log file
(Garib ... we should indeed do the XML one of these days !)
I think we have seen it before, but if you could send us a gzip of the
whole run dir,
or at least the last refmac log file, we will be able to tell you
exactly.
In a similar case, getting the newest refmac5 from York solved the
problem.
Since I can almost guarantee that any such anomalies are genuine bugs
in ARP/wARP 7.0
(and especially in the 'new' flex-warp module) it might be best to
email directly the authors,
so we can deal with it asap ...
(I am on ccp4bb detox, I read it once a day to avoid shouting to too
many people)
Tassos
On Jul 23, 2007, at 16:24, Craig McElroy wrote:
Hi all,
I am trying to use the new ARP/wARP to build a model starting from a
partially refined structure for the phases using the "Use pdb file as
it is"
option. When I run the program it quits after/during the first REFMAC
cycle
with the following message:
ERROR ('IndexError', ('list index out of range',), [' File
"/Users/gerrit/CProg/ARP_svn/pyWARP/CArc.py", line 78, in
checkAndProcess\n', ' File
"/Users/gerrit/CProg/ARP_svn/pyWARP/CRefmacController.py", line 43, in
checkAndProcess\n', ' File
"/Users/gerrit/CProg/ARP_svn/pyWARP/CRefmacController.py", line 107, in
_parse\n'])
--
ERROR => Ending JOB
--
I'm relatively sure I have everything installed properly, but it
seems the
program is trying to reference scripts that do not exist (i.e. there
is no
/Users/gerrit on my system and therefore no python scripts in
/Users/gerrit/CProg/ARP_svn/pyWARP/).
Any help that you could provide would
be appreciated. Thanks in advance.
Craig
--Craig McElroy, Ph.D.
Department of Molecular and Cellular Biochemistry
Ohio State University
483 Hamilton Hall
1645 Neil Ave.
Columbus, OH 43210
(614) 688-8630
Re: [ccp4bb] Help with coordinate file
Hello Mona, I am guessing you have the atom name,number and coordinates in your file. I did something like that and Openbabel will convert it to the pdb file you desire but as far as I know, you will have to assign a residue name to the atom yourself. I did this by superimposition on the original file and manually naming the atoms in a text editor. If all else fails, that is. Arti > Hello all, > > I have a coordinate file of an energy minimized molecule which was > apparently done using Chem 3D Pro. Does anyone know how I can convert > this to a pdb file? > > Thank you > Mona Rahman > > > -- > Mona N. Rahman, Ph.D. > Post-doctoral Fellow > Botterell Hall, Room 634 > Department of Biochemistry > Queen's University > Kingston, ON, K7L 3N6 > Tel: 613-533-6392 > E-mail: [EMAIL PROTECTED] > Arti S. Pandey Graduate Student Chemistry and Biochemistry Montana State University Bozeman,MT 59717
Re: [ccp4bb] Help with coordinate file
Thanks for the advice everyone. I downloaded the graphic interface for Open Babel but for some reason it's not converting my file. I'll play around more with this later but any hints would be greatly appreciated. On Tue, July 24, 2007 09:50, Seth Horne wrote: > Try Open Babel at http://openbabel.sourceforge.net/wiki/Main_Page > > Regards, > Seth > > > W. Seth Horne, Ph.D. > Department of Chemistry > University of Wisconsin > > > -Original Message- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of > Mona N. Rahman > Sent: Tuesday, July 24, 2007 8:32 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Help with coordinate file > > Hello all, > > I have a coordinate file of an energy minimized molecule which was > apparently done using Chem 3D Pro. Does anyone know how I can convert > this to a pdb file? > > Thank you > Mona Rahman > > > -- > Mona N. Rahman, Ph.D. > Post-doctoral Fellow > Botterell Hall, Room 634 > Department of Biochemistry > Queen's University > Kingston, ON, K7L 3N6 > Tel: 613-533-6392 > E-mail: [EMAIL PROTECTED] > > -- Mona N. Rahman, Ph.D. Post-doctoral Fellow Botterell Hall, Room 634 Department of Biochemistry Queen's University Kingston, ON, K7L 3N6 Tel: 613-533-6392 E-mail: [EMAIL PROTECTED]
[ccp4bb] Low B factors Resolved
First, Thank you all for the help and suggestions, it truly resolved the issue. First I reset the B factors to something close to the Wilson B average (53). Then making sure the B-solvent contribution flag was set and refining isotropic b-factor I reran the job. The B-factors now are reasonable and the negative density issues have been resolved. Using Babinet instead of simple scaling also brought down the R and Rfree though it did make the maps a little less defined and increased the B factors to a higher average B. Much more refining to do but I'm in a much better position now. Not to mention that my maps are a lot more interpretable. Thanks Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos & more. http://mobile.yahoo.com/go?refer=1GNXIC
Re: [ccp4bb] Help with coordinate file
