Re: [ccp4bb] Suggestions to improve resolution of protein crystals
Dear Saurabh I would like to share something that worked for me. I was in a similar situation, though my crystals weren't as beautiful as yours are. I followed Alexander McPherson's Crystallization of Biological Macromolecules and what ultimately worked is as follows: I did something called iterative seeding. That is, I took seeds from generation 1 and grew generation 2, then took seed from generation 2 to grow 3, and so on. It took me about 7-8 generations to get a crystal that was diffracting in the 3 angstrom range. I tried more generations, but the quality didn't really improve anymore. Afterward, I took these crystals and tried to desiccate them before data collection. The method that best worked for me was to dip it in a cryosolution with 5% glycerol --> keep it for 2 mins and then move to 10% glycerol and so on, up to 35% glycerol. You may want to standardize the cryosolution as well. I was able to get up to 2.6 angstrom data at home source. Hope this helps. *Regards* *Adarsh Kumar, PhD* *Suo Lab* *Florida State University College of Medicine* *Tallahassee, FL - 32304* On Sun, Mar 21, 2021 at 2:04 PM Saurabh Upadhyay wrote: > Dear All, > > I am trying to crystalize a protein, which occurs in monomeric (60kDa) and > tetrameric (240kDa) form. *The protein during crystallization was in > MES buffer pH-6 *and the method of crystallization was "*Sitting drop*" > in "*Proplex*" condition. Some of the conditions in which crystals were > obtained are: > > *1) 0.1M HEPES pH-7; 10% (w/v) PEG 4000* > *2) 0.1M Tris, pH-8; 8% (w/v) PEG 8000* > *3) 0.1M Tris, pH-8; 25% (v/v) PEG 400* > > For reference, I have attached the images of the crystals observed below. > > *However, the diffraction pattern obtained and the resolution of crystals > were very poor. Even some mosaicity has been observed. * > > Kindly suggest some methods or modifications, to improve the resolution > and diffraction pattern of the crystals obtained. > > Thanking You, > Sincerely, > Saurabh Upadhyay, > Ph.D. Scholar > c/o Dr. Ashok kumar Patel, > Kusuma School of Biological Sciences, > Indian Institute of Technology, Hauz Khas, > New Delhi-110016, India > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Post doc position available at Florida State University
Dear all One postdoctoral position is available immediately in an enzymology laboratory to elucidate mechanisms of DNA/RNA synthesis, DNA lesion bypass, and base excision repair catalyzed by various human and viral DNA/RNA polymerases, and to mechanistically investigate gene editing enzymes including CRISPR/Cas9 and Cas13a. Background in structural biology (X-ray crystallography and/or CryoEM), biophysics, protein purification, and recombinant DNA techniques is preferred. An important criterion for selection will be the ability of the desired individual to pursue independent research in an active multi-disciplinary setting. Interested candidates should send a CV and a statement describing experience, goals, and reasons for the interest in this position, and arrange to have three letters of recommendation sent to Dr. Zucai Suo, Eminent Professor and Dorian and John Blackmon Chair of Biomedical Science, Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL. Dr. Suo can be contacted by email (zucai@med.fsu.edu). Further information about the research projects in the Suo Lab can be obtained from https://med.fsu.edu/index.cfm?page=suolab.research. Employer: Florida State University College of Medicine Location: Tallahassee, Florida Salary: NIH guidelines for post-doctoral salaries + benefits Discipline: Life Sciences, Biochemistry, Biology, Biophysics, Structural Biology, and Biomedical Sciences Position Type: Full Time Organization Type: Academia Job Type: Postdoc To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] One postdoc position available at Florida State University
