Hi Qianglin, What type of system and Coot version are you using? I've just tried opening EMD-7472 with Coot 0.8.9.1 on a 64-bit Linux system and it opens the whole map correctly as long as the machine has enough memory available. (If there's not enough memory, Coot doesn't load part of the map, it just crashes with a segmentation fault or a std::bad_alloc error.)
One thing you could try is to convert your map to an MTZ file. Coot loads them in quite different ways so there's a chance an MTZ would work when the real-space map doesn't. The MTZ file might also be smaller, if the resolution of your map is lower than the Nyquist frequency of the map's grid sampling. As an example, EMD-7472 claims a resolution of 4.2 A but has a pixel spacing of 1.03 A. The map file is about 8 GB, but an MTZ calculated to 4.2 A resolution is only 1.3 GB. You can use Refmac to convert maps to MTZ files using the keyword SFCALC, but you might find it more convenient to use the "MRC to MTZ" task in CCPEM (http://www.ccpem.ac.uk/download.php), which will set all the necessary arguments for you. Best wishes, Colin -----Original Message----- From: Mailing list for users of COOT Crystallographic Software <[email protected]> On Behalf Of Paul Emsley Sent: 30 July 2018 23:20 To: [email protected] Subject: Re: open a large map On 30/07/18 22:20, Qianglin Fang wrote: > Thank you very much for the reply. I have already tried to use a large map > display radius. Acctually, I found this problem after trying this. I also > tried to open a map in EMDB (accession code: EMD-7472) which has a box size > of 1280, and got the same problem. > > > I see what you mean - that is a large map. I guess that clipper (which is what Coot is using as the container for maps) is running out of indices for the grid points (or some such). It would (as far as I understand) need a non-trivial infrastructure change to fix this problem. Paul. ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
