Re: [ccp4bb] crystals that dont diffract :( :(

Hi Careina, if you don't have grey hair (available in the lab), you can still mount crystals at room temperature. With a MiTeGen RT kit, very little skill is required to test crystal diffraction or even collect entire data sets at room temperature.

Re: [ccp4bb] Might be of interest to this group

Wouldn’t that be something for the PyMOL mailing list? All best - Andreas On Fri, 9 Feb 2018 at 20:38, David Schuller wrote: > http://www.cell.com/current-biology/fulltext/S0960-9822(18)30014-9 > A Novel Form of Stereo Vision in the Praying Mantis > Vivek Nityananda

Re: [ccp4bb] NMR or Homology Model as a MR model

Dear Nishant, Rosetta is a good suggestion. You can also use an ensemble of several related (superposed) structures as your search model. This will improve your chances of success. All best. Andreas On Tue, Aug 29, 2017 at 12:50 PM, Nishant Varshney wrote: > Dear

Re: [ccp4bb] Stable Refinement as Low(ish) resolution

Dear Rhys, I second Roger on the use of jelly-body refinement. In addition, give Buster a try. It sometimes does magic at lowish resolution. All best. Andreas On Thu, Jul 13, 2017 at 1:17 AM, Rhys Grinter wrote: > Dear All, > > I'm currently in the process of

Re: [ccp4bb] looking for paper describing optimisation of crystals using a screen kit as additive

Hi Sebastian, you're thinking about local sparse matrix screening. I've done this at a 90:10 ratio. Majeed, S., Ofek, G., Belachew, A., Huang, C.C., Zhou, T., and Kwong, P.D. Enhancing protein crystallization through precipitant synergy. Structure. 2003; 11: 1061–1070 All best. Andreas On

Re: [PyMOL] PyMOL for iPad issues

Dear João, type set grid_mode, on to see your models side by side. You might have to align them first. Use the command super model1, model2 for that. All best. Andreas On Tue, Feb 28, 2017 at 5:27 PM, João Oliveira Jr. wrote: > Hi > > Please, when using PyMOL

Re: [ccp4bb] Choosing test set for twin refinement, with multiple operators

Dear Andre, I agree with Jacob that P 42 21 2 might be the right space group, and that and R free of 33% isn't so bad. If your electron density is poor, that might just reflect the low resolution. Have you tried refinement with Buster? It has a way with low-resolution data. All best.

Re: [PyMOL] Coordinates of an atom

Dear Mohsen, when I Google "pymol coordinates atom", the top hit is this: https://pymolwiki.org/index.php/Get_Coordinates_I Worth a try. All best. Andreas On Thu, Dec 1, 2016 at 2:19 PM, Mohsen Chitsaz < mohsen.chit...@flinders.edu.au> wrote: > Hi all, > > > > Can anyone please help me

Re: [ccp4bb] XDS questions

Dear Wei, if you process your data with XDS, the best is probably to do the scaling in XDS (CORRECT) and be done with it. If you want to use Aimless for merging, you can turn off scaling with the ONLYMERGE keyword or use SCALES CONSTANT. All best. Andreas On Thu, Nov 17, 2016 at 9:40 PM,

Re: [PyMOL] on PDB

http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures Andreas On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu wrote: > Dear Shane, > > get_view is a nice command. Is any way to change the original PDB based on > what we get by set_view to get the new pdb? > >

Re: [PyMOL] on using pymol scripts

Dear Smith, right click on https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/centroid.py, select Save Link As. This is a good skill to have because it allows you to download all sorts of things from the internet. You can use Google Chrome, Mozilla Firefox and Microsoft Edge for

Re: [PyMOL] APBS problem

Hi Albert, I apologize that I take your email for a grumpy old man's rant, but I feel this mailing list is getting washed out with poorly formulated questions. What happened to specifying what OS you use, what version of PyMOL, what version of the apbs plugin. Also, to give answers, it would