Dear all One postdoctoral position is available immediately in an enzymology laboratory to elucidate mechanisms of DNA/RNA synthesis, DNA lesion bypass, and base excision repair catalyzed by various human and viral DNA/RNA polymerases, and to mechanistically investigate gene editing enzymes including CRISPR/Cas9 and Cas13a. Background in structural biology (X-ray crystallography and/or CryoEM), biophysics, protein purification, and recombinant DNA techniques is preferred. An important criterion for selection will be the ability of the desired individual to pursue independent research in an active multi-disciplinary setting. Interested candidates should send a CV and a statement describing experience, goals, and reasons for the interest in this position, and arrange to have three letters of recommendation sent to Dr. Zucai Suo, Eminent Professor and Dorian and John Blackmon Chair of Biomedical Science, Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL. Dr. Suo can be contacted by email (zucai@med.fsu.edu). Further information about the research projects in the Suo Lab can be obtained from https://med.fsu.edu/index.cfm?page=suolab.research. Employer: Florida State University College of Medicine Location: Tallahassee, Florida Salary: NIH guidelines for post-doctoral salaries + benefits Discipline: Life Sciences, Biochemistry, Biology, Biophysics, Structural Biology, and Biomedical Sciences Position Type: Full Time Organization Type: Academia Job Type: Postdoc To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density
Hi Jessica You may try the following (if you haven't already): 1. Try solving it using P222 space group. 2. Re-index using different axes. *Regards* *Adarsh Kumar* *Florida State University College of Medicine* *Tallahassee, FL - 32304* On Mon, Dec 16, 2019 at 2:30 PM Jessica Besaw wrote: > There have been two potential space groups: > > P212121 - Rfree = 36% > P21212 - Rfree = 45% > > Xtriage reports that twinning is unlikely. > > Cheers! > > Jessica > > > > > > On Mon, 16 Dec 2019 at 13:56, Jürgen Bosch wrote: > >> What’s your spacegroup ? RWork / RFree? >> >> Twinning by any chance? >> >> Jürgen >> >> __ >> Jürgen Bosch, Ph.D. >> Division of Pediatric Pulmonology and Allergy/Immunology >> Case Western Reserve University >> 2109 Adelbert Rd, BRB 835 >> Cleveland, OH 44106 >> Phone: 216.368.7565 >> Fax: 216.368.4223 >> https://www.linkedin.com/in/jubosch/ >> >> CEO & Co-Founder at InterRayBio, LLC >> >> Johns Hopkins University >> Bloomberg School of Public Health >> Department of Biochemistry & Molecular Biology >> >> On Dec 16, 2019, at 1:50 PM, Jessica Besaw wrote: >> >> I am crystallizing this membrane protein in a medium (bicelles) that >> forms lamella like sheets that stack on top of each other. >> >> The layer packing is shown below. Is this structure unreasonable? >> >> >> >> On Mon, 16 Dec 2019 at 13:38, Reza Khayat wrote: >> >>> Hi Jessica, >>> >>> >>> The gap between the two proteins is a bit troubling. Perhaps it's the >>> image, but why would a crystal form if there is no crystal contact between >>> the two proteins? >>> >>> >>> Reza >>> >>> >>> Reza Khayat, PhD >>> Assistant Professor >>> City College of New York >>> Department of Chemistry >>> New York, NY 10031 >>> -- >>> *From:* CCP4 bulletin board on behalf of Ashish >>> Kumar >>> *Sent:* Monday, December 16, 2019 1:24 PM >>> *To:* CCP4BB@JISCMAIL.AC.UK >>> *Subject:* [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric >>> unit does not fit density >>> >>> Hi Jessica, >>> >>> It may be possible because of wrong MR solution as well. How were your >>> stats after MR. >>> Also it is correct that it could be possible because of wrong space >>> group. >>> Try changing the Space group and repeat MR. >>> >>> Best Regards >>> Ashish >>> >>> On 16 Dec 2019 22:56, "Jessica Besaw" wrote: >>> >>> Dear community, >>> >>> I am having a lot of trouble solving a protein structure. I think my >>> problem may caused by incorrectly placed proteins in molecular replacement. >>> I have two proteins in my asymmetric unit. It appears that one protein fits >>> perfectly, and the other one has many errors. (See snapshots below). I have >>> tried deleting the parts of the protein (and even the whole protein) to try >>> and rebuild it in COOT, but it was a bit too difficult for me to solve. >>> >>> I would appreciate any and all suggestions for potential strategies >>> moving forward. >>> >>> Other information: >>> (1) 2.4 Angstrom >>> (2) 99% complete >>> (3) "Translational NCS may be present at a level that may complicate >>> refinement" >>> >>> Cheers! >>> >>> Jessica >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> -- >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0=MBjWbF0ZDC5tg1IQYg3-zjOPSn7yuF2KfXIxak9l0MA=E2hs1sz4cNOm0vRwjsoHzxqEyBnMO-5BfM18hOltqLI=> >>> >>> >>> >>> -- >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0=MBjWbF0ZDC5tg1IQYg3-zjOPSn7yuF2KfXIxak9l0MA=E2hs1sz4cNOm0vRwjsoHzxqEyBnMO-5BfM18hOltqLI=> >>> >>> -- >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >>> >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >> >> >> > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Postdoc position available in an enzymology laboratory at Florida State University