[EMAIL PROTECTED] wrote: Hello Mona, I am guessing you have the atom name,number and coordinates in your file. I did something like that and Openbabel will convert it to the pdb file you desire but as far as I know, you will have to assign a residue name to the atom yourself. I did this by superimposition on the original file and manually naming the atoms in a text editor. As has been pointed out on this BBS before, the text editor "nedit" is very good for this because of the ability to cut and paste columns, i.e rectangular selections of text. Hold down the control key and drag from upper right to lower left corner (or v.v.) to select the column with residue names, copy, then select the same area in the defective file and paste. (Make sure the two selections have the same number of residues and atoms in each residue) Get nedit (if you don't have it) from nedit.org or "yum install nedit"
Re: [ccp4bb] FPLC vs Duo Flow
Thanks to all those who responded. Here is a summary of the responses. Overall, there are mixed feelings, but there is a clear bias towards Akta, with a better service and durability – individual experiences with service might be due to geographical distributions? Filip ___ Original question: Hi, I believe this subject has been touched briefly before, but does anyone have any strong feelings before or against using an Akta FPLC/purifier versus a Biorad Duo Flow? The Biorad Duo instruments are significantly cheaper; are they however also 'as good' as GE Healthcare? I'm especially interested in comments from people who have used both instruments before. Cheers Filip ___ Hi Filip, I use both Biologic Duo Flow and Akta Explorer extensively. In my opinion the Biorad equipment is as good and realiable as the Akta for most routine uses. I generally prefer the Akta Explorer over the Biorad system but its mostly a personal preference. In my opinion, the following are the relative advantages of one system over the other. Advantages of Biorad: 1. It is easy to use and maintain/clean. 2. The software interface is straight forward and user firendly. The Akta software appears to deter new users! 3. The Biorad system is highly modular. So, upgrading the equipment or adding more capabilities is easy and cheap. 4. The system pressure is far lower than Akta at a particular flow rate. Advantages of Akta: 1. The Akta software is far superior in terms of capability (display/data analysis), although not as user friendly in terms of creating a program. 2. The fraction collectors are more robust and reliable, although the Biorad fraction collector seems to have improved. 3. The Akta system is less sensitive to air in the buffer and runs perfectly fine without degassing buffers. It is fairly easy to get air-trapped in the Biorad pump. I would not hesitate to chose the Duo Flow over the basic Akta FPLC if cost is a major concern. Hope this helps, -Anirban - Dear Filip, I would recommend getting a demo from the manufacturer. It's hard to decide based on other people's recommendations. Having said this I also must add that I am an avid fan of the AKTA systems, although their prices are high. Still, a Purifier can be obtained for around 30K, which is comparable with the 20K we have heard for the DuoFlow system with similar capacity. The DuoFlow is overall cheaper, however it also has the distinctly 80-ies feeling of a box-modular system. The fancy names of the components don't help either – for example, why does there have to be a special valve kit to double the performance of the standard 10 and 40 ml/min pumps? Everything has to be configured piece-by-piece and the software is somewhat clumsy, as compared to the sleek Unicow (Unicorn) that runs the AKTA systems. The advantages of the system are essentially the same as its disadvantages – namely that you can configure DuoFlow to be as simple or as complicated as you wish, and more importantly if money is tight – theoretically, additional pieces can be bought later as the money situation improves. The slight problem with this is that you get a system where individual components are ageing at different rates. So, as I said – ask the rep to bring you a system for a few days – they're pretty small so it shouldn't be a serious problem for them, especially if you can hint on trying to decide on it versus AKTA, or on the potential to buy more than one J Good luck, Artem Actually I have to take back the price comment. I cannot find a way to build something for less than 33-35K that'd be comparable to the 34K for AKTA Purifier. Perhaps they quote you different prices, though. Artem - Hi Filip, The support for the Akta machines since they have been bought by GE has been absolutely terrible in our experience. Their engineers know less about the machines than we do and that was not the case before they became part of the giant GE corporation. The Akta that we purchased had defective pumps and it took 6 months for them to acknowledge the problem and they agreed to replace them only when the Howard Hughes purchasing office threatened to take action against the company. So, the bottom line is the machines are well engineered thanks to the great design of the old Amersham engineers, but GE does not care about this market (chump change compared to the other stuff they sell). So as a result the price is high and the service has been terrible in our experience. Just my two cents. Good luck. Antonina Hi, In our lab we have background on both instruments, 2 Biorad and 2 Aktas. We got problems on both, minor ones on Aktas, major ones on Biorads, with expensive fixing on Aktas and cheaper fixings on Biorads, but efficient fixing on Aktas and unsolved problem