Re: [ccp4bb] Problem regarding output in ccp4i 6.5

Dear Deepa, there was a time when spaces in the names of foldera and files was a big nono in ccp4. Maybe it still is. Try changing New Folder to New_Folder or something else without a space. Best Andreas On Wed, Jun 3, 2015 at 6:09 AM, Deepa Raju deepakmraj...@gmail.com wrote: Dear all,

Re: [ccp4bb] Low Phaser RFZ

Hi Eric, What does your map look like? Do you see features that don't come from the search model? That's the key. That said, with a TFZ of above 10, I'd be rather positive about my prospects. Andreas On Tue, May 19, 2015 at 2:36 AM, Eric Karg 052044071b36-dmarc-requ...@jiscmail.ac.uk

Re: [COOT] SGI dials and coot?

You're probably better off getting a Powermate. The thing doesn't come close to dials in terms of convenience but it works smoothly with O, coot and PyMOL. Andreas On Mon, Jan 11, 2010 at 4:47 AM, Oliver Clarke cla...@wehi.edu.au wrote: Hi all, Apologies if this has been asked before -

[Bug 500973] Re: Kernel panic while installing Ubuntu 9.10

Hi Leann, it is reproducible. How do I capture the beginning? -- Kernel panic while installing Ubuntu 9.10 https://bugs.launchpad.net/bugs/500973 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list

[Bug 500973] Re: Kernel panic while installing Ubuntu 9.10

** Attachment added: Foto of the kernel panic http://launchpadlibrarian.net/37241322/2009-12-27%2023.01.31.jpg -- Kernel panic while installing Ubuntu 9.10 https://bugs.launchpad.net/bugs/500973 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed

[Bug 500973] [NEW] Kernel panic while installing Ubuntu 9.10

Public bug reported: When installing Ubuntu 9.10 on my Gericom Blockbuster Notebook (mobile AMD Athlon(tm) XP 2400+ @ 1794MHz, 512 KB Cache), the installer freezes after some time. Assuming that it is a kernel panic, I tried to switch to the console immediately, so I solved to make a screen

Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....

Hey Tommi, I am under the impression that Zbyszek Otwinowski has looked in depth at all of the structures that have now been retracted and has prepared a long manuscript detailing the evidence for fabrication and falsification. As far as I know, this manuscript hasn't been published yet

Re: [PyMOL] superimpose option

Hey Saeid, use the 'super' command. Type super protein1, protein2 For more information, check teh wiki. Andreas On Tue, Dec 8, 2009 at 7:07 AM, saeid mirzaei smirzae...@yahoo.com wrote: Hi everyone, could some one tell me I can use Pymol for superimposing two protein or not if so

Re: [PyMOL] how to get RMSD from align command

Hey Thomas, if you want to use align anyway, make sure to use the quite=0 option. The quiet option (if present) is set to zero by default for parsed PyMOL commands, but is not set for Python API calls. align is nearly equal to cmd.align(quiet=0) Thus, if you want to get rmsd output, include

[ccp4bb] ctruncate error (kind of)

Dear all, I'm converting intensities from scala to amplitudes with ctruncate like so: ctruncate -mtzin scala_protein_3_001_180.mtz -colin /*/*/[IMEAN,SIGIMEAN] The data are native. An mtz file is generated, and it looks ok, but ctruncate doesn't terminate properly. Instead, after Anisotropy

Re: [PyMOL] pymol does not open from a terminal

Maia, you have to install libpng and/or libpng-devel. Andreas On Fri, Sep 11, 2009 at 3:04 AM, Maia Cherney ch...@ualberta.ca wrote: Hi, Could you please help me with a pymol problem. I have ubuntu linux and I have pymol in the /usr/bin (comes with ubuntu installation) and also one in the

Re: [ccp4bb] Computer hardware and OS survey

As Warren pointed out, dual-boot is so 20th century it's surprising people still bother with it. For me, dual boot (never mind it was on a fantastic Thinkpad) was the major reason to go for OSX. I was simply too sick of it.. It might sound like heresy to true Macolytes but I feel I have now the