Dear all One postdoctoral position is available immediately in an enzymology laboratory to elucidate mechanisms of DNA/RNA synthesis, DNA lesion bypass, and base excision repair catalyzed by various human and viral DNA/RNA polymerases, and to mechanistically investigate gene editing enzymes including CRISPR/Cas9 and Cas13a. Background in structural biology (X-ray crystallography and/or CryoEM), biophysics, protein purification, and recombinant DNA techniques is preferred. Prior experience with DNA binding proteins would be an added advantage. An important criterion for selection will be the ability of the desired individual to pursue independent research in an active multi-disciplinary setting. Interested candidates should send a CV and a statement describing experience, goals, and reasons for the interest in this position, and arrange to have three letters of recommendation sent to: Dr. Zucai Suo Eminent Professor and Dorian and John Blackmon Chair of Biomedical Science Department of Biomedical Sciences Florida State University - College of Medicine Tallahassee, FL Email: zucai@med.fsu.edu Further information about the research projects in the Suo Lab can be obtained from https://med.fsu.edu/suolab/research The list of publications can be found at https://med.fsu.edu/suolab/publications Job Description: Employer: Florida State University College of Medicine Location: Tallahassee, Florida Salary: NIH guidelines for post-doctoral salaries + benefits Discipline: Life Sciences, Biochemistry, Biology, Biophysics, Structural Biology, and Biomedical Sciences Position Type: Full Time Organization Type: Academia Job Type: Postdoc To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Postdoc position available in an enzymology laboratory at Florida State University
One postdoctoral position is available immediately in an enzymology laboratory to elucidate mechanisms of DNA/RNA synthesis, DNA lesion bypass, and base excision repair catalyzed by various human and viral DNA/RNA polymerases, and to mechanistically investigate gene editing enzymes including CRISPR/Cas9 and Cas13a. Background in structural biology (X-ray crystallography and/or CryoEM), biophysics, protein purification, and recombinant DNA techniques is preferred. Prior experience with DNA binding proteins would be an added advantage. An important criterion for selection will be the ability of the desired individual to pursue independent research in an active multi-disciplinary setting. Interested candidates should send a CV and a statement describing experience, goals, and reasons for the interest in this position, and arrange to have three letters of recommendation sent to: Dr. Zucai Suo Eminent Professor and Dorian and John Blackmon Chair of Biomedical Science Department of Biomedical Sciences Florida State University - College of Medicine Tallahassee, FL Email: zucai@med.fsu.edu Further information about the research projects in the Suo Lab can be obtained from https://med.fsu.edu/suolab/research The list of publications can be found at https://med.fsu.edu/suolab/publications Job Description: Employer: Florida State University College of Medicine Location: Tallahassee, Florida Salary: NIH guidelines for post-doctoral salaries + benefits Discipline: Life Sciences, Biochemistry, Biology, Biophysics, Structural Biology, and Biomedical Sciences Position Type: Full Time Organization Type: Academia Job Type: Postdoc To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] One postdoc position available at Florida State University
