Re: [ccp4bb] making high res image in pymol
Thank you all for the suggestions. I lowered the hash-max and could get ray tracing to complete for line or even ribbon modes (to be honest line mode worked even without lowering the hash-max). But as Matthew pointed out, I could not get it to work in the cartoon mode. I think I am restricted here with my hardware limitations... Alex On Tue, Jan 28, 2014 at 2:20 PM, Yong Wang wrote: > Hi Alex, > > > > If you don't mind forgoing the ray tracing, you may try the draw command > to specifically set the resolution (and antialiasing) to your needs, and > then save the image. > > > > Yong > > > > > -- > > *Yong Wang, Ph.D. Research > Advisor, Discovery Chemistry Research* > > Eli Lilly & Company Phone: > 317-655-9145 > > Lilly Corporate Center DC 0403 Fax: 317-651-6333 > > Indianapolis, IN 46285 > wang_y...@lilly.com > > > > CONFIDENTIALITY NOTICE: This e-mail message from Eli Lilly and Company > (including all attachments) is for the sole use of the intended > recipient(s) and may contain confidential and privileged information. Any > unauthorized review, use, disclosure, copying or distribution is strictly > prohibited. If you are not the intended recipient, please contact the > sender by reply e-mail and destroy all copies of the original message. > > > > > > > > > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *A > K > > *Sent:* Tuesday, January 28, 2014 10:27 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] making high res image in pymol > > > > Hi all, > > I am trying to generate a high resolution figure of a molecule together > with its symmetry mates (250 A readius) for a poster. If I try to ray it, > the pymol session crashes (perhaps too many molecules are open). Using png > xxx.png, dpi=300 or dpi=600 command doesn't make any difference; the image > is still kind of low resolution for A0 or A1. Any idea how I can generate > this in pymol? (I am using the free version of pymol) > > Thank you in advance, > > Alex >
[ccp4bb] making high res image in pymol
Hi all, I am trying to generate a high resolution figure of a molecule together with its symmetry mates (250 A readius) for a poster. If I try to ray it, the pymol session crashes (perhaps too many molecules are open). Using png xxx.png, dpi=300 or dpi=600 command doesn't make any difference; the image is still kind of low resolution for A0 or A1. Any idea how I can generate this in pymol? (I am using the free version of pymol) Thank you in advance, Alex
Re: [ccp4bb] RNA for crystallization
Thanks for all suggestions. I am going to P32-label the RNA and see if it runs as a single species on the gel and if not, I'll do the HPLC. Alex On Mon, May 20, 2013 at 11:16 AM, Eugene Valkov wrote: > Hi Alex, > > If you do not have access to HPLC equipment, another alternative is > gel-purification using a PAGE setup under denaturing (urea) conditions. > This has the advantage of being fairly simple and effective for a range of > transcripts, but you will need a fairly large gel tank system to get good > resolution. Ke and Doudna 2004 review in Methods is an excellent starting > point for learning about practical issues involved in the crystallisation > of protein/RNA complexes and purification of RNA for this purpose. > > Hope this helps, > Eugene > > > > On 20 May 2013 15:20, A K wrote: > >> Dear all, >> I have a crystallization-related question. I am going to co-crystallize >> protein with RNA. I ordered a short (10 mer and 14 mer) RNA from Dharmacon >> but did not choose the purification option while ordering them due to the >> budget issues. How critical is to HPLC purify them before setting drops? >> Aren't RNA synthesis protocols reliable enough nowadays for such short RNAs? >> Thanks, >> Alex >> > > > > -- > Dr Eugene Valkov > > Division of Structural Studies > MRC Laboratory of Molecular Biology > Francis Crick Avenue > Cambridge Biomedical Campus > Cambridge CB2 0QH, U.K. > > Email: eval...@mrc-lmb.cam.ac.uk > Tel: +44 (0) 1223 407840 >
[ccp4bb] RNA for crystallization
Dear all, I have a crystallization-related question. I am going to co-crystallize protein with RNA. I ordered a short (10 mer and 14 mer) RNA from Dharmacon but did not choose the purification option while ordering them due to the budget issues. How critical is to HPLC purify them before setting drops? Aren't RNA synthesis protocols reliable enough nowadays for such short RNAs? Thanks, Alex
[ccp4bb] ./configure problem
Hi there, I am trying to install ccp4 on a scientific linux system. I've got stuck in the step where I need to configure the system. After sourcing ccp4.setup, I go to the main ccp4 folder and try ./configure help, but I get the error "bash: ./configure: No such file or directory". It looks as if the configure script has not been included in my tar file. The file I unzipped was called ccp4-6.3.0.1-arp-linux-x86_64.tar.gz. Any suggestion is highly appreciated. Alex
Re: [ccp4bb] Additives to bacterial cultures to improve solubility