[ccp4bb] reagarding CNS domain definitons
Hello to all, I'm a bit new to CNS. I am using CNS for rigid body refinement but i don't know how to define domains in the input file and also for annealated simulations which one I have to chose. I mean either "cartesian " or "torsion" molecular dynamics. Thanx in advance for your kind help. Krishna Ch PhD Student Hannover Medical School Hannover
[ccp4bb] phenix mtz to ccp4 mtz conversion
Hi, I have an mtz file from Phenix I am trying to convert for use in Refmac. The labels are currently: H K L I-obs SIGI-obs R-free-flags I can't seem to get it to work. I am using Import, it runs, spits out a new mtz, and then Refmac complains about the labels. What is the easiest way (ie what program in ccp4 and usig what parameters). Thanks, John Bruning
Re: [ccp4bb] phenix mtz to ccp4 mtz conversion
Use truncate to convert I-obs to F-obs. No format change is needed. Peter John Bruning wrote: Hi, I have an mtz file from Phenix I am trying to convert for use in Refmac. The labels are currently: H K L I-obs SIGI-obs R-free-flags I can't seem to get it to work. I am using Import, it runs, spits out a new mtz, and then Refmac complains about the labels. What is the easiest way (ie what program in ccp4 and usig what parameters). Thanks, John Bruning
Re: [ccp4bb] reagarding CNS domain definitons
Since I was reading it this afternoon again, I cant help but suggest to all refinement newbies and more experienced 'refiners' my favorite read: Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2156-68. Epub 2004 Nov 26. Introduction to macromolecular refinement. Tronrud DE. Howard Hughes Medical Institute and Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA. [EMAIL PROTECTED] The process of refinement is such a large problem in function minimization that even the computers of today cannot perform the calculations to properly fit X-ray diffraction data. Each of the refinement packages currently under development reduces the difficulty of this problem by utilizing a unique combination of targets, assumptions and optimization methods. This review summarizes the basic methods and underlying assumptions in the commonly used refinement packages. This information can guide the selection of a refinement package that is best suited for a particular refinement project. Tassos PS Krishna, your questions will at least be partially answered in that; you will also see there is no simple answer before you define your needs better. On 24 Jul 2007, at 20:07, krish wrote: Hello to all, I'm a bit new to CNS. I am using CNS for rigid body refinement but i don't know how to define domains in the input file and also for annealated simulations which one I have to chose. I mean either "cartesian " or "torsion" molecular dynamics. Thanx in advance for your kind help. Krishna Ch PhD Student Hannover Medical School Hannover
Re: [ccp4bb] Help with coordinate file
You might need to make sure that the input format you are entering is the correct one for the program that created the file. > Thanks for the advice everyone. I downloaded the graphic interface for > Open Babel but for some reason it's not converting my file. I'll play > around more with this later but any hints would be greatly appreciated. > > > On Tue, July 24, 2007 09:50, Seth Horne wrote: >> Try Open Babel at http://openbabel.sourceforge.net/wiki/Main_Page >> >> Regards, >> Seth >> >> >> W. Seth Horne, Ph.D. >> Department of Chemistry >> University of Wisconsin >> >> >> -Original Message- >> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of >> Mona N. Rahman >> Sent: Tuesday, July 24, 2007 8:32 AM >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: [ccp4bb] Help with coordinate file >> >> Hello all, >> >> I have a coordinate file of an energy minimized molecule which was >> apparently done using Chem 3D Pro. Does anyone know how I can convert >> this to a pdb file? >> >> Thank you >> Mona Rahman >> >> >> -- >> Mona N. Rahman, Ph.D. >> Post-doctoral Fellow >> Botterell Hall, Room 634 >> Department of Biochemistry >> Queen's University >> Kingston, ON, K7L 3N6 >> Tel: 613-533-6392 >> E-mail: [EMAIL PROTECTED] >> >> > > > -- > Mona N. Rahman, Ph.D. > Post-doctoral Fellow > Botterell Hall, Room 634 > Department of Biochemistry > Queen's University > Kingston, ON, K7L 3N6 > Tel: 613-533-6392 > E-mail: [EMAIL PROTECTED] > Arti S. Pandey Graduate Student Chemistry and Biochemistry Montana State University Bozeman,MT 59717