Dear all One postdoctoral position is available immediately in an enzymology laboratory to elucidate mechanisms of DNA/RNA synthesis, DNA lesion bypass, and base excision repair catalyzed by various human and viral DNA/RNA polymerases, and to mechanistically investigate gene editing enzymes including CRISPR/Cas9 and Cas13a. Background in structural biology (X-ray crystallography and/or CryoEM), biophysics, protein purification, and recombinant DNA techniques is preferred. An important criterion for selection will be the ability of the desired individual to pursue independent research in an active multi-disciplinary setting. Interested candidates should send a CV and a statement describing experience, goals, and reasons for the interest in this position, and arrange to have three letters of recommendation sent to Dr. Zucai Suo, Eminent Professor and Dorian and John Blackmon Chair of Biomedical Science, Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL. Dr. Suo can be contacted by email (zucai@med.fsu.edu). Further information about the research projects in the Suo Lab can be obtained from https://med.fsu.edu/index.cfm?page=suolab.research. A list of recent publications is available at https://med.fsu.edu/suolab/publications. Employer: Florida State University College of Medicine Location: Tallahassee, Florida Salary: NIH guidelines for post-doctoral salaries + benefits Discipline: Life Sciences, Biochemistry, Biology, Biophysics, Structural Biology, and Biomedical Sciences Position Type: Full Time Organization Type: Academia Job Type: Postdoc Regards Adarsh Kumar, PhD Suo Lab Florida State University School of Medicine Tallahassee, FL - 32304 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation
Hello everyone Just wanted to update that PNY stereo connector worked. In summary, I have the following items now: OS: Ubuntu 16.04 LTS Graphics : Quadro P4000 Stereo connector: PNY ( http://accessories.dell.com/sna/productdetail.aspx?c=us=en=bsd=111=A7035595 ) Monitor: Asus VG248QE Used method detailed in the following link: https://devtalk.nvidia.com/default/topic/1004126/general-discussion/nvidia-3d-stereo-under-linux-ubuntu-16/ Thank you for all your help. *Regards* *Adarsh Kumar, PhD* *Suo Lab* *Florida State University College of Medicine* *Tallahassee, FL - 32304* On Wed, Jan 9, 2019 at 7:32 AM Philippe BENAS < 0d88e888355a-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi Dirk, > > Thanks a lot for your post. It will be indeed really helpful in our lab. > > Best regards, > Philippe > > -- > Philippe BENAS, Ph.D. > > ARN UPR 9002 CNRS > IBMC Strasbourg > 15, rue René Descartes > F-67084 STRASBOURG cedex > +33.3.8841.7109 > E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr > URLs: http://www-ibmc.u-strasbg.fr/ , > http://www-ibmc.u-strasbg.fr/spip-arn/ > -- > > > > -- > *De :* Dirk Kostrewa > *À :* CCP4BB@JISCMAIL.AC.UK > *Envoyé le :* Mardi 8 janvier 2019 10h01 > *Objet :* Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu > workstation > > Dear colleagues, > > since approximately end of last year, there is indeed a 3D stereo > problem under CentOS/Scientific Linux 7.6. I found the odd reason for > this by a small warning message in the Xorg-log file and some > trial-and-error and just want to share this with you, in case, you come > across the same problem: > > My xorg.conf contains the usual switch-off of the composite extension, > since this is incompatible with 3D stereo: > > Section "Extensions" > Option "Composite" "Disable" > EndSection > > However, in recent Xorg-log files, there is a warning that the extension > "Composite" is not recognized, but the extension "COMPOSITE" is loaded. > This doesn't lead to 3D stereo problems on the KDE desktop, but disables > 3D stereo on the MATE and probably the XFCE desktop. The solution is > both odd and easy - you have to modify the composite option in your > xorg.conf as follows: > > Section "Extensions" > Option "COMPOSITE" "Disable" > EndSection > > I have no idea, since when Xorg is case-sensitive, or whether this has > anything to do with the Nvidia driver (I use the one from ELRepo). > Anyway, this solution appears to work. > > Best wishes, > > Dirk. > > On 20.12.18 22:28, Kay Diederichs wrote: > > Unfortunately, monitors with built-in emitter are no longer being > manufactured. The NVIDIA website has not been updated for years. So that > path leads nowhere. > > > > Stereo has worked well for us (for existing monitors with built-in > emitter, and with Quadro cards /USB emitter) until and including CentOS > 7.5. Recently, this stopped after updating to CentOS 7.6 - coot finds the > stereo-capable hardware