Mark, you can try low percentage of ethanol as well, as it increases the expression of some chaperones (can't find the paper right now!). Alex > On Tue, Feb 26, 2013 at 2:08 AM, Mark J van Raaij > wrote: > >> Dear All, >> >> We are considering trying additives to bacterial cultures to see if they >> improve solubility of some proteins we express: L-arginine, glycyl-glycine, >> sorbitol and betaine. I would be glad to receive recommendations and >> experiences, also if they haven't worked. >> Side-question: should we get cell culture-certified compounds, or would >> "normal", much more economical ones suffice? (i.e. are they likely to >> contain side-products that would affect bacterial growth?). >> >> Greetings, >> >> Mark >> >> Mark J van Raaij >> Lab 20B >> Dpto de Estructura de Macromoleculas >> Centro Nacional de Biotecnologia - CSIC >> c/Darwin 3 >> E-28049 Madrid, Spain >> tel. (+34) 91 585 4616 >> http://www.cnb.csic.es/~mjvanraaij >> >> > > > -- > David J. Leibly > Graduate Student, Yeates Lab > Dept. Chem & Biochem > Univ. of California, Los Angeles > Boyer Hall 269B > (310) 825-8901 >
Re: [ccp4bb] GeForce Graphics cards
Hi Zhijie, thanks for the link. I was actually referring to that post. Can you please tell me what graphics card you are using? Alex On Wed, Feb 13, 2013 at 6:16 PM, Zhijie Li wrote: > ** > Hi, > > Since it is mentioned, I would like to take this chance to clarify: > > We have used the Zalman and LG 2342P under Linux, Windows(XP and 7) and a > VM Windows within a Linux system, on either desktop (with a minimal > on-board graphic chip) or laptops. The monitor is quite plug-and-play in > all cases we have tested. According to the internet, these monitors also > work with Macs for stereo game play and stereo video viewing. > > In regard to the crystallographic software, the Zalman mode is supported > by COOT, Chimera, and the new Pymol (but not the 0.99) - we have tested > them all in both Linux and Windows. > > Passive 3D only requires the graphic program to send out the left and > right images in alternating lines. To my understanding this suggests that > it is independent of OS or graphic cards. But f > or Mac users, I think the first thing to check is whether the Mac COOT and > Chimera has a Zalman mode option. > > Here's the link to my previous reply on the BB regarding our experience > with the Zalman and LG D2342: > http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg28113.html > > Zhijie > > > > *From:* S K > *Sent:* Wednesday, February 13, 2013 3:37 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] GeForce Graphics cards > > Harry, > > I found this on pymol wiki "NVidia 3D NVision kit only supports DirectX > software for GeForce (gaming cards) on Windows; users are reporting that > they are not able to run PyMOL with NVision with these cards. Get a newer > model low end quadro (> G8x graphics core) without the 3 pin mini din (e.g. > Quadro 370) or with the 3 pin mini din (e.g. Quadro 3700) for Windows." and > this too " The GeForce cards do not support windowed openGL stereo, so we > do not support these series of cards for the NVision 3D solution. For > linux, you must have a quadro card that has a 3 pin mini din connector. The > cheapest/oldest card that will work with linux is the Quadro 3700.*WARNING > *: The Quadro FX1400 does not support 3d vision stereo on Windows7 or > Linux. " This was posted there a while ago and I was wondering if there > has been any update to that which has not been posted. > > Regarding the passive monitors, I think they are compatible with linux, > after all we have been using zalman for long time, which is technically a > passive 3D monitor. I also found posts on the ccp4bb from people happily > using LG D2342P monitor, though linux or windows was not mentioned. > > A > > On Wed, Feb 13, 2013 at 3:21 PM, Harry Mark Greenblatt < > harry.greenbl...@weizmann.ac.il> wrote: > >> BS"D >> >> Dear Alex, >> >> >> I'm not sure why you think the new Geforce cards will be an issue. >> Please clarify. >> >> As far as stereo is concerned, Geforce cards only give stereo under >> Windows, not Linux. If you want stereo under Linux you need the Quadro >> cards with the stereo option (for example, Quadro 4000 or 5000). Not all >> Quadro cards support this option, and so would only give stereo under >> Windows, like the Geforce cards. >> >> Not sure about the passive type of stereo; I have a feeling that will >> also only work under Windows. I'm also not sure it works with Pymol and >> Coot. Perhaps someone can clarify this. >> >> As far as I know the stereo under Linux is only the active variety, using >> the NVidia 3D Vision glasses. >> >> Harry >> >> >> >> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Alex >> Kavian [alek6...@gmail.com] >> Sent: Wednesday, February 13, 2013 9:47 PM >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: [ccp4bb] GeForce Graphics cards >> >> Hi there, >> >> I have an off-toptic question about Graphics card. My searches on >> pymolwiki and ccp4bb archives resulted in the following conclusion: Coot >> and pymol are not compatible with the new GeForce graphics cards. Hoewver, >> most of the posts I found were from 2009 and 2010. Does anyone here have >> any experience with GeForce 660 or 680 for stereo applications of Coot, >> Pymol or UCSF chimera? Will quadro cards work equally smooth in the stereo >> mode of these programs? Do 3D applications put too much pressure on the >> Graphics card which would justify installing dual Graphics card? (not sure >> if is relevant, but just for the record, we want to buy passive 3D monitor >> due to the budget restrictions). >> >> Thanks, >> Alex >> > >