Re: [PyMOL] exploding proteins

Hey Warren, unfortunately, none of your suggestions fixes the problem (which isn't really one anyway as I never use the lines representation). If I set both ati_bugs and nvidia_bugs, the display is completely messed up. https://fileexchange.imperial.ac.uk/files/dfc7e41276/ati_nvidia.png I'll

[PyMOL] exploding proteins

Dear all, I just checked out PyMOL 1.1r0 revision 3367 via subversion. When I open any old pdb file (eg. fetch 1ubq), the protein is displayed as if irradiated with a free-electron laser ( https://fileexchange.imperial.ac.uk/files/5b706c5efa/lines.png). The cartoon

Re: [ccp4bb] xtalview and mifit

Hey Ethan, all, On Feb 6, 2008 1:02 AM, Ethan Merritt [EMAIL PROTECTED] wrote: The problem is that both Fedora and Suse 10.3 currently ship with a broken xorg library. This is a known problem (Google for details), but I do not know if there is a fixed version available for download. Now,

Re: [PyMOL] viewport report?

Hey Thomas, try this: width,height = cmd.get_session()['main'][0:2] print width, height or print (cmd.get_session()['main'][0:2]) Andreas Thomas Stout wrote: Hi All -- I have a rather old session file that I would like to replicate in a new session file. Essentially, I want to carry

Re: [PyMOL] pymol in the background

Hey Gordon, I don't quite understand your problem. Pymol can be run in the background (or even remotely) by calling it as pymol -qc script.py When you want to use it interactively, the shell it was started from is used for all sorts of output. Why do you need this shell? Just open

Re: [ccp4bb] post-doc possibility in newcastle

You'd need quite a large French press or meat grinder to crack the cells and get the protein. William Scott wrote: On Thu, 20 Sep 2007 17:23:05 +0100 R. J. Lewis [EMAIL PROTECTED] wrote: a large signalling complex called the 'stressosome' from B. subtilis. -

Re: [ccp4bb] Stereo grpahics and Virtual Reality

For the benefit of overworked and stressed-out graduate students and post-docs, funding agencies need to be convinced that the remotes cannot be bought without the console. Andreas Stephen Graham wrote: Full VR systems with motion tracking and are now affordable to most labs (~$2500 for

Re: [ccp4bb] libstdc++.so.5: cannot open shared object file: No such file or directory

This is an old version of the c++ libraries. You get it by installing compat-libstdc++-33 Andreas Paul Kraft wrote: Hiys, I've got an hp pavillion dv2000 with a 64x2 processor and I loaded the redhat version of CCP4-6.0.2. I tried loading it manually but there was no configure or make

Re: [PyMOL] between views

Tassos, Dirk, sorry for the very late reply, but I've just now finished going through a few hundred list mails that had accumulated. For converting scenes to movies, Joel Bard's slerpy is really shweet. Check it out at http://www.pymolwiki.org/index.php/Slerpy. What I do is the following -

[PyMOL] transparency cross-fading

Hey all, I've run into the following problem while making some movies with MacPyMOL 0.99rc6. I have a protein in surface representation that I start with transparency = 0 and a cavity (voidoo-created map) as surface with transparency = 1. In other words, the protein surface is visible, the

Re: [PyMOL] protein cartoon/floating sidechains/ligands

Hey Gary, in order to have sidechains be attached to your cartoon representation, the cartoons must not be smoothened. set cartoon_flat_sheets, off will do that. Be warned that your sheets will look like the ocean beyond the reef of Tunnels beach. To get just a sidechain, type show sticks,

Re: [PyMOL] image metadata plugin

I was actually thinking about a related approach. Could one include a feature in PyMOL allowing the user to save notes with a session? I've really come to like saving sessions but going back to them later I often wonder what the objects are exactly, what the views were meant to represent, which