and reports the switch to stereo, but the monitor > does not flip the pictures. We are investigating. We are using the Nvidia > drivers through the EPEL repository. > > > > best, > > > > Kay > > > > > > On Thu, 20 Dec 2018 16:11:56 -0500, David Schuller > wrote: > > > >> I can see two possible paths here: > >> > >> 1) Make the card work with an emitter > >> > >> or 2) Switch to a monitor with a built-in emitter > >> > >> Datasheet on the graphics card: > >> < > https://www.nvidia.com/content/dam/en-zz/Solutions/design-visualization/productspage/quadro/quadro-desktop/quadro-pascal-p4000-data-sheet-us-nvidia-704358-r2-web.pdf > > > >> > >> "3D Stereo support with Stereo Connector1 > >> ... > >> 1 VGA/DVI/HDMI/stereo support via adapter/connector/bracket" > >> > >> The task then is to identify the correct bracket to work with this card, > >> and find a source for purchase. > >> Something like this: > >> > >> > https://www.bhphotovideo.com/c/product/652465-REG/PNY_Technologies_900_50762__000_Stereo_Bracket_for_Quadro.html > >> "PNY Technoligies Stereo Bracket for Quadro FX 3800" > >>> Is this part also compatible with the Quadro P4000? I do not know. > >> http://www8.hp.com/h20195/v2/GetPDF.aspx/c04658472.pdf > >> "NVidia 3D Stereo Bracket... > >> Supports NVIDIA Quadro® K4000, K5000, K6000, K4200,
Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation - Fwd: 3D graphics under linux for coot, pymol and chimera
Hi Wim Thank you for sharing your experience. I have almost the same setup, except for the stereo connector. i will place order for that today and will share how things go from there. *Regards* *Adarsh Kumar, PhD* *Suo Lab* *Florida State University College of Medicine* *Tallahassee, FL - 32304* On Fri, Dec 21, 2018 at 2:19 AM Wim Burmeister wrote: > Hello, > I re-post my contribution from 17 may 2017. > Software versions and hardware may be obsolete, but some of the > information may still help. > Best > Wim > > > Forwarded Message > Subject: 3D graphics under linux for coot, pymol and chimera > Date: Wed, 17 May 2017 12:27:21 +0200 > From: Wim Burmeister > To: CCP4 Bulletin Board > > Hello, > > we just wanted to share our experience in finding a configuration which > allows to use 3D graphics under linux using Nvidia GeForce 3D glasses. > > We had quite a hard time to find a configurations which works correctly. > > We finally used Debian linux with a xfce desktop. Other recent desktops > use a tiling which is not compatible with 3D graphics. > > The hardware consists of > > >- a DELL Precision T5810 desktop computer with an Nvidia Quadro M4000 >(8 Gbyte memory, 4 DP) graphics card >- Nvidia GeForce 3D Vision 2 (NVIDIA GEF 3D VISION 2 GLASSES KIT) >active stereo glasses >- a stereo connector PNY Quadro 4000 3D for the synchronization of >graphics card and glasses >- an ASUS 24" LED 3D - VG248QE display >- a DisplayPort-DisplayPort cable > > The Nvidia linux drivers from version 367.57 can handle the current > version of the Nvidia glasses. > > For an obscure reason a direct DP-DP connection between graphics card and > display is absolutely required in order to obtain fully working stereo. If > a DP-DVI dual link adapter is used, the stereo does not work on the top and > the bottom part of the screen. This is true for a native DELL active > adaptor or generic models. The exact reason remains unresolved, but the > solution is to use a direct DP-DP connection. This limits the available > choice of displays which require 120 Hz for 1080*1980 screen resolution and > a DP input. We have been choosing a “Nvidia 3D ready” model. > > There has been a considerate about of exchange about this problem on > > > https://devtalk.nvidia.com/default/topic/992892/linux/partially-working-stereoscopic-effect-with-3d-vision-under-debian-linux/ > > The setup comes with a price tag of about 1600 € free of taxes. > > coot, pymol and chimera work straight without problems in hardware stereo > mode. The experience is absolutely great. > > Best > > Wim > -- > > Wim Burmeister > Professeur > Institut de Biologie Structurale (IBS) CIBB > 71 avenue des Martyrs > CS 20192 > 38044 Grenoble Cedex 9, FRANCE > E-mail: wim.burmeis...@ibs.fr > Tel:+33 (0) 457 42 87 41 Fax: +33 (0) 476 20 94 00 > website > <http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/> > > > > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation
Thank you, Guenter. I will keep that in mind. *Regards* *Adarsh Kumar, PhD* *Suo Lab* *Florida State University College of Medicine* *Tallahassee, FL - 32304* On Thu, Dec 20, 2018 at 5:33 PM Guenter Fritz < guenter.fritz.phenix.c...@gmail.com> wrote: > Dear Adarsh, > > just an add-on to the instructions of the others. Since GNOME is not > anymore compatible with stereo, we use successfully Xubuntu (18.04) with > NVIDIA drivers. > Best , Guenter > > Hello everyone > > > > We have just purchased a Dell workstation for crystallography data > analysis. We were trying to use Nvidia 3D vision 2 glasses with it, but > failed to do so. Please help me out with this one. Some relevant > information is as follows: > > OS: Ubuntu 16.04 LTS > > Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket) > > Monitor: Asus VG248QE > > > > Thanks and regards > > Adarsh Kumar > > Suo Lab > > Florida State University College of Medicine > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation
Hi Did you use 3-DIN connector? Regards Adarsh Kumar, PhD Suo lab Florida State University School of Medicine Tallahassee FL - 32304 On Thu, Dec 20, 2018, 16:48 Guillermo Montoya we are using a similar setup ( i do not know if the asus monitor is the > same) > and I managed to make it work following this > > > https://devtalk.nvidia.com/default/topic/1004126/general-discussion/nvidia-3d-stereo-under-linux-ubuntu-16/ > > but you need to use metacity as window manager > > I hope it helps > > best > > > G. > > > > On 20 Dec 2018, at 21:45, Adarsh Kumar > wrote: > > > > Hello everyone > > > > We have just purchased a Dell workstation for crystallography data > analysis. We were trying to use Nvidia 3D vision 2 glasses with it, but > failed to do so. Please help me out with this one. Some relevant > information is as follows: > > OS: Ubuntu 16.04 LTS > > Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket) > > Monitor: Asus VG248QE > > > > Thanks and regards > > Adarsh Kumar > > Suo Lab > > Florida State University College of Medicine > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation
Thank you Jim. I will try that. *Regards* *Adarsh Kumar, PhD* *Suo Lab* *Florida State University College of Medicine* *Tallahassee, FL - 32304* On Thu, Dec 20, 2018 at 3:55 PM Jim Fairman wrote: > If you want to use it with linux, the 3-pin connector is required. You > can buy a cable that plugs into an output on the video card and then > provides an "Nvidia 3D Stereo Bracket" 3-pin adapter to plug the little > pyramid into. > > Here is a link to Dell's site, but you can get it elsewhere as well: > http://accessories.dell.com/sna/productdetail.aspx?c=us=en=fed=16=A7035595 > > I can vouch for the VG248QE monitors working with 3D Vision 2, I have 2 of > them. > > Cheers, Jim > -- > Jim Fairman > C: 1-240-479-6575 > > > On Thu, Dec 20, 2018 at 12:46 PM Adarsh Kumar > wrote: > >> Hello everyone >> >> We have just purchased a Dell workstation for crystallography data >> analysis. We were trying to use Nvidia 3D vision 2 glasses with it, but >> failed to do so. Please help me out with this one. Some relevant >> information is as follows: >> OS: Ubuntu 16.04 LTS >> Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket) >> Monitor: Asus VG248QE >> >> Thanks and regards >> Adarsh Kumar >> Suo Lab >> Florida State University College of Medicine >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >> > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation
Hello everyone We have just purchased a Dell workstation for crystallography data analysis. We were trying to use Nvidia 3D vision 2 glasses with it, but failed to do so. Please help me out with this one. Some relevant information is as follows: OS: Ubuntu 16.04 LTS Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket) Monitor: Asus VG248QE Thanks and regards Adarsh Kumar Suo Lab Florida State University College of Medicine To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] One postdoc position available at Florida State University