Re: [ccp4bb] off-topic Apple computer question

Steve, Steve Lane wrote: Given the current situation at Apple, particularly their shift in focus and revenue percentage from computers to other types of devices, i.e. iPods, either/both of the above reasons for refusal to do the work are plausible. are you saying one shouldn't buy one's

Re: [PyMOL] Showing the surface

Hi Michael, try to set a low resolution in addition to the increased VdW radii. Play around with the following set of commands: set gaussian_resolution, 9.0 # or whatever looks best map_new mapName, gaussian, 3.0, object # number is separation between grid lines, 1 is way too detailed for low

Re: [ccp4bb]: carriers for crystallization plates

*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** I second Bernhard's suggestions. Find a Styrofoam container that's just big enough for your plates. Pad the gaps left by the short sides of the trays with paper

[ccp4bb]: ccp4 user meeting

Just a quick question to all participants of the ccp4 user meeting in January. Do most people stay in Reading Saturday night, or will the place be deserted? I'm asking because I'd like to benefit the most from the brain power at the meeting, and if there's a chance to have an insightful

Re: [ccp4bb]: laptop for ccp4i

The good thing with a PC notebook is that you get a usable touchpad and an ALT key that lets you access menus without taking your hands off the keyboard, the lack of both of which drives me up the wall every time I sit in front of a Mac portable. How to decide on a notebook? Sit in front of

Re: [PyMOL] Show residues and sticks

The other day I got annoyed always having to type and not (name c,n,ca) when I want to see sidechains without the mainchain. The attached script takes care of this. run sidechain.py sidechain resi 34 (instead of show sticks, resi 34 and not (name c,n,ca)) Andreas Andrea Spitaleri wrote:

Re: [PyMOL] Show residues and sticks

) [ and not:] [ show sticks, resi 34 and not (name c,n,ca) ] Chris also pointed out that this feature exists somewhere in the pymol GUI (For whatever selection, under the show menu, at the bottom there is sidechain - lines, sticks, spheres). Thanks. Andreas Andreas Forster wrote: The other day

Re: [PyMOL] differential helix transparency

Hey Satinder, transparency can only be set for objects, not for selections. Thus, you have to create different objects corresponding to your helices. Like so: create helix1, i. 23:30 # wherever your first helix is create helix2and3, i. 40:45 or i. 70:83 # the other two helices show

Re: GLIBC problems (was Re: [ccp4bb]: NCS edits in coot)

*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** There's surely a difference whether you take care of your own computer or whether you're trying to make a local network run smoothly. My laptop, which used to be

Re: [PyMOL] PyMOL-users Digest, Vol 5, Issue 22

Oh, works like a charm. (If you're a bit more descriptive about your problem, we can help you better.) Andreas surendra negi wrote: Is there any 32 bit version of pymol? I am unable to install it in XP - Original Message

Re: [PyMOL] Problems with rendering and saving

Hey Florian, I'd say it's a limitation of your graphics card. Others should correct me if I'm wrong. In any case, on my computer, I can write a 6400x4800 pixel2 file. PyMOLpng test ScenePNG: wrote 6400x4800 pixel image to file test.png. A different question is why I or you would want to

[ccp4bb]: yummy packages (was redhat WS3 and Xfree problems)

*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** I second Kevin's point. Don't install packages manually. Let yum or apt take care of it. If you add livna.org to your list of repositories, most of your laptop

[ccp4bb]: summary crystal tray database

*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** Hey all, I've been reminded recently that I owe the list a summary of responses obtained concerning crystal tray databases. There are actually a large number of

Re: [PyMOL] One-Button Mice on Macs

Warren, what's up with this? Pymol and one-button mouse?? What's next? Pymol on abacus? Wouldn't it rather be time to remind Apple to provide ergonomic equipment? Andreas ps. I would be interested in hearing if anyone has found an ingenious use for the dozens of shiny slick white

pserver: no such repository

Hello, when I want to access my cvs repository via pserver, i get the error /var/lib/cvs: no such repository. I tried this from two different machines (one of them was the machine with the repository on its harddisc), so its not a networking problem. I can access the repository locally with