Dear all One postdoctoral position is available immediately in an enzymology laboratory to elucidate mechanisms of DNA/RNA synthesis, DNA lesion bypass, and base excision repair catalyzed by various human and viral DNA/RNA polymerases, and to mechanistically investigate gene editing enzymes including CRISPR/Cas9 and Cas13a. Background in structural biology (X-ray crystallography and/or CryoEM), biophysics, protein purification, and recombinant DNA techniques is preferred. An important criterion for selection will be the ability of the desired individual to pursue independent research in an active multi-disciplinary setting. Interested candidates should send a CV and a statement describing experience, goals, and reasons for the interest in this position, and arrange to have three letters of recommendation sent to Dr. Zucai Suo, Eminent Professor and Dorian and John Blackmon Chair of Biomedical Science, Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL. Dr. Suo can be contacted by email (zucai@med.fsu.edu). Further information about the research projects in the Suo Lab can be obtained from https://med.fsu.edu/index.cfm?page=suolab.research. Employer: Florida State University College of Medicine Location: Tallahassee, Florida Salary: NIH guidelines for post-doctoral salaries + benefits Discipline: Life Sciences, Biochemistry, Biology, Biophysics, Structural Biology, and Biomedical Sciences Position Type: Full Time Organization Type: Academia Job Type: Postdoc Regards Adarsh Kumar, PhD Suo Lab Florida State University School of Medicine Tallahassee, FL - 32304 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Postdoc position available at Florida State University
Dear all One postdoctoral position is available immediately in an enzymology laboratory to elucidate mechanisms of DNA/RNA synthesis, DNA lesion bypass, and base excision repair catalyzed by various human and viral DNA/RNA polymerases, and to mechanistically investigate gene editing enzymes including CRISPR/Cas9 and Cas13a. Background in structural biology (X-ray crystallography and/or CryoEM), biophysics, protein purification, and recombinant DNA techniques is preferred. An important criterion for selection will be the ability of the desired individual to pursue independent research in an active multi-disciplinary setting. Interested candidates should send a CV and a statement describing experience, goals, and reasons for the interest in this position, and arrange to have three letters of recommendation sent to: Dr. Zucai Suo, Eminent Professor and Dorian and John Blackmon Chair of Biomedical Science, Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL. Dr. Suo can be contacted by email (zucai@med.fsu.edu). Further information about the research projects in the Suo Lab can be obtained from https://u.osu.edu/suolab/. Employer: Florida State University College of Medicine Location: Tallahassee, Florida Salary: NIH guidelines for post-doctoral salaries + benefits Discipline: Life Sciences, Biochemistry, Biology, Biophysics, Structural Biology, and Biomedical Sciences Position Type: Full Time Organization Type: Academia Job Type: Postdoc *Regards* *Adarsh Kumar, PhD* *Suo Lab* *Florida State University School of Medicine* *Tallahassee, FL - 32304* To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] on unit cell and asymmetric unit
Dear John A unit cell can be produced by the symmetry operations on an asymmetric unit. So, in your summary, if you just include number of copies in the asymmetric unit along with the space group, it should do the job. On Sat, Feb 4, 2017 at 4:37 PM, < 0ef8f1cfe4cc-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear All, > > Some papers write in the way that how many copies of proteins exist in the > crystal unit cell (for example, in each unit cell there was monomer or > dimer or 3 proteins), some write in the way that how many copies of > proteins exist in the crystal assymetric unit. > > I am writing a paragraph to sumarize how many copies of proteins exist in > the crystal unit cell or in the crystal assymetric unit, based on > published papers. In this situation can I treat unit cell and assymetric > unit as same, especially if I need to prepare a table to indicate the > copies of proteins in the unit cell or asymmetric unit? > > I am looking forward to getting a reply from you. > > Best regards. > > John > -- *Regards.* *Adarsh Kumar* *Senior Research Fellow (SPMF)* *Dr. S. Karthikeyan's Group (Protein Crystallography Unit)* *Dept. of Protein Science and Engineering* *Institute of Microbial Technology (CSIR)* *Sector 39A, Chandigarh - 160036* *India*
